metadata: run_metadata: 196 rows where devstage_curation_coarse = "Embryo" and experiment.library

196 rows where devstage_curation_coarse = "Embryo" and experiment.library_selection = "RANDOM"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	sample.description	sample.title	sample.alias	sample.centername	sample.attributes	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.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
5795	5795	ERR1698352	ERX1767860	ERS1417534	ERP018188	PRJEB16335	RNA seq of the zebrafish danio rerio brain post developmental exposure to 17a ethinylestradiol	E-MTAB-5173	Transcriptome Analysis	17a ethinylestradiol EE2 is a synthetic estrogen commonly used as an active substance in oral contraceptives. It is frequently found in waste water effluent and raise concern due to its persistent nature. EE2 binds to estrogen receptors with similar affinity to oestradiol and acts as one of the most potent hormone mimics found in the environment. Estrogen is involved in many aspects of the development of the neuroendocrine system influencing both brain structure and behavior. We and others have reported a significant effect on non reproductive behaviors in adult fish and in recent studies we found that developmental exposure to EE2 resulted in an anxiogenic phenotype as adults even post a long remediation period. In this study we aim to study possible mechanisms behind the behavior alterations of zebrafish developmentally exposed to EE2 by sequencing the whole brain transcriptome. Zebrafish embryos were exposed to 0 2.14 and 7.34 ng/L EE2 from 1 day to 80 dpf post the exposure period a remediation period of 120 days followed before the fish were sampled. 3 male brains from the control group 0 ng/L and the 2.14 ng/L group were sampled and 3 female brains from the control group 0 ng/L and 7.34 ng/L were sampled.	ENA FIRST PUBLIC:2017 10 02\|ENA LAST UPDATE:2016 10 19\|ArrayExpress:E MTAB 5173	Protocols: RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich Germany EE2 exposure. Fish exposed to 0 2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA	IonXpressRNA 012 up 058 12	SAMEA4518355	School of Natural Science, Technology and Environmental Studies Sodertorn University	ENA first public:2017 10 02\|ENA last update:2016 10 19\|External Id:SAMEA4518355\|INSDC center alias:School of Natural Science Technology and Environmental Studies Sodertorn University\|INSDC center name:School of Natural Science Technology and Environmental Studies Sodertorn University\|INSDC first public:2017 10 02T17:05:16Z\|INSDC last update:2016 10 19T13:53:59Z\|INSDC status:public\|Submitter Id:E MTAB 5173:IonXpressRNA 012 up 058 12\|age:200\|broker name:ArrayExpress\|common name:zebrafish\|organism part:brain\|sample name:E MTAB 5173:IonXpressRNA 012 up 058 12\|sex:male	Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol	E MTAB 5173:IonXpressRNA 012 up 058 12 s	IonXpressRNA 012 up 058 12 s	RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol	RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich Germany EE2 exposure. Fish exposed to 0 2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA	Experimental Factor: male:sex\|Experimental Factor: 17 ethinylestradiol:compound\|Experimental Factor: 2.14:dose	RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ION_TORRENT	Ion Torrent Proton		ERP018188	Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17Î± ethinylestradiol	ENA FIRST PUBLIC:2017 10 02\|ENA LAST UPDATE:2018 11 16	IonXpressRNA_012_up_058_12.fastq.gz	fastq	2535299006.0	33956077.0	E MTAB 5173:IonXpressRNA 012 up 058 12	0:74.66	A:719061985;C:581906269;G:579932234;T:654398518;N:0	74		719061985	581906269	579932234	654398518	0	ERX1767860	ERS1417534	ERA739176	School of Natural Science, Technology and Environmental Studies Sodertorn University\|European Nucleotide Archive	School of Natural Science, Technology and Environmental Studies Sodertorn University\|European Nucleotide Archive	1	0.7343		0.34119		0.7359		0.48406		66		B		usable mapping rate	ion_torrent	ion_torrent	full_length	random_priming	ribozero	bulk	unknown	unknown	Sweden	2016-10-19	Pharyngula	Embryo	Brain	Nervous System
5796	5796	ERR1698351	ERX1767859	ERS1417533	ERP018188	PRJEB16335	RNA seq of the zebrafish danio rerio brain post developmental exposure to 17a ethinylestradiol	E-MTAB-5173	Transcriptome Analysis	17a ethinylestradiol EE2 is a synthetic estrogen commonly used as an active substance in oral contraceptives. It is frequently found in waste water effluent and raise concern due to its persistent nature. EE2 binds to estrogen receptors with similar affinity to oestradiol and acts as one of the most potent hormone mimics found in the environment. Estrogen is involved in many aspects of the development of the neuroendocrine system influencing both brain structure and behavior. We and others have reported a significant effect on non reproductive behaviors in adult fish and in recent studies we found that developmental exposure to EE2 resulted in an anxiogenic phenotype as adults even post a long remediation period. In this study we aim to study possible mechanisms behind the behavior alterations of zebrafish developmentally exposed to EE2 by sequencing the whole brain transcriptome. Zebrafish embryos were exposed to 0 2.14 and 7.34 ng/L EE2 from 1 day to 80 dpf post the exposure period a remediation period of 120 days followed before the fish were sampled. 3 male brains from the control group 0 ng/L and the 2.14 ng/L group were sampled and 3 female brains from the control group 0 ng/L and 7.34 ng/L were sampled.	ENA FIRST PUBLIC:2017 10 02\|ENA LAST UPDATE:2016 10 19\|ArrayExpress:E MTAB 5173	Protocols: RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich Germany EE2 exposure. Fish exposed to 0 2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA	IonXpressRNA 011 up 058 11	SAMEA4518354	School of Natural Science, Technology and Environmental Studies Sodertorn University	ENA first public:2017 10 02\|ENA last update:2016 10 19\|External Id:SAMEA4518354\|INSDC center alias:School of Natural Science Technology and Environmental Studies Sodertorn University\|INSDC center name:School of Natural Science Technology and Environmental Studies Sodertorn University\|INSDC first public:2017 10 02T17:05:16Z\|INSDC last update:2016 10 19T13:53:59Z\|INSDC status:public\|Submitter Id:E MTAB 5173:IonXpressRNA 011 up 058 11\|age:200\|broker name:ArrayExpress\|common name:zebrafish\|organism part:brain\|sample name:E MTAB 5173:IonXpressRNA 011 up 058 11\|sex:male	Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol	E MTAB 5173:IonXpressRNA 011 up 058 11 s	IonXpressRNA 011 up 058 11 s	RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol	RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich Germany EE2 exposure. Fish exposed to 0 2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA	Experimental Factor: male:sex\|Experimental Factor: 17 ethinylestradiol:compound\|Experimental Factor: 2.14:dose	RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ION_TORRENT	Ion Torrent Proton		ERP018188	Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17Î± ethinylestradiol	ENA FIRST PUBLIC:2017 10 02\|ENA LAST UPDATE:2018 11 16	IonXpressRNA_011_up_058_11.fastq.gz	fastq	3400774471.0	38709756.0	E MTAB 5173:IonXpressRNA 011 up 058 11	0:87.85	A:948991439;C:793389977;G:792539547;T:865853508;N:0	87		948991439	793389977	792539547	865853508	0	ERX1767859	ERS1417533	ERA739176	School of Natural Science, Technology and Environmental Studies Sodertorn University\|European Nucleotide Archive	School of Natural Science, Technology and Environmental Studies Sodertorn University\|European Nucleotide Archive	1	0.63968		0.27033		0.75213		0.47966		139		B		usable mapping rate	ion_torrent	ion_torrent	full_length	random_priming	ribozero	bulk	unknown	unknown	Sweden	2016-10-19	Pharyngula	Embryo	Brain	Nervous System
5797	5797	ERR1698350	ERX1767858	ERS1417532	ERP018188	PRJEB16335	RNA seq of the zebrafish danio rerio brain post developmental exposure to 17a ethinylestradiol	E-MTAB-5173	Transcriptome Analysis	17a ethinylestradiol EE2 is a synthetic estrogen commonly used as an active substance in oral contraceptives. It is frequently found in waste water effluent and raise concern due to its persistent nature. EE2 binds to estrogen receptors with similar affinity to oestradiol and acts as one of the most potent hormone mimics found in the environment. Estrogen is involved in many aspects of the development of the neuroendocrine system influencing both brain structure and behavior. We and others have reported a significant effect on non reproductive behaviors in adult fish and in recent studies we found that developmental exposure to EE2 resulted in an anxiogenic phenotype as adults even post a long remediation period. In this study we aim to study possible mechanisms behind the behavior alterations of zebrafish developmentally exposed to EE2 by sequencing the whole brain transcriptome. Zebrafish embryos were exposed to 0 2.14 and 7.34 ng/L EE2 from 1 day to 80 dpf post the exposure period a remediation period of 120 days followed before the fish were sampled. 3 male brains from the control group 0 ng/L and the 2.14 ng/L group were sampled and 3 female brains from the control group 0 ng/L and 7.34 ng/L were sampled.	ENA FIRST PUBLIC:2017 10 02\|ENA LAST UPDATE:2016 10 19\|ArrayExpress:E MTAB 5173	Protocols: RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich Germany EE2 exposure. Fish exposed to 0 2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA	IonXpressRNA 010 up 058 10	SAMEA4518353	School of Natural Science, Technology and Environmental Studies Sodertorn University	ENA first public:2017 10 02\|ENA last update:2016 10 19\|External Id:SAMEA4518353\|INSDC center alias:School of Natural Science Technology and Environmental Studies Sodertorn University\|INSDC center name:School of Natural Science Technology and Environmental Studies Sodertorn University\|INSDC first public:2017 10 02T17:05:16Z\|INSDC last update:2016 10 19T13:53:59Z\|INSDC status:public\|Submitter Id:E MTAB 5173:IonXpressRNA 010 up 058 10\|age:200\|broker name:ArrayExpress\|common name:zebrafish\|organism part:brain\|sample name:E MTAB 5173:IonXpressRNA 010 up 058 10\|sex:male	Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol	E MTAB 5173:IonXpressRNA 010 up 058 10 s	IonXpressRNA 010 up 058 10 s	RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol	RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich Germany EE2 exposure. Fish exposed to 0 2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA	Experimental Factor: male:sex\|Experimental Factor: 17 ethinylestradiol:compound\|Experimental Factor: 2.14:dose	RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ION_TORRENT	Ion Torrent Proton		ERP018188	Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17Î± ethinylestradiol	ENA FIRST PUBLIC:2017 10 02\|ENA LAST UPDATE:2018 11 16	IonXpressRNA_010_up_058_10.fastq.gz	fastq	3502667998.0	39204781.0	E MTAB 5173:IonXpressRNA 010 up 058 10	0:89.34	A:976977303;C:803330255;G:808731995;T:913628445;N:0	89		976977303	803330255	808731995	913628445	0	ERX1767858	ERS1417532	ERA739176	School of Natural Science, Technology and Environmental Studies Sodertorn University\|European Nucleotide Archive	School of Natural Science, Technology and Environmental Studies Sodertorn University\|European Nucleotide Archive	1	0.65846		0.2815		0.74028		0.47784		86		B		usable mapping rate	ion_torrent	ion_torrent	full_length	random_priming	ribozero	bulk	unknown	unknown	Sweden	2016-10-19	Pharyngula	Embryo	Brain	Nervous System
5798	5798	ERR1698349	ERX1767857	ERS1417531	ERP018188	PRJEB16335	RNA seq of the zebrafish danio rerio brain post developmental exposure to 17a ethinylestradiol	E-MTAB-5173	Transcriptome Analysis	17a ethinylestradiol EE2 is a synthetic estrogen commonly used as an active substance in oral contraceptives. It is frequently found in waste water effluent and raise concern due to its persistent nature. EE2 binds to estrogen receptors with similar affinity to oestradiol and acts as one of the most potent hormone mimics found in the environment. Estrogen is involved in many aspects of the development of the neuroendocrine system influencing both brain structure and behavior. We and others have reported a significant effect on non reproductive behaviors in adult fish and in recent studies we found that developmental exposure to EE2 resulted in an anxiogenic phenotype as adults even post a long remediation period. In this study we aim to study possible mechanisms behind the behavior alterations of zebrafish developmentally exposed to EE2 by sequencing the whole brain transcriptome. Zebrafish embryos were exposed to 0 2.14 and 7.34 ng/L EE2 from 1 day to 80 dpf post the exposure period a remediation period of 120 days followed before the fish were sampled. 3 male brains from the control group 0 ng/L and the 2.14 ng/L group were sampled and 3 female brains from the control group 0 ng/L and 7.34 ng/L were sampled.	ENA FIRST PUBLIC:2017 10 02\|ENA LAST UPDATE:2016 10 19\|ArrayExpress:E MTAB 5173	Protocols: RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich Germany EE2 exposure. Fish exposed to 0 2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA	IonXpressRNA 009 up 058 9	SAMEA4518352	School of Natural Science, Technology and Environmental Studies Sodertorn University	ENA first public:2017 10 02\|ENA last update:2016 10 19\|External Id:SAMEA4518352\|INSDC center alias:School of Natural Science Technology and Environmental Studies Sodertorn University\|INSDC center name:School of Natural Science Technology and Environmental Studies Sodertorn University\|INSDC first public:2017 10 02T17:05:16Z\|INSDC last update:2016 10 19T13:53:59Z\|INSDC status:public\|Submitter Id:E MTAB 5173:IonXpressRNA 009 up 058 9\|age:200\|broker name:ArrayExpress\|common name:zebrafish\|organism part:brain\|sample name:E MTAB 5173:IonXpressRNA 009 up 058 9\|sex:male	Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol	E MTAB 5173:IonXpressRNA 009 up 058 9 s	IonXpressRNA 009 up 058 9 s	RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol	RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich Germany EE2 exposure. Fish exposed to 0 2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA	Experimental Factor: male:sex\|Experimental Factor: n1:compound	RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ION_TORRENT	Ion Torrent Proton		ERP018188	Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17Î± ethinylestradiol	ENA FIRST PUBLIC:2017 10 02\|ENA LAST UPDATE:2018 11 16	IonXpressRNA_009_up_058_9.fastq.gz	fastq	3575088264.0	39745481.0	E MTAB 5173:IonXpressRNA 009 up 058 9	0:89.95	A:1011474126;C:809896078;G:807471974;T:946246086;N:0	89		1011474126	809896078	807471974	946246086	0	ERX1767857	ERS1417531	ERA739176	School of Natural Science, Technology and Environmental Studies Sodertorn University\|European Nucleotide Archive	School of Natural Science, Technology and Environmental Studies Sodertorn University\|European Nucleotide Archive	1	0.65266		0.30274		0.75286		0.48527		94		B		usable mapping rate	ion_torrent	ion_torrent	full_length	random_priming	ribozero	bulk	unknown	unknown	Sweden	2016-10-19	Pharyngula	Embryo	Brain	Nervous System
5799	5799	ERR1698348	ERX1767856	ERS1417530	ERP018188	PRJEB16335	RNA seq of the zebrafish danio rerio brain post developmental exposure to 17a ethinylestradiol	E-MTAB-5173	Transcriptome Analysis	17a ethinylestradiol EE2 is a synthetic estrogen commonly used as an active substance in oral contraceptives. It is frequently found in waste water effluent and raise concern due to its persistent nature. EE2 binds to estrogen receptors with similar affinity to oestradiol and acts as one of the most potent hormone mimics found in the environment. Estrogen is involved in many aspects of the development of the neuroendocrine system influencing both brain structure and behavior. We and others have reported a significant effect on non reproductive behaviors in adult fish and in recent studies we found that developmental exposure to EE2 resulted in an anxiogenic phenotype as adults even post a long remediation period. In this study we aim to study possible mechanisms behind the behavior alterations of zebrafish developmentally exposed to EE2 by sequencing the whole brain transcriptome. Zebrafish embryos were exposed to 0 2.14 and 7.34 ng/L EE2 from 1 day to 80 dpf post the exposure period a remediation period of 120 days followed before the fish were sampled. 3 male brains from the control group 0 ng/L and the 2.14 ng/L group were sampled and 3 female brains from the control group 0 ng/L and 7.34 ng/L were sampled.	ENA FIRST PUBLIC:2017 10 02\|ENA LAST UPDATE:2016 10 19\|ArrayExpress:E MTAB 5173	Protocols: RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich Germany EE2 exposure. Fish exposed to 0 2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA	IonXpressRNA 008 up 058 8	SAMEA4518351	School of Natural Science, Technology and Environmental Studies Sodertorn University	ENA first public:2017 10 02\|ENA last update:2016 10 19\|External Id:SAMEA4518351\|INSDC center alias:School of Natural Science Technology and Environmental Studies Sodertorn University\|INSDC center name:School of Natural Science Technology and Environmental Studies Sodertorn University\|INSDC first public:2017 10 02T17:05:16Z\|INSDC last update:2016 10 19T13:53:59Z\|INSDC status:public\|Submitter Id:E MTAB 5173:IonXpressRNA 008 up 058 8\|age:200\|broker name:ArrayExpress\|common name:zebrafish\|organism part:brain\|sample name:E MTAB 5173:IonXpressRNA 008 up 058 8\|sex:male	Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol	E MTAB 5173:IonXpressRNA 008 up 058 8 s	IonXpressRNA 008 up 058 8 s	RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol	RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich Germany EE2 exposure. Fish exposed to 0 2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA	Experimental Factor: male:sex\|Experimental Factor: n1:compound	RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ION_TORRENT	Ion Torrent Proton		ERP018188	Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17Î± ethinylestradiol	ENA FIRST PUBLIC:2017 10 02\|ENA LAST UPDATE:2018 11 16	IonXpressRNA_008_up_058_8.fastq.gz	fastq	3259710114.0	38530802.0	E MTAB 5173:IonXpressRNA 008 up 058 8	0:84.60	A:916053004;C:755694888;G:751125332;T:836836890;N:0	84		916053004	755694888	751125332	836836890	0	ERX1767856	ERS1417530	ERA739176	School of Natural Science, Technology and Environmental Studies Sodertorn University\|European Nucleotide Archive	School of Natural Science, Technology and Environmental Studies Sodertorn University\|European Nucleotide Archive	1	0.70995		0.31365		0.74781		0.48846		61		B		usable mapping rate	ion_torrent	ion_torrent	full_length	random_priming	ribozero	bulk	unknown	unknown	Sweden	2016-10-19	Pharyngula	Embryo	Brain	Nervous System
5800	5800	ERR1698347	ERX1767855	ERS1417529	ERP018188	PRJEB16335	RNA seq of the zebrafish danio rerio brain post developmental exposure to 17a ethinylestradiol	E-MTAB-5173	Transcriptome Analysis	17a ethinylestradiol EE2 is a synthetic estrogen commonly used as an active substance in oral contraceptives. It is frequently found in waste water effluent and raise concern due to its persistent nature. EE2 binds to estrogen receptors with similar affinity to oestradiol and acts as one of the most potent hormone mimics found in the environment. Estrogen is involved in many aspects of the development of the neuroendocrine system influencing both brain structure and behavior. We and others have reported a significant effect on non reproductive behaviors in adult fish and in recent studies we found that developmental exposure to EE2 resulted in an anxiogenic phenotype as adults even post a long remediation period. In this study we aim to study possible mechanisms behind the behavior alterations of zebrafish developmentally exposed to EE2 by sequencing the whole brain transcriptome. Zebrafish embryos were exposed to 0 2.14 and 7.34 ng/L EE2 from 1 day to 80 dpf post the exposure period a remediation period of 120 days followed before the fish were sampled. 3 male brains from the control group 0 ng/L and the 2.14 ng/L group were sampled and 3 female brains from the control group 0 ng/L and 7.34 ng/L were sampled.	ENA FIRST PUBLIC:2017 10 02\|ENA LAST UPDATE:2016 10 19\|ArrayExpress:E MTAB 5173	Protocols: RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich Germany EE2 exposure. Fish exposed to 0 2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA	IonXpressRNA 007 up 058 7	SAMEA4518350	School of Natural Science, Technology and Environmental Studies Sodertorn University	ENA first public:2017 10 02\|ENA last update:2016 10 19\|External Id:SAMEA4518350\|INSDC center alias:School of Natural Science Technology and Environmental Studies Sodertorn University\|INSDC center name:School of Natural Science Technology and Environmental Studies Sodertorn University\|INSDC first public:2017 10 02T17:05:16Z\|INSDC last update:2016 10 19T13:53:59Z\|INSDC status:public\|Submitter Id:E MTAB 5173:IonXpressRNA 007 up 058 7\|age:200\|broker name:ArrayExpress\|common name:zebrafish\|organism part:brain\|sample name:E MTAB 5173:IonXpressRNA 007 up 058 7\|sex:male	Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol	E MTAB 5173:IonXpressRNA 007 up 058 7 s	IonXpressRNA 007 up 058 7 s	RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol	RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich Germany EE2 exposure. Fish exposed to 0 2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA	Experimental Factor: male:sex\|Experimental Factor: n1:compound	RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ION_TORRENT	Ion Torrent Proton		ERP018188	Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17Î± ethinylestradiol	ENA FIRST PUBLIC:2017 10 02\|ENA LAST UPDATE:2018 11 16	IonXpressRNA_007_up_058_7.fastq.gz	fastq	2307842164.0	28984666.0	E MTAB 5173:IonXpressRNA 007 up 058 7	0:79.62	A:634041732;C:548565089;G:545418985;T:579816358;N:0	79		634041732	548565089	545418985	579816358	0	ERX1767855	ERS1417529	ERA739176	School of Natural Science, Technology and Environmental Studies Sodertorn University\|European Nucleotide Archive	School of Natural Science, Technology and Environmental Studies Sodertorn University\|European Nucleotide Archive	1	0.67542		0.2817		0.74168		0.47224		37		B		usable mapping rate	ion_torrent	ion_torrent	full_length	random_priming	ribozero	bulk	unknown	unknown	Sweden	2016-10-19	Pharyngula	Embryo	Brain	Nervous System
5801	5801	ERR1698346	ERX1767854	ERS1417528	ERP018188	PRJEB16335	RNA seq of the zebrafish danio rerio brain post developmental exposure to 17a ethinylestradiol	E-MTAB-5173	Transcriptome Analysis	17a ethinylestradiol EE2 is a synthetic estrogen commonly used as an active substance in oral contraceptives. It is frequently found in waste water effluent and raise concern due to its persistent nature. EE2 binds to estrogen receptors with similar affinity to oestradiol and acts as one of the most potent hormone mimics found in the environment. Estrogen is involved in many aspects of the development of the neuroendocrine system influencing both brain structure and behavior. We and others have reported a significant effect on non reproductive behaviors in adult fish and in recent studies we found that developmental exposure to EE2 resulted in an anxiogenic phenotype as adults even post a long remediation period. In this study we aim to study possible mechanisms behind the behavior alterations of zebrafish developmentally exposed to EE2 by sequencing the whole brain transcriptome. Zebrafish embryos were exposed to 0 2.14 and 7.34 ng/L EE2 from 1 day to 80 dpf post the exposure period a remediation period of 120 days followed before the fish were sampled. 3 male brains from the control group 0 ng/L and the 2.14 ng/L group were sampled and 3 female brains from the control group 0 ng/L and 7.34 ng/L were sampled.	ENA FIRST PUBLIC:2017 10 02\|ENA LAST UPDATE:2016 10 19\|ArrayExpress:E MTAB 5173	Protocols: RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich Germany EE2 exposure. Fish exposed to 0 2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA	IonXpressRNA 006 up 058 6	SAMEA4518349	School of Natural Science, Technology and Environmental Studies Sodertorn University	ENA first public:2017 10 02\|ENA last update:2016 10 19\|External Id:SAMEA4518349\|INSDC center alias:School of Natural Science Technology and Environmental Studies Sodertorn University\|INSDC center name:School of Natural Science Technology and Environmental Studies Sodertorn University\|INSDC first public:2017 10 02T17:05:16Z\|INSDC last update:2016 10 19T13:53:59Z\|INSDC status:public\|Submitter Id:E MTAB 5173:IonXpressRNA 006 up 058 6\|age:200\|broker name:ArrayExpress\|common name:zebrafish\|organism part:brain\|sample name:E MTAB 5173:IonXpressRNA 006 up 058 6\|sex:female	Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol	E MTAB 5173:IonXpressRNA 006 up 058 6 s	IonXpressRNA 006 up 058 6 s	RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol	RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich Germany EE2 exposure. Fish exposed to 0 2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA	Experimental Factor: female:sex\|Experimental Factor: 17 ethinylestradiol:compound\|Experimental Factor: 7.34:dose	RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ION_TORRENT	Ion Torrent Proton		ERP018188	Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17Î± ethinylestradiol	ENA FIRST PUBLIC:2017 10 02\|ENA LAST UPDATE:2018 11 16	IonXpressRNA_006_up_058_6.fastq.gz	fastq	2239484857.0	27021234.0	E MTAB 5173:IonXpressRNA 006 up 058 6	0:82.88	A:637326624;C:506830056;G:503508207;T:591819970;N:0	82		637326624	506830056	503508207	591819970	0	ERX1767854	ERS1417528	ERA739176	School of Natural Science, Technology and Environmental Studies Sodertorn University\|European Nucleotide Archive	School of Natural Science, Technology and Environmental Studies Sodertorn University\|European Nucleotide Archive	1	0.66441		0.31904		0.74905		0.47154		122		B		usable mapping rate	ion_torrent	ion_torrent	full_length	random_priming	ribozero	bulk	unknown	unknown	Sweden	2016-10-19	Pharyngula	Embryo	Brain	Nervous System
5802	5802	ERR1698345	ERX1767853	ERS1417527	ERP018188	PRJEB16335	RNA seq of the zebrafish danio rerio brain post developmental exposure to 17a ethinylestradiol	E-MTAB-5173	Transcriptome Analysis	17a ethinylestradiol EE2 is a synthetic estrogen commonly used as an active substance in oral contraceptives. It is frequently found in waste water effluent and raise concern due to its persistent nature. EE2 binds to estrogen receptors with similar affinity to oestradiol and acts as one of the most potent hormone mimics found in the environment. Estrogen is involved in many aspects of the development of the neuroendocrine system influencing both brain structure and behavior. We and others have reported a significant effect on non reproductive behaviors in adult fish and in recent studies we found that developmental exposure to EE2 resulted in an anxiogenic phenotype as adults even post a long remediation period. In this study we aim to study possible mechanisms behind the behavior alterations of zebrafish developmentally exposed to EE2 by sequencing the whole brain transcriptome. Zebrafish embryos were exposed to 0 2.14 and 7.34 ng/L EE2 from 1 day to 80 dpf post the exposure period a remediation period of 120 days followed before the fish were sampled. 3 male brains from the control group 0 ng/L and the 2.14 ng/L group were sampled and 3 female brains from the control group 0 ng/L and 7.34 ng/L were sampled.	ENA FIRST PUBLIC:2017 10 02\|ENA LAST UPDATE:2016 10 19\|ArrayExpress:E MTAB 5173	Protocols: RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich Germany EE2 exposure. Fish exposed to 0 2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA	IonXpressRNA 005 up 058 5	SAMEA4518348	School of Natural Science, Technology and Environmental Studies Sodertorn University	ENA first public:2017 10 02\|ENA last update:2016 10 19\|External Id:SAMEA4518348\|INSDC center alias:School of Natural Science Technology and Environmental Studies Sodertorn University\|INSDC center name:School of Natural Science Technology and Environmental Studies Sodertorn University\|INSDC first public:2017 10 02T17:05:16Z\|INSDC last update:2016 10 19T13:53:59Z\|INSDC status:public\|Submitter Id:E MTAB 5173:IonXpressRNA 005 up 058 5\|age:200\|broker name:ArrayExpress\|common name:zebrafish\|organism part:brain\|sample name:E MTAB 5173:IonXpressRNA 005 up 058 5\|sex:female	Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol	E MTAB 5173:IonXpressRNA 005 up 058 5 s	IonXpressRNA 005 up 058 5 s	RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol	RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich Germany EE2 exposure. Fish exposed to 0 2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA	Experimental Factor: female:sex\|Experimental Factor: 17 ethinylestradiol:compound\|Experimental Factor: 7.34:dose	RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ION_TORRENT	Ion Torrent Proton		ERP018188	Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17Î± ethinylestradiol	ENA FIRST PUBLIC:2017 10 02\|ENA LAST UPDATE:2018 11 16	IonXpressRNA_005_up_058_5.fastq.gz	fastq	2920608487.0	39573075.0	E MTAB 5173:IonXpressRNA 005 up 058 5	0:73.80	A:814851327;C:678116994;G:691911192;T:735728974;N:0	73		814851327	678116994	691911192	735728974	0	ERX1767853	ERS1417527	ERA739176	School of Natural Science, Technology and Environmental Studies Sodertorn University\|European Nucleotide Archive	School of Natural Science, Technology and Environmental Studies Sodertorn University\|European Nucleotide Archive	1	0.60005		0.25542		0.76481		0.4886		12		B		usable mapping rate	ion_torrent	ion_torrent	full_length	random_priming	ribozero	bulk	unknown	unknown	Sweden	2016-10-19	Pharyngula	Embryo	Brain	Nervous System
5803	5803	ERR1698344	ERX1767852	ERS1417526	ERP018188	PRJEB16335	RNA seq of the zebrafish danio rerio brain post developmental exposure to 17a ethinylestradiol	E-MTAB-5173	Transcriptome Analysis	17a ethinylestradiol EE2 is a synthetic estrogen commonly used as an active substance in oral contraceptives. It is frequently found in waste water effluent and raise concern due to its persistent nature. EE2 binds to estrogen receptors with similar affinity to oestradiol and acts as one of the most potent hormone mimics found in the environment. Estrogen is involved in many aspects of the development of the neuroendocrine system influencing both brain structure and behavior. We and others have reported a significant effect on non reproductive behaviors in adult fish and in recent studies we found that developmental exposure to EE2 resulted in an anxiogenic phenotype as adults even post a long remediation period. In this study we aim to study possible mechanisms behind the behavior alterations of zebrafish developmentally exposed to EE2 by sequencing the whole brain transcriptome. Zebrafish embryos were exposed to 0 2.14 and 7.34 ng/L EE2 from 1 day to 80 dpf post the exposure period a remediation period of 120 days followed before the fish were sampled. 3 male brains from the control group 0 ng/L and the 2.14 ng/L group were sampled and 3 female brains from the control group 0 ng/L and 7.34 ng/L were sampled.	ENA FIRST PUBLIC:2017 10 02\|ENA LAST UPDATE:2016 10 19\|ArrayExpress:E MTAB 5173	Protocols: RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich Germany EE2 exposure. Fish exposed to 0 2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA	IonXpressRNA 004 up 058 4	SAMEA4518347	School of Natural Science, Technology and Environmental Studies Sodertorn University	ENA first public:2017 10 02\|ENA last update:2016 10 19\|External Id:SAMEA4518347\|INSDC center alias:School of Natural Science Technology and Environmental Studies Sodertorn University\|INSDC center name:School of Natural Science Technology and Environmental Studies Sodertorn University\|INSDC first public:2017 10 02T17:05:16Z\|INSDC last update:2016 10 19T13:53:59Z\|INSDC status:public\|Submitter Id:E MTAB 5173:IonXpressRNA 004 up 058 4\|age:200\|broker name:ArrayExpress\|common name:zebrafish\|organism part:brain\|sample name:E MTAB 5173:IonXpressRNA 004 up 058 4\|sex:female	Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol	E MTAB 5173:IonXpressRNA 004 up 058 4 s	IonXpressRNA 004 up 058 4 s	RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol	RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich Germany EE2 exposure. Fish exposed to 0 2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA	Experimental Factor: female:sex\|Experimental Factor: 17 ethinylestradiol:compound\|Experimental Factor: 7.34:dose	RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ION_TORRENT	Ion Torrent Proton		ERP018188	Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17Î± ethinylestradiol	ENA FIRST PUBLIC:2017 10 02\|ENA LAST UPDATE:2018 11 16	IonXpressRNA_004_up_058_4.fastq.gz	fastq	2989727396.0	37953454.0	E MTAB 5173:IonXpressRNA 004 up 058 4	0:78.77	A:802963810;C:722434772;G:742850530;T:721478284;N:0	78		802963810	722434772	742850530	721478284	0	ERX1767852	ERS1417526	ERA739176	School of Natural Science, Technology and Environmental Studies Sodertorn University\|European Nucleotide Archive	School of Natural Science, Technology and Environmental Studies Sodertorn University\|European Nucleotide Archive	1	0.76402		0.32503		0.74241		0.4815		128		B		usable mapping rate	ion_torrent	ion_torrent	full_length	random_priming	ribozero	bulk	unknown	unknown	Sweden	2016-10-19	Pharyngula	Embryo	Brain	Nervous System
5804	5804	ERR1698343	ERX1767851	ERS1417525	ERP018188	PRJEB16335	RNA seq of the zebrafish danio rerio brain post developmental exposure to 17a ethinylestradiol	E-MTAB-5173	Transcriptome Analysis	17a ethinylestradiol EE2 is a synthetic estrogen commonly used as an active substance in oral contraceptives. It is frequently found in waste water effluent and raise concern due to its persistent nature. EE2 binds to estrogen receptors with similar affinity to oestradiol and acts as one of the most potent hormone mimics found in the environment. Estrogen is involved in many aspects of the development of the neuroendocrine system influencing both brain structure and behavior. We and others have reported a significant effect on non reproductive behaviors in adult fish and in recent studies we found that developmental exposure to EE2 resulted in an anxiogenic phenotype as adults even post a long remediation period. In this study we aim to study possible mechanisms behind the behavior alterations of zebrafish developmentally exposed to EE2 by sequencing the whole brain transcriptome. Zebrafish embryos were exposed to 0 2.14 and 7.34 ng/L EE2 from 1 day to 80 dpf post the exposure period a remediation period of 120 days followed before the fish were sampled. 3 male brains from the control group 0 ng/L and the 2.14 ng/L group were sampled and 3 female brains from the control group 0 ng/L and 7.34 ng/L were sampled.	ENA FIRST PUBLIC:2017 10 02\|ENA LAST UPDATE:2016 10 19\|ArrayExpress:E MTAB 5173	Protocols: RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich Germany EE2 exposure. Fish exposed to 0 2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA	IonXpressRNA 003 up 058 3	SAMEA4518346	School of Natural Science, Technology and Environmental Studies Sodertorn University	ENA first public:2017 10 02\|ENA last update:2016 10 19\|External Id:SAMEA4518346\|INSDC center alias:School of Natural Science Technology and Environmental Studies Sodertorn University\|INSDC center name:School of Natural Science Technology and Environmental Studies Sodertorn University\|INSDC first public:2017 10 02T17:05:16Z\|INSDC last update:2016 10 19T13:53:59Z\|INSDC status:public\|Submitter Id:E MTAB 5173:IonXpressRNA 003 up 058 3\|age:200\|broker name:ArrayExpress\|common name:zebrafish\|organism part:brain\|sample name:E MTAB 5173:IonXpressRNA 003 up 058 3\|sex:female	Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol	E MTAB 5173:IonXpressRNA 003 up 058 3 s	IonXpressRNA 003 up 058 3 s	RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol	RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich Germany EE2 exposure. Fish exposed to 0 2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA	Experimental Factor: female:sex\|Experimental Factor: n1:compound	RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ION_TORRENT	Ion Torrent Proton		ERP018188	Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17Î± ethinylestradiol	ENA FIRST PUBLIC:2017 10 02\|ENA LAST UPDATE:2018 11 16	IonXpressRNA_003_up_058_3.fastq.gz	fastq	4068383115.0	41996847.0	E MTAB 5173:IonXpressRNA 003 up 058 3	0:96.87	A:1133167706;C:944306379;G:948626944;T:1042282086;N:0	96		1133167706	944306379	948626944	1042282086	0	ERX1767851	ERS1417525	ERA739176	School of Natural Science, Technology and Environmental Studies Sodertorn University\|European Nucleotide Archive	School of Natural Science, Technology and Environmental Studies Sodertorn University\|European Nucleotide Archive	1	0.54804		0.22334		0.76353		0.49163		93		B		usable mapping rate	ion_torrent	ion_torrent	full_length	random_priming	ribozero	bulk	unknown	unknown	Sweden	2016-10-19	Pharyngula	Embryo	Brain	Nervous System
5805	5805	ERR1698342	ERX1767850	ERS1417524	ERP018188	PRJEB16335	RNA seq of the zebrafish danio rerio brain post developmental exposure to 17a ethinylestradiol	E-MTAB-5173	Transcriptome Analysis	17a ethinylestradiol EE2 is a synthetic estrogen commonly used as an active substance in oral contraceptives. It is frequently found in waste water effluent and raise concern due to its persistent nature. EE2 binds to estrogen receptors with similar affinity to oestradiol and acts as one of the most potent hormone mimics found in the environment. Estrogen is involved in many aspects of the development of the neuroendocrine system influencing both brain structure and behavior. We and others have reported a significant effect on non reproductive behaviors in adult fish and in recent studies we found that developmental exposure to EE2 resulted in an anxiogenic phenotype as adults even post a long remediation period. In this study we aim to study possible mechanisms behind the behavior alterations of zebrafish developmentally exposed to EE2 by sequencing the whole brain transcriptome. Zebrafish embryos were exposed to 0 2.14 and 7.34 ng/L EE2 from 1 day to 80 dpf post the exposure period a remediation period of 120 days followed before the fish were sampled. 3 male brains from the control group 0 ng/L and the 2.14 ng/L group were sampled and 3 female brains from the control group 0 ng/L and 7.34 ng/L were sampled.	ENA FIRST PUBLIC:2017 10 02\|ENA LAST UPDATE:2016 10 19\|ArrayExpress:E MTAB 5173	Protocols: RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich Germany EE2 exposure. Fish exposed to 0 2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA	IonXpressRNA 002 up 058 2	SAMEA4518345	School of Natural Science, Technology and Environmental Studies Sodertorn University	ENA first public:2017 10 02\|ENA last update:2016 10 19\|External Id:SAMEA4518345\|INSDC center alias:School of Natural Science Technology and Environmental Studies Sodertorn University\|INSDC center name:School of Natural Science Technology and Environmental Studies Sodertorn University\|INSDC first public:2017 10 02T17:05:16Z\|INSDC last update:2016 10 19T13:53:59Z\|INSDC status:public\|Submitter Id:E MTAB 5173:IonXpressRNA 002 up 058 2\|age:200\|broker name:ArrayExpress\|common name:zebrafish\|organism part:brain\|sample name:E MTAB 5173:IonXpressRNA 002 up 058 2\|sex:female	Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol	E MTAB 5173:IonXpressRNA 002 up 058 2 s	IonXpressRNA 002 up 058 2 s	RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol	RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich Germany EE2 exposure. Fish exposed to 0 2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA	Experimental Factor: female:sex\|Experimental Factor: n1:compound	RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ION_TORRENT	Ion Torrent Proton		ERP018188	Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17Î± ethinylestradiol	ENA FIRST PUBLIC:2017 10 02\|ENA LAST UPDATE:2018 11 16	IonXpressRNA_002_up_058_2.fastq.gz	fastq	2679963893.0	33552723.0	E MTAB 5173:IonXpressRNA 002 up 058 2	0:79.87	A:709092431;C:635329399;G:670478210;T:665063853;N:0	79		709092431	635329399	670478210	665063853	0	ERX1767850	ERS1417524	ERA739176	School of Natural Science, Technology and Environmental Studies Sodertorn University\|European Nucleotide Archive	School of Natural Science, Technology and Environmental Studies Sodertorn University\|European Nucleotide Archive	1	0.43283		0.18649		0.81178		0.52885		116		B		usable mapping rate	ion_torrent	ion_torrent	full_length	random_priming	ribozero	bulk	unknown	unknown	Sweden	2016-10-19	Pharyngula	Embryo	Brain	Nervous System
5806	5806	ERR1698341	ERX1767849	ERS1417523	ERP018188	PRJEB16335	RNA seq of the zebrafish danio rerio brain post developmental exposure to 17a ethinylestradiol	E-MTAB-5173	Transcriptome Analysis	17a ethinylestradiol EE2 is a synthetic estrogen commonly used as an active substance in oral contraceptives. It is frequently found in waste water effluent and raise concern due to its persistent nature. EE2 binds to estrogen receptors with similar affinity to oestradiol and acts as one of the most potent hormone mimics found in the environment. Estrogen is involved in many aspects of the development of the neuroendocrine system influencing both brain structure and behavior. We and others have reported a significant effect on non reproductive behaviors in adult fish and in recent studies we found that developmental exposure to EE2 resulted in an anxiogenic phenotype as adults even post a long remediation period. In this study we aim to study possible mechanisms behind the behavior alterations of zebrafish developmentally exposed to EE2 by sequencing the whole brain transcriptome. Zebrafish embryos were exposed to 0 2.14 and 7.34 ng/L EE2 from 1 day to 80 dpf post the exposure period a remediation period of 120 days followed before the fish were sampled. 3 male brains from the control group 0 ng/L and the 2.14 ng/L group were sampled and 3 female brains from the control group 0 ng/L and 7.34 ng/L were sampled.	ENA FIRST PUBLIC:2017 10 02\|ENA LAST UPDATE:2016 10 19\|ArrayExpress:E MTAB 5173	Protocols: RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich Germany EE2 exposure. Fish exposed to 0 2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA	IonXpressRNA 001 up 058 1	SAMEA4518344	School of Natural Science, Technology and Environmental Studies Sodertorn University	ENA first public:2017 10 02\|ENA last update:2016 10 19\|External Id:SAMEA4518344\|INSDC center alias:School of Natural Science Technology and Environmental Studies Sodertorn University\|INSDC center name:School of Natural Science Technology and Environmental Studies Sodertorn University\|INSDC first public:2017 10 02T17:05:16Z\|INSDC last update:2016 10 19T13:53:59Z\|INSDC status:public\|Submitter Id:E MTAB 5173:IonXpressRNA 001 up 058 1\|age:200\|broker name:ArrayExpress\|common name:zebrafish\|organism part:brain\|sample name:E MTAB 5173:IonXpressRNA 001 up 058 1\|sex:female	Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol	E MTAB 5173:IonXpressRNA 001 up 058 1 s	IonXpressRNA 001 up 058 1 s	RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol	RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich Germany EE2 exposure. Fish exposed to 0 2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA	Experimental Factor: female:sex\|Experimental Factor: n1:compound	RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ION_TORRENT	Ion Torrent Proton		ERP018188	Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17Î± ethinylestradiol	ENA FIRST PUBLIC:2017 10 02\|ENA LAST UPDATE:2018 11 16	IonXpressRNA_001_up_058_1.fastq.gz	fastq	3358902499.0	39857024.0	E MTAB 5173:IonXpressRNA 001 up 058 1	0:84.27	A:933405205;C:784111716;G:780404241;T:860981337;N:0	84		933405205	784111716	780404241	860981337	0	ERX1767849	ERS1417523	ERA739176	School of Natural Science, Technology and Environmental Studies Sodertorn University\|European Nucleotide Archive	School of Natural Science, Technology and Environmental Studies Sodertorn University\|European Nucleotide Archive	1	0.71789		0.33159		0.76619		0.514		56		B		usable mapping rate	ion_torrent	ion_torrent	full_length	random_priming	ribozero	bulk	unknown	unknown	Sweden	2016-10-19	Pharyngula	Embryo	Brain	Nervous System
8088	8088	ERR034127	ERX012653	ERS032268	ERP000635	PRJEB2512	The Zebrafish transcriptome during early development	KI-BN-JKE-DRERIO-RNASEQ-2011	Transcriptome Analysis	Background: Zebrafish Danio rerio is an important model for the study of early vertebrate development. The transition from fertilized egg to embryo is accompanied by a multitude of changes in gene expression and the transcriptional events that underlie these processes have not been fully characterized. In this study we use RNA Seq to characterize and compare the transcriptome of four early developmental stages in zebrafish on a global scale. Results: An average of 79M total reads were detected from the different stages. Out of the total number of reads 65% 73% reads were successfully mapped to the zebrafish genome and 36% 44% out of those were uniquely mapped. The total number of detected unique gene transcripts was 11187 of which 10096 of these were already present at 1 cell stage. The largest number of common transcripts was observed between 1 cell stage and 16 cell stage. An enrichment of gene transcripts with molecular functions of DNA binding protein folding and processing as well as metal ion binding was observed with progression of development. To confirm our RNA Seq results and to further investigate the developmental expression of specific genes the transcript levels of a subset of genes were analyzed using TaqMan® array micro fluidic card TLDA. Conclusion: Clustering analysis of the detected transcripts show a majority of gene transcripts being present at steady levels with a minority of the gene transcripts clustering as increasing or decreasing in expression during development. Developmental stages pre MBT were similar when comparing highly expressed genes whereas 50% epiboly stage differed from the earlier three stages in highly expressed genes number of uniquely expressed genes and enrichment of GO molecular functions.		RNA extracted from zebrafish embryo at 50% epiboly stage	zebrafish embryo 50 epiboly	SAMEA791629	Department of Biosciences and Nutrition, Karolinska Institutet, Sweden	ENA first public:2011 06 09\|ENA last update:2018 03 08\|External Id:SAMEA791629\|INSDC center alias:KI BN\|INSDC center name:Department of Biosciences and Nutrition Karolinska Institutet Sweden\|INSDC first public:2011 06 09T11:04:10Z\|INSDC last update:2018 03 08T15:26:39Z\|INSDC status:public\|Submitter Id:KI BN JKE DRERIO RNASEQ 2011 50epiboly\|common name:zebrafish\|sample name:KI BN JKE DRERIO RNASEQ 2011 50epiboly\|sex:mixed\|strain:Tuebingen	Transcriptome profiling of early zebrafish development	KI BN JKE DRERIO RNASEQ 2011 50epiboly	JKE Drerio rna seq	Transcriptome profiling of 50% epiboly stages of zebrafish embryos.	Total RNA was extracted from approximately 150 embryos per developmental stage using Trireagent Sigma Aldrich. The total RNA was then processed further according to the Small RNA Expression Kit Applied Biosystems.		RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ABI_SOLID	AB SOLiD System 3.0	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</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>	ERP000635	AB SOLiD System 3.0 sequencing; Transcriptome profiling of early zebrafish development	ENA FIRST PUBLIC:2011 06 09\|ENA LAST UPDATE:2018 11 16	KI-BN-JKE-DRERIO-RNASEQ-2011-50epiboly.csfasta.gz KI-BN-JKE-DRERIO-RNASEQ-2011-50epiboly_QV.qual.gz	SOLiD_native SOLiD_native	3929903550.0	78598071.0	KI BN JKE DRERIO RNASEQ 2011 50epiboly	0:50		50							ERX012653	ERS032268	ERA029959	KI-BN\|Department of Biosciences and Nutrition	Department of Biosciences and Nutrition, Karolinska Institutet, Sweden	1	0.60757		0.09893		0.94899		0.77821		50		B		usable mapping rate	legacy	early	unknown	random_priming	unknown	bulk	unknown	unknown	Sweden	2011-06-09	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
8089	8089	ERR034126	ERX012652	ERS032267	ERP000635	PRJEB2512	The Zebrafish transcriptome during early development	KI-BN-JKE-DRERIO-RNASEQ-2011	Transcriptome Analysis	Background: Zebrafish Danio rerio is an important model for the study of early vertebrate development. The transition from fertilized egg to embryo is accompanied by a multitude of changes in gene expression and the transcriptional events that underlie these processes have not been fully characterized. In this study we use RNA Seq to characterize and compare the transcriptome of four early developmental stages in zebrafish on a global scale. Results: An average of 79M total reads were detected from the different stages. Out of the total number of reads 65% 73% reads were successfully mapped to the zebrafish genome and 36% 44% out of those were uniquely mapped. The total number of detected unique gene transcripts was 11187 of which 10096 of these were already present at 1 cell stage. The largest number of common transcripts was observed between 1 cell stage and 16 cell stage. An enrichment of gene transcripts with molecular functions of DNA binding protein folding and processing as well as metal ion binding was observed with progression of development. To confirm our RNA Seq results and to further investigate the developmental expression of specific genes the transcript levels of a subset of genes were analyzed using TaqMan® array micro fluidic card TLDA. Conclusion: Clustering analysis of the detected transcripts show a majority of gene transcripts being present at steady levels with a minority of the gene transcripts clustering as increasing or decreasing in expression during development. Developmental stages pre MBT were similar when comparing highly expressed genes whereas 50% epiboly stage differed from the earlier three stages in highly expressed genes number of uniquely expressed genes and enrichment of GO molecular functions.		RNA extracted from zebrafish embryo at 512 cell stage	zebrafish embryo 512 cell	SAMEA791632	Department of Biosciences and Nutrition, Karolinska Institutet, Sweden	ENA first public:2011 06 09\|ENA last update:2018 03 08\|External Id:SAMEA791632\|INSDC center alias:KI BN\|INSDC center name:Department of Biosciences and Nutrition Karolinska Institutet Sweden\|INSDC first public:2011 06 09T11:04:10Z\|INSDC last update:2018 03 08T15:26:39Z\|INSDC status:public\|Submitter Id:KI BN JKE DRERIO RNASEQ 2011 512cell\|common name:zebrafish\|sample name:KI BN JKE DRERIO RNASEQ 2011 512cell\|sex:mixed\|strain:Tuebingen	Transcriptome profiling of early zebrafish development	KI BN JKE DRERIO RNASEQ 2011 512cell	JKE Drerio rna seq	Transcriptome profiling of 512 cell stage of zebrafish embryos.	Total RNA was extracted from approximately 150 embryos per developmental stage using Trireagent Sigma Aldrich. The total RNA was then processed further according to the Small RNA Expression Kit Applied Biosystems.		RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ABI_SOLID	AB SOLiD System 3.0	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</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>	ERP000635	AB SOLiD System 3.0 sequencing; Transcriptome profiling of early zebrafish development	ENA FIRST PUBLIC:2011 06 09\|ENA LAST UPDATE:2018 11 16	KI-BN-JKE-DRERIO-RNASEQ-2011-512cell.csfasta.gz KI-BN-JKE-DRERIO-RNASEQ-2011-512cell_QV.qual.gz	SOLiD_native SOLiD_native	3918756250.0	78375125.0	KI BN JKE DRERIO RNASEQ 2011 512cell	0:50		50							ERX012652	ERS032267	ERA029959	KI-BN\|Department of Biosciences and Nutrition	Department of Biosciences and Nutrition, Karolinska Institutet, Sweden	1	0.63824		0.09111		0.91969		0.73496		50		B		usable mapping rate	legacy	early	unknown	random_priming	unknown	bulk	unknown	unknown	Sweden	2011-06-09	Blastula	Embryo	Embryo Imprecise	All anatomical structures
8090	8090	ERR034125	ERX012651	ERS032266	ERP000635	PRJEB2512	The Zebrafish transcriptome during early development	KI-BN-JKE-DRERIO-RNASEQ-2011	Transcriptome Analysis	Background: Zebrafish Danio rerio is an important model for the study of early vertebrate development. The transition from fertilized egg to embryo is accompanied by a multitude of changes in gene expression and the transcriptional events that underlie these processes have not been fully characterized. In this study we use RNA Seq to characterize and compare the transcriptome of four early developmental stages in zebrafish on a global scale. Results: An average of 79M total reads were detected from the different stages. Out of the total number of reads 65% 73% reads were successfully mapped to the zebrafish genome and 36% 44% out of those were uniquely mapped. The total number of detected unique gene transcripts was 11187 of which 10096 of these were already present at 1 cell stage. The largest number of common transcripts was observed between 1 cell stage and 16 cell stage. An enrichment of gene transcripts with molecular functions of DNA binding protein folding and processing as well as metal ion binding was observed with progression of development. To confirm our RNA Seq results and to further investigate the developmental expression of specific genes the transcript levels of a subset of genes were analyzed using TaqMan® array micro fluidic card TLDA. Conclusion: Clustering analysis of the detected transcripts show a majority of gene transcripts being present at steady levels with a minority of the gene transcripts clustering as increasing or decreasing in expression during development. Developmental stages pre MBT were similar when comparing highly expressed genes whereas 50% epiboly stage differed from the earlier three stages in highly expressed genes number of uniquely expressed genes and enrichment of GO molecular functions.		RNA extracted from zebrafish embryo at 16 cell stage	zebrafish embryo 16 cell	SAMEA791631	Department of Biosciences and Nutrition, Karolinska Institutet, Sweden	ENA first public:2011 06 09\|ENA last update:2018 03 08\|External Id:SAMEA791631\|INSDC center alias:KI BN\|INSDC center name:Department of Biosciences and Nutrition Karolinska Institutet Sweden\|INSDC first public:2011 06 09T11:04:10Z\|INSDC last update:2018 03 08T15:26:39Z\|INSDC status:public\|Submitter Id:KI BN JKE DRERIO RNASEQ 2011 16cell\|common name:zebrafish\|sample name:KI BN JKE DRERIO RNASEQ 2011 16cell\|sex:mixed\|strain:Tuebingen	Transcriptome profiling of early zebrafish development	KI BN JKE DRERIO RNASEQ 2011 16cell	JKE Drerio rna seq	Transcriptome profiling of 16 cell stage of zebrafish embryos.	Total RNA was extracted from approximately 150 embryos per developmental stage using Trireagent Sigma Aldrich. The total RNA was then processed further according to the Small RNA Expression Kit Applied Biosystems.		RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ABI_SOLID	AB SOLiD System 3.0	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</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>	ERP000635	AB SOLiD System 3.0 sequencing; Transcriptome profiling of early zebrafish development	ENA FIRST PUBLIC:2011 06 09\|ENA LAST UPDATE:2018 11 16	KI-BN-JKE-DRERIO-RNASEQ-2011-16cell.csfasta.gz KI-BN-JKE-DRERIO-RNASEQ-2011-16cell_QV.qual.gz	SOLiD_native SOLiD_native	4256756500.0	85135130.0	KI BN JKE DRERIO RNASEQ 2011 16cell	0:50		50							ERX012651	ERS032266	ERA029959	KI-BN\|Department of Biosciences and Nutrition	Department of Biosciences and Nutrition, Karolinska Institutet, Sweden	1	0.57946		0.08115		0.91896		0.72164		50		B		usable mapping rate	legacy	early	unknown	random_priming	unknown	bulk	unknown	unknown	Sweden	2011-06-09	Cleavage	Embryo	Embryo Imprecise	All anatomical structures
8091	8091	ERR034124	ERX012650	ERS032265	ERP000635	PRJEB2512	The Zebrafish transcriptome during early development	KI-BN-JKE-DRERIO-RNASEQ-2011	Transcriptome Analysis	Background: Zebrafish Danio rerio is an important model for the study of early vertebrate development. The transition from fertilized egg to embryo is accompanied by a multitude of changes in gene expression and the transcriptional events that underlie these processes have not been fully characterized. In this study we use RNA Seq to characterize and compare the transcriptome of four early developmental stages in zebrafish on a global scale. Results: An average of 79M total reads were detected from the different stages. Out of the total number of reads 65% 73% reads were successfully mapped to the zebrafish genome and 36% 44% out of those were uniquely mapped. The total number of detected unique gene transcripts was 11187 of which 10096 of these were already present at 1 cell stage. The largest number of common transcripts was observed between 1 cell stage and 16 cell stage. An enrichment of gene transcripts with molecular functions of DNA binding protein folding and processing as well as metal ion binding was observed with progression of development. To confirm our RNA Seq results and to further investigate the developmental expression of specific genes the transcript levels of a subset of genes were analyzed using TaqMan® array micro fluidic card TLDA. Conclusion: Clustering analysis of the detected transcripts show a majority of gene transcripts being present at steady levels with a minority of the gene transcripts clustering as increasing or decreasing in expression during development. Developmental stages pre MBT were similar when comparing highly expressed genes whereas 50% epiboly stage differed from the earlier three stages in highly expressed genes number of uniquely expressed genes and enrichment of GO molecular functions.		RNA extracted from zebrafish embryo at 1 cell stage	zebrafish embryo 1 cell	SAMEA791630	Department of Biosciences and Nutrition, Karolinska Institutet, Sweden	ENA first public:2011 06 09\|ENA last update:2018 03 08\|External Id:SAMEA791630\|INSDC center alias:KI BN\|INSDC center name:Department of Biosciences and Nutrition Karolinska Institutet Sweden\|INSDC first public:2011 06 09T11:04:10Z\|INSDC last update:2018 03 08T15:26:39Z\|INSDC status:public\|Submitter Id:KI BN JKE DRERIO RNASEQ 2011 1cell\|common name:zebrafish\|sample name:KI BN JKE DRERIO RNASEQ 2011 1cell\|sex:mixed\|strain:Tuebingen	Transcriptome profiling of early zebrafish development	KI BN JKE DRERIO RNASEQ 2011 1cell	JKE Drerio rna seq	Transcriptome profiling of 1 cell stage of zebrafish embryos.	Total RNA was extracted from approximately 150 embryos per developmental stage using Trireagent Sigma Aldrich. The total RNA was then processed further according to the Small RNA Expression Kit Applied Biosystems.		RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ABI_SOLID	AB SOLiD System 3.0	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</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>	ERP000635	AB SOLiD System 3.0 sequencing; Transcriptome profiling of early zebrafish development	ENA FIRST PUBLIC:2011 06 09\|ENA LAST UPDATE:2018 11 16	KI-BN-JKE-DRERIO-RNASEQ-2011-1cell.csfasta.gz KI-BN-JKE-DRERIO-RNASEQ-2011-1cell_QV.qual.gz	SOLiD_native SOLiD_native	3676380950.0	73527619.0	KI BN JKE DRERIO RNASEQ 2011 1cell	0:50		50							ERX012650	ERS032265	ERA029959	KI-BN\|Department of Biosciences and Nutrition	Department of Biosciences and Nutrition, Karolinska Institutet, Sweden	1	0.64855		0.08432		0.9052		0.74223		50		B		usable mapping rate	legacy	early	unknown	random_priming	unknown	bulk	unknown	unknown	Sweden	2011-06-09	Zygote	Embryo	Embryo Imprecise	All anatomical structures
10060	10060	ERR4795364	ERX4665135	ERS5281176	ERP124847	PRJEB41113	Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	E-MTAB-9727	Transcriptome Analysis	The mesothelium forms epithelial membranes that line the bodies cavities and surround the internal organs. Mesothelia widely contribute to organ homeostasis and regeneration and their dysregulation can result in congenital anomalies of the viscera ventral wall defects and mesothelioma tumors. Nonetheless the embryonic ontogeny and developmental regulation of mesothelium formation has remained uncharted. Here we combine genetic lineage tracing in toto live imaging and single cell transcriptomics in zebrafish to track mesothelial progenitor origins from the lateral plate mesoderm LPM. Our single cell analysis uncovers a post gastrulation gene expression signature centered on hand2 that delineates distinct progenitor populations within the forming LPM. Combining gene expression analysis and imaging of transgenic reporter zebrafish embryos we chart the origin of mesothelial progenitors to the lateral most hand2 expressing LPM and confirm evolutionary conservation in mouse. Our time lapse imaging of transgenic hand2 reporter embryos captures zebrafish mesothelium formation documenting the coordinated cell movements that form pericardium and visceral and parietal peritoneum. We establish that the primordial germ cells migrate associated with the forming mesothelium as ventral migration boundary. Functionally hand2 mutants fail to close the ventral mesothelium due to perturbed migration of mesothelium progenitors. Analyzing mouse and human mesothelioma tumors hypothesized to emerge from transformed mesothelium we find de novo expression of LPM associated transcription factors and in particular of Hand2 indicating the re initiation of a developmental transcriptional program in mesothelioma. Taken together our work outlines a genetic and developmental signature of mesothelial origins centered around Hand2 contributing to our understanding of mesothelial pathologies and mesothelioma.	ENA FIRST PUBLIC:2022 01 14\|ENA LAST UPDATE:2022 01 14	Protocols: Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse trans…	Sample 4	E MTAB 9727:Sample 4		isolate:not applicable\|organism:Danio rerio\|sex:mixed\|age:10\|developmental stage:tailbud stage\|organism part:lateral plate mesoderm plate\|genotype:drl:mCherry\|ENA FIRST PUBLIC:2021 04 01\|ENA LAST UPDATE:2021 09 01	NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	E MTAB 9727:Sample 4 s	Sample 4 s	Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription an…	Experimental Factor: replicate:lateral plate mesoderm plate 4	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	RANDOM	SINGLE	ILLUMINA	NextSeq 500		ERP124847	NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	ENA FIRST PUBLIC:2022 01 14\|ENA LAST UPDATE:2022 01 14	SN4_AH2TW3BGX5_S1_R1_cat.fastq.gz	fastq	5410723202.0	71707309.0	E MTAB 9727:Sample 4	0:75.46 1:0	A:1330416803;C:531269504;G:734031980;T:2814959249;N:45666	75	0	1330416803	531269504	734031980	2814959249	45666	ERX4665135	ERS5281176	ERA3048543	University of Zurich\|European Nucleotide Archive	University of Zurich\|European Nucleotide Archive	1	0.33614		0.21532		0.99019		0.41002		76		B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Switzerland	2021-04-01	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
10061	10061	ERR4795365	ERX4665135	ERS5281176	ERP124847	PRJEB41113	Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	E-MTAB-9727	Transcriptome Analysis	The mesothelium forms epithelial membranes that line the bodies cavities and surround the internal organs. Mesothelia widely contribute to organ homeostasis and regeneration and their dysregulation can result in congenital anomalies of the viscera ventral wall defects and mesothelioma tumors. Nonetheless the embryonic ontogeny and developmental regulation of mesothelium formation has remained uncharted. Here we combine genetic lineage tracing in toto live imaging and single cell transcriptomics in zebrafish to track mesothelial progenitor origins from the lateral plate mesoderm LPM. Our single cell analysis uncovers a post gastrulation gene expression signature centered on hand2 that delineates distinct progenitor populations within the forming LPM. Combining gene expression analysis and imaging of transgenic reporter zebrafish embryos we chart the origin of mesothelial progenitors to the lateral most hand2 expressing LPM and confirm evolutionary conservation in mouse. Our time lapse imaging of transgenic hand2 reporter embryos captures zebrafish mesothelium formation documenting the coordinated cell movements that form pericardium and visceral and parietal peritoneum. We establish that the primordial germ cells migrate associated with the forming mesothelium as ventral migration boundary. Functionally hand2 mutants fail to close the ventral mesothelium due to perturbed migration of mesothelium progenitors. Analyzing mouse and human mesothelioma tumors hypothesized to emerge from transformed mesothelium we find de novo expression of LPM associated transcription factors and in particular of Hand2 indicating the re initiation of a developmental transcriptional program in mesothelioma. Taken together our work outlines a genetic and developmental signature of mesothelial origins centered around Hand2 contributing to our understanding of mesothelial pathologies and mesothelioma.	ENA FIRST PUBLIC:2022 01 14\|ENA LAST UPDATE:2022 01 14	Protocols: Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse trans…	Sample 4	E MTAB 9727:Sample 4		isolate:not applicable\|organism:Danio rerio\|sex:mixed\|age:10\|developmental stage:tailbud stage\|organism part:lateral plate mesoderm plate\|genotype:drl:mCherry\|ENA FIRST PUBLIC:2021 04 01\|ENA LAST UPDATE:2021 09 01	NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	E MTAB 9727:Sample 4 s	Sample 4 s	Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription an…	Experimental Factor: replicate:lateral plate mesoderm plate 4	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	RANDOM	SINGLE	ILLUMINA	NextSeq 500		ERP124847	NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	ENA FIRST PUBLIC:2022 01 14\|ENA LAST UPDATE:2022 01 14	SN4_AH2TW3BGX5_S1_R2_cat.fastq.gz	fastq	5414184547.0	71707309.0	E MTAB 9727:Sample 4 1	0:0 1:75.50	A:1582938104;C:1052565419;G:1177180395;T:1600161662;N:1338967	0	75	1582938104	1052565419	1177180395	1600161662	1338967	ERX4665135	ERS5281176	ERA3048543	University of Zurich\|European Nucleotide Archive	University of Zurich\|European Nucleotide Archive	1	0.84976		0.28521		0.85038		0.5124		75		B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Switzerland	2021-04-01	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
10062	10062	ERR4795362	ERX4665134	ERS5281175	ERP124847	PRJEB41113	Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	E-MTAB-9727	Transcriptome Analysis	The mesothelium forms epithelial membranes that line the bodies cavities and surround the internal organs. Mesothelia widely contribute to organ homeostasis and regeneration and their dysregulation can result in congenital anomalies of the viscera ventral wall defects and mesothelioma tumors. Nonetheless the embryonic ontogeny and developmental regulation of mesothelium formation has remained uncharted. Here we combine genetic lineage tracing in toto live imaging and single cell transcriptomics in zebrafish to track mesothelial progenitor origins from the lateral plate mesoderm LPM. Our single cell analysis uncovers a post gastrulation gene expression signature centered on hand2 that delineates distinct progenitor populations within the forming LPM. Combining gene expression analysis and imaging of transgenic reporter zebrafish embryos we chart the origin of mesothelial progenitors to the lateral most hand2 expressing LPM and confirm evolutionary conservation in mouse. Our time lapse imaging of transgenic hand2 reporter embryos captures zebrafish mesothelium formation documenting the coordinated cell movements that form pericardium and visceral and parietal peritoneum. We establish that the primordial germ cells migrate associated with the forming mesothelium as ventral migration boundary. Functionally hand2 mutants fail to close the ventral mesothelium due to perturbed migration of mesothelium progenitors. Analyzing mouse and human mesothelioma tumors hypothesized to emerge from transformed mesothelium we find de novo expression of LPM associated transcription factors and in particular of Hand2 indicating the re initiation of a developmental transcriptional program in mesothelioma. Taken together our work outlines a genetic and developmental signature of mesothelial origins centered around Hand2 contributing to our understanding of mesothelial pathologies and mesothelioma.	ENA FIRST PUBLIC:2022 01 14\|ENA LAST UPDATE:2022 01 14	Protocols: Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse trans…	Sample 3	E MTAB 9727:Sample 3		isolate:not applicable\|organism:Danio rerio\|sex:mixed\|age:10\|developmental stage:tailbud stage\|organism part:lateral plate mesoderm plate\|genotype:drl:mCherry\|ENA FIRST PUBLIC:2021 04 01\|ENA LAST UPDATE:2021 09 01	NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	E MTAB 9727:Sample 3 s	Sample 3 s	Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription an…	Experimental Factor: replicate:lateral plate mesoderm plate 3	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	RANDOM	SINGLE	ILLUMINA	NextSeq 500		ERP124847	NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	ENA FIRST PUBLIC:2022 01 14\|ENA LAST UPDATE:2022 01 14	SN3_AHY3WGBGX3_S7_R1_cat.fastq.gz	fastq	4823193891.0	63965519.0	E MTAB 9727:Sample 3	0:75.40 1:0	A:1323978162;C:446831209;G:581746343;T:2470114091;N:524086	75	0	1323978162	446831209	581746343	2470114091	524086	ERX4665134	ERS5281175	ERA3048543	University of Zurich\|European Nucleotide Archive	University of Zurich\|European Nucleotide Archive	1	0.36549		0.19722		0.95552		0.4702		76		B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Switzerland	2021-04-01	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
10063	10063	ERR4795363	ERX4665134	ERS5281175	ERP124847	PRJEB41113	Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	E-MTAB-9727	Transcriptome Analysis	The mesothelium forms epithelial membranes that line the bodies cavities and surround the internal organs. Mesothelia widely contribute to organ homeostasis and regeneration and their dysregulation can result in congenital anomalies of the viscera ventral wall defects and mesothelioma tumors. Nonetheless the embryonic ontogeny and developmental regulation of mesothelium formation has remained uncharted. Here we combine genetic lineage tracing in toto live imaging and single cell transcriptomics in zebrafish to track mesothelial progenitor origins from the lateral plate mesoderm LPM. Our single cell analysis uncovers a post gastrulation gene expression signature centered on hand2 that delineates distinct progenitor populations within the forming LPM. Combining gene expression analysis and imaging of transgenic reporter zebrafish embryos we chart the origin of mesothelial progenitors to the lateral most hand2 expressing LPM and confirm evolutionary conservation in mouse. Our time lapse imaging of transgenic hand2 reporter embryos captures zebrafish mesothelium formation documenting the coordinated cell movements that form pericardium and visceral and parietal peritoneum. We establish that the primordial germ cells migrate associated with the forming mesothelium as ventral migration boundary. Functionally hand2 mutants fail to close the ventral mesothelium due to perturbed migration of mesothelium progenitors. Analyzing mouse and human mesothelioma tumors hypothesized to emerge from transformed mesothelium we find de novo expression of LPM associated transcription factors and in particular of Hand2 indicating the re initiation of a developmental transcriptional program in mesothelioma. Taken together our work outlines a genetic and developmental signature of mesothelial origins centered around Hand2 contributing to our understanding of mesothelial pathologies and mesothelioma.	ENA FIRST PUBLIC:2022 01 14\|ENA LAST UPDATE:2022 01 14	Protocols: Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse trans…	Sample 3	E MTAB 9727:Sample 3		isolate:not applicable\|organism:Danio rerio\|sex:mixed\|age:10\|developmental stage:tailbud stage\|organism part:lateral plate mesoderm plate\|genotype:drl:mCherry\|ENA FIRST PUBLIC:2021 04 01\|ENA LAST UPDATE:2021 09 01	NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	E MTAB 9727:Sample 3 s	Sample 3 s	Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription an…	Experimental Factor: replicate:lateral plate mesoderm plate 3	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	RANDOM	SINGLE	ILLUMINA	NextSeq 500		ERP124847	NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	ENA FIRST PUBLIC:2022 01 14\|ENA LAST UPDATE:2022 01 14	SN3_AHY3WGBGX3_S7_R2_cat.fastq.gz	fastq	4828889391.0	63965519.0	E MTAB 9727:Sample 3 1	0:0 1:75.49	A:1434099697;C:964508763;G:893584575;T:1534727600;N:1968756	0	75	1434099697	964508763	893584575	1534727600	1968756	ERX4665134	ERS5281175	ERA3048543	University of Zurich\|European Nucleotide Archive	University of Zurich\|European Nucleotide Archive	1	0.85811		0.26231		0.82731		0.48618		76		B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Switzerland	2021-04-01	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
10064	10064	ERR4795360	ERX4665133	ERS5281174	ERP124847	PRJEB41113	Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	E-MTAB-9727	Transcriptome Analysis	The mesothelium forms epithelial membranes that line the bodies cavities and surround the internal organs. Mesothelia widely contribute to organ homeostasis and regeneration and their dysregulation can result in congenital anomalies of the viscera ventral wall defects and mesothelioma tumors. Nonetheless the embryonic ontogeny and developmental regulation of mesothelium formation has remained uncharted. Here we combine genetic lineage tracing in toto live imaging and single cell transcriptomics in zebrafish to track mesothelial progenitor origins from the lateral plate mesoderm LPM. Our single cell analysis uncovers a post gastrulation gene expression signature centered on hand2 that delineates distinct progenitor populations within the forming LPM. Combining gene expression analysis and imaging of transgenic reporter zebrafish embryos we chart the origin of mesothelial progenitors to the lateral most hand2 expressing LPM and confirm evolutionary conservation in mouse. Our time lapse imaging of transgenic hand2 reporter embryos captures zebrafish mesothelium formation documenting the coordinated cell movements that form pericardium and visceral and parietal peritoneum. We establish that the primordial germ cells migrate associated with the forming mesothelium as ventral migration boundary. Functionally hand2 mutants fail to close the ventral mesothelium due to perturbed migration of mesothelium progenitors. Analyzing mouse and human mesothelioma tumors hypothesized to emerge from transformed mesothelium we find de novo expression of LPM associated transcription factors and in particular of Hand2 indicating the re initiation of a developmental transcriptional program in mesothelioma. Taken together our work outlines a genetic and developmental signature of mesothelial origins centered around Hand2 contributing to our understanding of mesothelial pathologies and mesothelioma.	ENA FIRST PUBLIC:2022 01 14\|ENA LAST UPDATE:2022 01 14	Protocols: Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse trans…	Sample 2	E MTAB 9727:Sample 2		isolate:not applicable\|organism:Danio rerio\|sex:mixed\|age:10\|developmental stage:tailbud stage\|organism part:lateral plate mesoderm plate\|genotype:drl:mCherry\|ENA FIRST PUBLIC:2021 04 01\|ENA LAST UPDATE:2021 09 01	NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	E MTAB 9727:Sample 2 s	Sample 2 s	Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription an…	Experimental Factor: replicate:lateral plate mesoderm plate 2	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	RANDOM	SINGLE	ILLUMINA	NextSeq 500		ERP124847	NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	ENA FIRST PUBLIC:2022 01 14\|ENA LAST UPDATE:2022 01 14	SN2_AHY3WGBGX3_S6_R1_cat.fastq.gz	fastq	5598371393.0	74235388.0	E MTAB 9727:Sample 2	0:75.41 1:0	A:1526486973;C:558020193;G:717587491;T:2795646081;N:630655	75	0	1526486973	558020193	717587491	2795646081	630655	ERX4665133	ERS5281174	ERA3048543	University of Zurich\|European Nucleotide Archive	University of Zurich\|European Nucleotide Archive	1	0.28059		0.19252		0.96404		0.4874		75		B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Switzerland	2021-04-01	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
10065	10065	ERR4795361	ERX4665133	ERS5281174	ERP124847	PRJEB41113	Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	E-MTAB-9727	Transcriptome Analysis	The mesothelium forms epithelial membranes that line the bodies cavities and surround the internal organs. Mesothelia widely contribute to organ homeostasis and regeneration and their dysregulation can result in congenital anomalies of the viscera ventral wall defects and mesothelioma tumors. Nonetheless the embryonic ontogeny and developmental regulation of mesothelium formation has remained uncharted. Here we combine genetic lineage tracing in toto live imaging and single cell transcriptomics in zebrafish to track mesothelial progenitor origins from the lateral plate mesoderm LPM. Our single cell analysis uncovers a post gastrulation gene expression signature centered on hand2 that delineates distinct progenitor populations within the forming LPM. Combining gene expression analysis and imaging of transgenic reporter zebrafish embryos we chart the origin of mesothelial progenitors to the lateral most hand2 expressing LPM and confirm evolutionary conservation in mouse. Our time lapse imaging of transgenic hand2 reporter embryos captures zebrafish mesothelium formation documenting the coordinated cell movements that form pericardium and visceral and parietal peritoneum. We establish that the primordial germ cells migrate associated with the forming mesothelium as ventral migration boundary. Functionally hand2 mutants fail to close the ventral mesothelium due to perturbed migration of mesothelium progenitors. Analyzing mouse and human mesothelioma tumors hypothesized to emerge from transformed mesothelium we find de novo expression of LPM associated transcription factors and in particular of Hand2 indicating the re initiation of a developmental transcriptional program in mesothelioma. Taken together our work outlines a genetic and developmental signature of mesothelial origins centered around Hand2 contributing to our understanding of mesothelial pathologies and mesothelioma.	ENA FIRST PUBLIC:2022 01 14\|ENA LAST UPDATE:2022 01 14	Protocols: Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse trans…	Sample 2	E MTAB 9727:Sample 2		isolate:not applicable\|organism:Danio rerio\|sex:mixed\|age:10\|developmental stage:tailbud stage\|organism part:lateral plate mesoderm plate\|genotype:drl:mCherry\|ENA FIRST PUBLIC:2021 04 01\|ENA LAST UPDATE:2021 09 01	NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	E MTAB 9727:Sample 2 s	Sample 2 s	Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription an…	Experimental Factor: replicate:lateral plate mesoderm plate 2	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	RANDOM	SINGLE	ILLUMINA	NextSeq 500		ERP124847	NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	ENA FIRST PUBLIC:2022 01 14\|ENA LAST UPDATE:2022 01 14	SN2_AHY3WGBGX3_S6_R2_cat.fastq.gz	fastq	5600151371.0	74235388.0	E MTAB 9727:Sample 2 1	0:0 1:75.44	A:1850568176;C:1035622971;G:1071138281;T:1640475883;N:2346060	0	75	1850568176	1035622971	1071138281	1640475883	2346060	ERX4665133	ERS5281174	ERA3048543	University of Zurich\|European Nucleotide Archive	University of Zurich\|European Nucleotide Archive	1	0.7679		0.30371		0.82651		0.43401		75		B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Switzerland	2021-04-01	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
10066	10066	ERR4795358	ERX4665132	ERS5281173	ERP124847	PRJEB41113	Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	E-MTAB-9727	Transcriptome Analysis	The mesothelium forms epithelial membranes that line the bodies cavities and surround the internal organs. Mesothelia widely contribute to organ homeostasis and regeneration and their dysregulation can result in congenital anomalies of the viscera ventral wall defects and mesothelioma tumors. Nonetheless the embryonic ontogeny and developmental regulation of mesothelium formation has remained uncharted. Here we combine genetic lineage tracing in toto live imaging and single cell transcriptomics in zebrafish to track mesothelial progenitor origins from the lateral plate mesoderm LPM. Our single cell analysis uncovers a post gastrulation gene expression signature centered on hand2 that delineates distinct progenitor populations within the forming LPM. Combining gene expression analysis and imaging of transgenic reporter zebrafish embryos we chart the origin of mesothelial progenitors to the lateral most hand2 expressing LPM and confirm evolutionary conservation in mouse. Our time lapse imaging of transgenic hand2 reporter embryos captures zebrafish mesothelium formation documenting the coordinated cell movements that form pericardium and visceral and parietal peritoneum. We establish that the primordial germ cells migrate associated with the forming mesothelium as ventral migration boundary. Functionally hand2 mutants fail to close the ventral mesothelium due to perturbed migration of mesothelium progenitors. Analyzing mouse and human mesothelioma tumors hypothesized to emerge from transformed mesothelium we find de novo expression of LPM associated transcription factors and in particular of Hand2 indicating the re initiation of a developmental transcriptional program in mesothelioma. Taken together our work outlines a genetic and developmental signature of mesothelial origins centered around Hand2 contributing to our understanding of mesothelial pathologies and mesothelioma.	ENA FIRST PUBLIC:2022 01 14\|ENA LAST UPDATE:2022 01 14	Protocols: Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse trans…	Sample 1	E MTAB 9727:Sample 1		isolate:not applicable\|organism:Danio rerio\|sex:mixed\|age:10\|developmental stage:tailbud stage\|organism part:lateral plate mesoderm plate\|genotype:drl:mCherry\|ENA FIRST PUBLIC:2021 04 01\|ENA LAST UPDATE:2021 09 01	NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	E MTAB 9727:Sample 1 s	Sample 1 s	Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription an…	Experimental Factor: replicate:lateral plate mesoderm plate 1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	RANDOM	SINGLE	ILLUMINA	NextSeq 500		ERP124847	NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	ENA FIRST PUBLIC:2022 01 14\|ENA LAST UPDATE:2022 01 14	SN1_AHY3WGBGX3_S5_R1_cat.fastq.gz	fastq	4996502316.0	66258508.0	E MTAB 9727:Sample 1	0:75.41 1:0	A:1330744174;C:451622042;G:591151500;T:2622422664;N:561936	75	0	1330744174	451622042	591151500	2622422664	561936	ERX4665132	ERS5281173	ERA3048543	University of Zurich\|European Nucleotide Archive	University of Zurich\|European Nucleotide Archive	1	0.29754		0.17671		0.9669		0.45463		75		B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Switzerland	2021-04-01	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
10067	10067	ERR4795359	ERX4665132	ERS5281173	ERP124847	PRJEB41113	Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	E-MTAB-9727	Transcriptome Analysis	The mesothelium forms epithelial membranes that line the bodies cavities and surround the internal organs. Mesothelia widely contribute to organ homeostasis and regeneration and their dysregulation can result in congenital anomalies of the viscera ventral wall defects and mesothelioma tumors. Nonetheless the embryonic ontogeny and developmental regulation of mesothelium formation has remained uncharted. Here we combine genetic lineage tracing in toto live imaging and single cell transcriptomics in zebrafish to track mesothelial progenitor origins from the lateral plate mesoderm LPM. Our single cell analysis uncovers a post gastrulation gene expression signature centered on hand2 that delineates distinct progenitor populations within the forming LPM. Combining gene expression analysis and imaging of transgenic reporter zebrafish embryos we chart the origin of mesothelial progenitors to the lateral most hand2 expressing LPM and confirm evolutionary conservation in mouse. Our time lapse imaging of transgenic hand2 reporter embryos captures zebrafish mesothelium formation documenting the coordinated cell movements that form pericardium and visceral and parietal peritoneum. We establish that the primordial germ cells migrate associated with the forming mesothelium as ventral migration boundary. Functionally hand2 mutants fail to close the ventral mesothelium due to perturbed migration of mesothelium progenitors. Analyzing mouse and human mesothelioma tumors hypothesized to emerge from transformed mesothelium we find de novo expression of LPM associated transcription factors and in particular of Hand2 indicating the re initiation of a developmental transcriptional program in mesothelioma. Taken together our work outlines a genetic and developmental signature of mesothelial origins centered around Hand2 contributing to our understanding of mesothelial pathologies and mesothelioma.	ENA FIRST PUBLIC:2022 01 14\|ENA LAST UPDATE:2022 01 14	Protocols: Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse trans…	Sample 1	E MTAB 9727:Sample 1		isolate:not applicable\|organism:Danio rerio\|sex:mixed\|age:10\|developmental stage:tailbud stage\|organism part:lateral plate mesoderm plate\|genotype:drl:mCherry\|ENA FIRST PUBLIC:2021 04 01\|ENA LAST UPDATE:2021 09 01	NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	E MTAB 9727:Sample 1 s	Sample 1 s	Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription an…	Experimental Factor: replicate:lateral plate mesoderm plate 1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	RANDOM	SINGLE	ILLUMINA	NextSeq 500		ERP124847	NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	ENA FIRST PUBLIC:2022 01 14\|ENA LAST UPDATE:2022 01 14	SN1_AHY3WGBGX3_S5_R2_cat.fastq.gz	fastq	4999908389.0	66258508.0	E MTAB 9727:Sample 1 1	0:0 1:75.46	A:1591945117;C:933968124;G:986108614;T:1485824022;N:2062512	0	75	1591945117	933968124	986108614	1485824022	2062512	ERX4665132	ERS5281173	ERA3048543	University of Zurich\|European Nucleotide Archive	University of Zurich\|European Nucleotide Archive	1	0.81333		0.2466		0.83027		0.51572		75		B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Switzerland	2021-04-01	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
11238	11238	ERR10782555	ERX10233132	ERS14439197	ERP144048	PRJEB58983	RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling	E-MTAB-12503	Transcriptome Analysis	Defects in blood development are a major contributor to complex congenital anomalies. Thrombocytopenia Absent Radius TAR Syndrome is a rare congenital disease presenting with reduced blood platelets megakaryocytic thrombocytopenia and forelimb anomalies concurrent with variable heart and kidney defects caused by hypomorphic RBM8A/Y14 gene function. RBM8A encodes a component of the ubiquitous exon junction complex involved in mRNA splicing transport and nonsense mediated decay. How perturbing a general mRNA processing factor causes the distinct phenotypes of TAR Syndrome remains unknown. Here we connect zebrafish rbm8a perturbation to early hematopoiesis defects via attenuated planar cell polarity PCP signaling involved in controlling developmental cell arrangements. Combining different genetic means to reduce rbm8a function we find a significant reduction of cd41 positive thrombocytes in hypomorphic rbm8a larvae. Transcriptomics analysis documents rbm8a mutant zebrafish embryos already post gastrulation accumulate mRNAs with erroneously included introns a hallmark of defective nonsense mediated decay. Affected mRNAs include transcripts encoding components of the non canonical Wnt pathway involved in PCP signaling and rbm8a mutant embryos show hallmarks of Wnt/PCP dependent early convergent extension defects. We establish that reduced rbm8a function synergizes with perturbations in Wnt/PCP pathway genes including wnt5b wnt11f2 fzd7a and vangl2. Following axis formation rbm8a perturbation impairs the migration and architecture of the lateral plate mesoderm LPM that forms the hematopoietic cardiovascular kidney and forelimb skeleton progenitors. Subsequently rbm8a perturbation impairs expression of early hematopoietic/endothelial genes including runx1a kdrl sox7 and the megakaryocyte regulator gfi1aa. Lastly we document similar hematopoietic defects upon loss of vangl2. Together our data link reduced rbm8a function to LPM migration and hematopoietic defects via attenuated Wnt/PCP signaling. Our…	ENA FIRST PUBLIC:2023 03 31\|ENA LAST UPDATE:2023 03 31	Protocols: Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined pooled embryos by Trizol LS extraction as per manufacturerâ€™s guidelines Invitrogen with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.	Sample 6	E MTAB 12503:Sample 6		strain:mixed AB and Tubingen\|ENA FIRST PUBLIC:2023 03 31\|individual:20170530.A 6\|organism:Danio rerio\|organism:Danio rerio\|ENA LAST UPDATE:2023 03 31\|scientific name:Danio rerio\|common name:zebrafish\|organism part:embryo\|age:10\|developmental stage:bud\|genotype:wild type genotype\|ENA FIRST PUBLIC:2023 03 31\|ENA LAST UPDATE:2023 03 31	Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling	E MTAB 12503:Sample 6 p	Sample 6 p	RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling	Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined pooled embryos by Trizol LS extraction as per manufacturerâ€™s guidelines Invitrogen with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.	Experimental Factor: developmental stage:bud\|Experimental Factor: genotype:wild type genotype	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	RANDOM	PAIRED	ILLUMINA	Illumina HiSeq 4000		ERP144048	Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling	ENA FIRST PUBLIC:2023 03 31\|ENA LAST UPDATE:2023 03 31	20170530.A-6_R1.fastq.gz 20170530.A-6_R2.fastq.gz	fastq fastq	14809693138.0	49038719.0	E MTAB 12503:20170530.A 6 R	0:151 1:151	A:4069749497;C:3367864217;G:3430269434;T:3928390721;N:13419269	151	151	4069749497	3367864217	3430269434	3928390721	13419269	ERX10233132	ERS14439197	ERA20162442	University of Zurich\|European Nucleotide Archive	University of Zurich\|European Nucleotide Archive	2	0.83945	0.69977	0.27269	0.22488	0.74523	0.77654	0.4899	0.4358	151	151	B	B	biological fallback assumption	illumina	hiseq_era	unknown	random_priming	trueseq	sc	unknown	unknown	Switzerland	2023-03-31	Multi-stage	Embryo	Whole Organism	All anatomical structures
11239	11239	ERR10782554	ERX10233131	ERS14439196	ERP144048	PRJEB58983	RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling	E-MTAB-12503	Transcriptome Analysis	Defects in blood development are a major contributor to complex congenital anomalies. Thrombocytopenia Absent Radius TAR Syndrome is a rare congenital disease presenting with reduced blood platelets megakaryocytic thrombocytopenia and forelimb anomalies concurrent with variable heart and kidney defects caused by hypomorphic RBM8A/Y14 gene function. RBM8A encodes a component of the ubiquitous exon junction complex involved in mRNA splicing transport and nonsense mediated decay. How perturbing a general mRNA processing factor causes the distinct phenotypes of TAR Syndrome remains unknown. Here we connect zebrafish rbm8a perturbation to early hematopoiesis defects via attenuated planar cell polarity PCP signaling involved in controlling developmental cell arrangements. Combining different genetic means to reduce rbm8a function we find a significant reduction of cd41 positive thrombocytes in hypomorphic rbm8a larvae. Transcriptomics analysis documents rbm8a mutant zebrafish embryos already post gastrulation accumulate mRNAs with erroneously included introns a hallmark of defective nonsense mediated decay. Affected mRNAs include transcripts encoding components of the non canonical Wnt pathway involved in PCP signaling and rbm8a mutant embryos show hallmarks of Wnt/PCP dependent early convergent extension defects. We establish that reduced rbm8a function synergizes with perturbations in Wnt/PCP pathway genes including wnt5b wnt11f2 fzd7a and vangl2. Following axis formation rbm8a perturbation impairs the migration and architecture of the lateral plate mesoderm LPM that forms the hematopoietic cardiovascular kidney and forelimb skeleton progenitors. Subsequently rbm8a perturbation impairs expression of early hematopoietic/endothelial genes including runx1a kdrl sox7 and the megakaryocyte regulator gfi1aa. Lastly we document similar hematopoietic defects upon loss of vangl2. Together our data link reduced rbm8a function to LPM migration and hematopoietic defects via attenuated Wnt/PCP signaling. Our…	ENA FIRST PUBLIC:2023 03 31\|ENA LAST UPDATE:2023 03 31	Protocols: Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined pooled embryos by Trizol LS extraction as per manufacturerâ€™s guidelines Invitrogen with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.	Sample 5	E MTAB 12503:Sample 5		strain:mixed AB and Tubingen\|ENA FIRST PUBLIC:2023 03 31\|individual:20170530.A 5\|organism:Danio rerio\|organism:Danio rerio\|ENA LAST UPDATE:2023 03 31\|scientific name:Danio rerio\|common name:zebrafish\|organism part:embryo\|age:10\|developmental stage:bud\|genotype:wild type genotype\|ENA FIRST PUBLIC:2023 03 31\|ENA LAST UPDATE:2023 03 31	Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling	E MTAB 12503:Sample 5 p	Sample 5 p	RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling	Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined pooled embryos by Trizol LS extraction as per manufacturerâ€™s guidelines Invitrogen with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.	Experimental Factor: developmental stage:bud\|Experimental Factor: genotype:wild type genotype	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	RANDOM	PAIRED	ILLUMINA	Illumina HiSeq 4000		ERP144048	Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling	ENA FIRST PUBLIC:2023 03 31\|ENA LAST UPDATE:2023 03 31	20170530.A-5_R1.fastq.gz 20170530.A-5_R2.fastq.gz	fastq fastq	14954968728.0	49519764.0	E MTAB 12503:20170530.A 5 R	0:151 1:151	A:4063340262;C:3440933120;G:3455723079;T:3981396987;N:13575280	151	151	4063340262	3440933120	3455723079	3981396987	13575280	ERX10233131	ERS14439196	ERA20162442	University of Zurich\|European Nucleotide Archive	University of Zurich\|European Nucleotide Archive	2	0.85891	0.86859	0.28842	0.28866	0.7349	0.75051	0.45532	0.49145	151	151	B	B	biological fallback assumption	illumina	hiseq_era	unknown	random_priming	trueseq	sc	unknown	unknown	Switzerland	2023-03-31	Multi-stage	Embryo	Whole Organism	All anatomical structures
11240	11240	ERR10782553	ERX10233130	ERS14439195	ERP144048	PRJEB58983	RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling	E-MTAB-12503	Transcriptome Analysis	Defects in blood development are a major contributor to complex congenital anomalies. Thrombocytopenia Absent Radius TAR Syndrome is a rare congenital disease presenting with reduced blood platelets megakaryocytic thrombocytopenia and forelimb anomalies concurrent with variable heart and kidney defects caused by hypomorphic RBM8A/Y14 gene function. RBM8A encodes a component of the ubiquitous exon junction complex involved in mRNA splicing transport and nonsense mediated decay. How perturbing a general mRNA processing factor causes the distinct phenotypes of TAR Syndrome remains unknown. Here we connect zebrafish rbm8a perturbation to early hematopoiesis defects via attenuated planar cell polarity PCP signaling involved in controlling developmental cell arrangements. Combining different genetic means to reduce rbm8a function we find a significant reduction of cd41 positive thrombocytes in hypomorphic rbm8a larvae. Transcriptomics analysis documents rbm8a mutant zebrafish embryos already post gastrulation accumulate mRNAs with erroneously included introns a hallmark of defective nonsense mediated decay. Affected mRNAs include transcripts encoding components of the non canonical Wnt pathway involved in PCP signaling and rbm8a mutant embryos show hallmarks of Wnt/PCP dependent early convergent extension defects. We establish that reduced rbm8a function synergizes with perturbations in Wnt/PCP pathway genes including wnt5b wnt11f2 fzd7a and vangl2. Following axis formation rbm8a perturbation impairs the migration and architecture of the lateral plate mesoderm LPM that forms the hematopoietic cardiovascular kidney and forelimb skeleton progenitors. Subsequently rbm8a perturbation impairs expression of early hematopoietic/endothelial genes including runx1a kdrl sox7 and the megakaryocyte regulator gfi1aa. Lastly we document similar hematopoietic defects upon loss of vangl2. Together our data link reduced rbm8a function to LPM migration and hematopoietic defects via attenuated Wnt/PCP signaling. Our…	ENA FIRST PUBLIC:2023 03 31\|ENA LAST UPDATE:2023 03 31	Protocols: Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined pooled embryos by Trizol LS extraction as per manufacturerâ€™s guidelines Invitrogen with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.	Sample 2	E MTAB 12503:Sample 2		strain:mixed AB and Tubingen\|ENA FIRST PUBLIC:2023 03 31\|individual:20170530.A 2\|organism:Danio rerio\|organism:Danio rerio\|ENA LAST UPDATE:2023 03 31\|scientific name:Danio rerio\|common name:zebrafish\|organism part:embryo\|age:24\|developmental stage:pharyngula prim 5\|genotype:wild type genotype\|ENA FIRST PUBLIC:2023 03 31\|ENA LAST UPDATE:2023 03 31	Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling	E MTAB 12503:Sample 2 p	Sample 2 p	RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling	Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined pooled embryos by Trizol LS extraction as per manufacturerâ€™s guidelines Invitrogen with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.	Experimental Factor: developmental stage:pharyngula prim 5\|Experimental Factor: genotype:wild type genotype	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	RANDOM	PAIRED	ILLUMINA	Illumina HiSeq 4000		ERP144048	Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling	ENA FIRST PUBLIC:2023 03 31\|ENA LAST UPDATE:2023 03 31	20170530.A-2_R1.fastq.gz 20170530.A-2_R2.fastq.gz	fastq fastq	16267571562.0	53866131.0	E MTAB 12503:20170530.A 2 R	0:151 1:151	A:4395815325;C:3765428574;G:3780844712;T:4310729283;N:14753668	151	151	4395815325	3765428574	3780844712	4310729283	14753668	ERX10233130	ERS14439195	ERA20162442	University of Zurich\|European Nucleotide Archive	University of Zurich\|European Nucleotide Archive	2	0.86977	0.8727	0.28497	0.28427	0.70763	0.72301	0.47478	0.47986	151	151	B	B	biological fallback assumption	illumina	hiseq_era	unknown	random_priming	trueseq	sc	unknown	unknown	Switzerland	2023-03-31	Pharyngula	Embryo	Whole Organism	All anatomical structures
11241	11241	ERR10782552	ERX10233129	ERS14439194	ERP144048	PRJEB58983	RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling	E-MTAB-12503	Transcriptome Analysis	Defects in blood development are a major contributor to complex congenital anomalies. Thrombocytopenia Absent Radius TAR Syndrome is a rare congenital disease presenting with reduced blood platelets megakaryocytic thrombocytopenia and forelimb anomalies concurrent with variable heart and kidney defects caused by hypomorphic RBM8A/Y14 gene function. RBM8A encodes a component of the ubiquitous exon junction complex involved in mRNA splicing transport and nonsense mediated decay. How perturbing a general mRNA processing factor causes the distinct phenotypes of TAR Syndrome remains unknown. Here we connect zebrafish rbm8a perturbation to early hematopoiesis defects via attenuated planar cell polarity PCP signaling involved in controlling developmental cell arrangements. Combining different genetic means to reduce rbm8a function we find a significant reduction of cd41 positive thrombocytes in hypomorphic rbm8a larvae. Transcriptomics analysis documents rbm8a mutant zebrafish embryos already post gastrulation accumulate mRNAs with erroneously included introns a hallmark of defective nonsense mediated decay. Affected mRNAs include transcripts encoding components of the non canonical Wnt pathway involved in PCP signaling and rbm8a mutant embryos show hallmarks of Wnt/PCP dependent early convergent extension defects. We establish that reduced rbm8a function synergizes with perturbations in Wnt/PCP pathway genes including wnt5b wnt11f2 fzd7a and vangl2. Following axis formation rbm8a perturbation impairs the migration and architecture of the lateral plate mesoderm LPM that forms the hematopoietic cardiovascular kidney and forelimb skeleton progenitors. Subsequently rbm8a perturbation impairs expression of early hematopoietic/endothelial genes including runx1a kdrl sox7 and the megakaryocyte regulator gfi1aa. Lastly we document similar hematopoietic defects upon loss of vangl2. Together our data link reduced rbm8a function to LPM migration and hematopoietic defects via attenuated Wnt/PCP signaling. Our…	ENA FIRST PUBLIC:2023 03 31\|ENA LAST UPDATE:2023 03 31	Protocols: Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined pooled embryos by Trizol LS extraction as per manufacturerâ€™s guidelines Invitrogen with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.	Sample 1	E MTAB 12503:Sample 1		strain:mixed AB and Tubingen\|ENA FIRST PUBLIC:2023 03 31\|individual:20170530.A 1\|organism:Danio rerio\|organism:Danio rerio\|ENA LAST UPDATE:2023 03 31\|scientific name:Danio rerio\|common name:zebrafish\|organism part:embryo\|age:24\|developmental stage:pharyngula prim 5\|genotype:wild type genotype\|ENA FIRST PUBLIC:2023 03 31\|ENA LAST UPDATE:2023 03 31	Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling	E MTAB 12503:Sample 1 p	Sample 1 p	RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling	Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined pooled embryos by Trizol LS extraction as per manufacturerâ€™s guidelines Invitrogen with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.	Experimental Factor: developmental stage:pharyngula prim 5\|Experimental Factor: genotype:wild type genotype	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	RANDOM	PAIRED	ILLUMINA	Illumina HiSeq 4000		ERP144048	Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling	ENA FIRST PUBLIC:2023 03 31\|ENA LAST UPDATE:2023 03 31	20170530.A-1_R1.fastq.gz 20170530.A-1_R2.fastq.gz	fastq fastq	15446599662.0	51147681.0	E MTAB 12503:20170530.A 1 R	0:151 1:151	A:4289931639;C:3451135010;G:3474244788;T:4217248893;N:14039332	151	151	4289931639	3451135010	3474244788	4217248893	14039332	ERX10233129	ERS14439194	ERA20162442	University of Zurich\|European Nucleotide Archive	University of Zurich\|European Nucleotide Archive	2	0.90114	0.90507	0.32128	0.32127	0.70232	0.71956	0.47336	0.47528	151	151	B	B	biological fallback assumption	illumina	hiseq_era	unknown	random_priming	trueseq	sc	unknown	unknown	Switzerland	2023-03-31	Pharyngula	Embryo	Whole Organism	All anatomical structures
11242	11242	ERR10782551	ERX10233128	ERS14439193	ERP144048	PRJEB58983	RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling	E-MTAB-12503	Transcriptome Analysis	Defects in blood development are a major contributor to complex congenital anomalies. Thrombocytopenia Absent Radius TAR Syndrome is a rare congenital disease presenting with reduced blood platelets megakaryocytic thrombocytopenia and forelimb anomalies concurrent with variable heart and kidney defects caused by hypomorphic RBM8A/Y14 gene function. RBM8A encodes a component of the ubiquitous exon junction complex involved in mRNA splicing transport and nonsense mediated decay. How perturbing a general mRNA processing factor causes the distinct phenotypes of TAR Syndrome remains unknown. Here we connect zebrafish rbm8a perturbation to early hematopoiesis defects via attenuated planar cell polarity PCP signaling involved in controlling developmental cell arrangements. Combining different genetic means to reduce rbm8a function we find a significant reduction of cd41 positive thrombocytes in hypomorphic rbm8a larvae. Transcriptomics analysis documents rbm8a mutant zebrafish embryos already post gastrulation accumulate mRNAs with erroneously included introns a hallmark of defective nonsense mediated decay. Affected mRNAs include transcripts encoding components of the non canonical Wnt pathway involved in PCP signaling and rbm8a mutant embryos show hallmarks of Wnt/PCP dependent early convergent extension defects. We establish that reduced rbm8a function synergizes with perturbations in Wnt/PCP pathway genes including wnt5b wnt11f2 fzd7a and vangl2. Following axis formation rbm8a perturbation impairs the migration and architecture of the lateral plate mesoderm LPM that forms the hematopoietic cardiovascular kidney and forelimb skeleton progenitors. Subsequently rbm8a perturbation impairs expression of early hematopoietic/endothelial genes including runx1a kdrl sox7 and the megakaryocyte regulator gfi1aa. Lastly we document similar hematopoietic defects upon loss of vangl2. Together our data link reduced rbm8a function to LPM migration and hematopoietic defects via attenuated Wnt/PCP signaling. Our…	ENA FIRST PUBLIC:2023 03 31\|ENA LAST UPDATE:2023 03 31	Protocols: Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined pooled embryos by Trizol LS extraction as per manufacturerâ€™s guidelines Invitrogen with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.	Sample 7	E MTAB 12503:Sample 7		strain:mixed AB and Tubingen\|ENA FIRST PUBLIC:2023 03 31\|individual:20170530.A 7\|organism:Danio rerio\|organism:Danio rerio\|ENA LAST UPDATE:2023 03 31\|scientific name:Danio rerio\|common name:zebrafish\|organism part:embryo\|age:10\|developmental stage:bud\|genotype:rbm8a d5/d5\|ENA FIRST PUBLIC:2023 03 31\|ENA LAST UPDATE:2023 03 31	Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling	E MTAB 12503:Sample 7 p	Sample 7 p	RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling	Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined pooled embryos by Trizol LS extraction as per manufacturerâ€™s guidelines Invitrogen with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.	Experimental Factor: developmental stage:bud\|Experimental Factor: genotype:rbm8a d5/d5	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	RANDOM	PAIRED	ILLUMINA	Illumina HiSeq 4000		ERP144048	Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling	ENA FIRST PUBLIC:2023 03 31\|ENA LAST UPDATE:2023 03 31	20170530.A-7_R1.fastq.gz 20170530.A-7_R2.fastq.gz	fastq fastq	12726557236.0	42140918.0	E MTAB 12503:20170530.A 7 R	0:151 1:151	A:3510176970;C:2879679978;G:2932244172;T:3392911734;N:11544382	151	151	3510176970	2879679978	2932244172	3392911734	11544382	ERX10233128	ERS14439193	ERA20162442	University of Zurich\|European Nucleotide Archive	University of Zurich\|European Nucleotide Archive	2	0.88531	0.88678	0.33279	0.3329	0.73545	0.74992	0.52548	0.52864	151	151	B	B	biological fallback assumption	illumina	hiseq_era	unknown	random_priming	trueseq	sc	unknown	unknown	Switzerland	2023-03-31	Multi-stage	Embryo	Whole Organism	All anatomical structures
11243	11243	ERR10782550	ERX10233127	ERS14439192	ERP144048	PRJEB58983	RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling	E-MTAB-12503	Transcriptome Analysis	Defects in blood development are a major contributor to complex congenital anomalies. Thrombocytopenia Absent Radius TAR Syndrome is a rare congenital disease presenting with reduced blood platelets megakaryocytic thrombocytopenia and forelimb anomalies concurrent with variable heart and kidney defects caused by hypomorphic RBM8A/Y14 gene function. RBM8A encodes a component of the ubiquitous exon junction complex involved in mRNA splicing transport and nonsense mediated decay. How perturbing a general mRNA processing factor causes the distinct phenotypes of TAR Syndrome remains unknown. Here we connect zebrafish rbm8a perturbation to early hematopoiesis defects via attenuated planar cell polarity PCP signaling involved in controlling developmental cell arrangements. Combining different genetic means to reduce rbm8a function we find a significant reduction of cd41 positive thrombocytes in hypomorphic rbm8a larvae. Transcriptomics analysis documents rbm8a mutant zebrafish embryos already post gastrulation accumulate mRNAs with erroneously included introns a hallmark of defective nonsense mediated decay. Affected mRNAs include transcripts encoding components of the non canonical Wnt pathway involved in PCP signaling and rbm8a mutant embryos show hallmarks of Wnt/PCP dependent early convergent extension defects. We establish that reduced rbm8a function synergizes with perturbations in Wnt/PCP pathway genes including wnt5b wnt11f2 fzd7a and vangl2. Following axis formation rbm8a perturbation impairs the migration and architecture of the lateral plate mesoderm LPM that forms the hematopoietic cardiovascular kidney and forelimb skeleton progenitors. Subsequently rbm8a perturbation impairs expression of early hematopoietic/endothelial genes including runx1a kdrl sox7 and the megakaryocyte regulator gfi1aa. Lastly we document similar hematopoietic defects upon loss of vangl2. Together our data link reduced rbm8a function to LPM migration and hematopoietic defects via attenuated Wnt/PCP signaling. Our…	ENA FIRST PUBLIC:2023 03 31\|ENA LAST UPDATE:2023 03 31	Protocols: Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined pooled embryos by Trizol LS extraction as per manufacturerâ€™s guidelines Invitrogen with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.	Sample 4	E MTAB 12503:Sample 4		strain:mixed AB and Tubingen\|ENA FIRST PUBLIC:2023 03 31\|individual:20170530.A 4\|organism:Danio rerio\|organism:Danio rerio\|ENA LAST UPDATE:2023 03 31\|scientific name:Danio rerio\|common name:zebrafish\|organism part:embryo\|age:24\|developmental stage:pharyngula prim 5\|genotype:rbm8a d5/d5\|ENA FIRST PUBLIC:2023 03 31\|ENA LAST UPDATE:2023 03 31	Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling	E MTAB 12503:Sample 4 p	Sample 4 p	RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling	Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined pooled embryos by Trizol LS extraction as per manufacturerâ€™s guidelines Invitrogen with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.	Experimental Factor: developmental stage:pharyngula prim 5\|Experimental Factor: genotype:rbm8a d5/d5	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	RANDOM	PAIRED	ILLUMINA	Illumina HiSeq 4000		ERP144048	Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling	ENA FIRST PUBLIC:2023 03 31\|ENA LAST UPDATE:2023 03 31	20170530.A-4_R1.fastq.gz 20170530.A-4_R2.fastq.gz	fastq fastq	15697575554.0	51978727.0	E MTAB 12503:20170530.A 4 R	0:151 1:151	A:4256444510;C:3622485921;G:3650190489;T:4154211501;N:14243133	151	151	4256444510	3622485921	3650190489	4154211501	14243133	ERX10233127	ERS14439192	ERA20162442	University of Zurich\|European Nucleotide Archive	University of Zurich\|European Nucleotide Archive	2	0.87714	0.88071	0.29319	0.29235	0.69844	0.7164	0.47594	0.47385	151	151	B	B	biological fallback assumption	illumina	hiseq_era	unknown	random_priming	trueseq	sc	unknown	unknown	Switzerland	2023-03-31	Pharyngula	Embryo	Whole Organism	All anatomical structures
11244	11244	ERR10782549	ERX10233126	ERS14439191	ERP144048	PRJEB58983	RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling	E-MTAB-12503	Transcriptome Analysis	Defects in blood development are a major contributor to complex congenital anomalies. Thrombocytopenia Absent Radius TAR Syndrome is a rare congenital disease presenting with reduced blood platelets megakaryocytic thrombocytopenia and forelimb anomalies concurrent with variable heart and kidney defects caused by hypomorphic RBM8A/Y14 gene function. RBM8A encodes a component of the ubiquitous exon junction complex involved in mRNA splicing transport and nonsense mediated decay. How perturbing a general mRNA processing factor causes the distinct phenotypes of TAR Syndrome remains unknown. Here we connect zebrafish rbm8a perturbation to early hematopoiesis defects via attenuated planar cell polarity PCP signaling involved in controlling developmental cell arrangements. Combining different genetic means to reduce rbm8a function we find a significant reduction of cd41 positive thrombocytes in hypomorphic rbm8a larvae. Transcriptomics analysis documents rbm8a mutant zebrafish embryos already post gastrulation accumulate mRNAs with erroneously included introns a hallmark of defective nonsense mediated decay. Affected mRNAs include transcripts encoding components of the non canonical Wnt pathway involved in PCP signaling and rbm8a mutant embryos show hallmarks of Wnt/PCP dependent early convergent extension defects. We establish that reduced rbm8a function synergizes with perturbations in Wnt/PCP pathway genes including wnt5b wnt11f2 fzd7a and vangl2. Following axis formation rbm8a perturbation impairs the migration and architecture of the lateral plate mesoderm LPM that forms the hematopoietic cardiovascular kidney and forelimb skeleton progenitors. Subsequently rbm8a perturbation impairs expression of early hematopoietic/endothelial genes including runx1a kdrl sox7 and the megakaryocyte regulator gfi1aa. Lastly we document similar hematopoietic defects upon loss of vangl2. Together our data link reduced rbm8a function to LPM migration and hematopoietic defects via attenuated Wnt/PCP signaling. Our…	ENA FIRST PUBLIC:2023 03 31\|ENA LAST UPDATE:2023 03 31	Protocols: Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined pooled embryos by Trizol LS extraction as per manufacturerâ€™s guidelines Invitrogen with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.	Sample 3	E MTAB 12503:Sample 3		strain:mixed AB and Tubingen\|ENA FIRST PUBLIC:2023 03 31\|individual:20170530.A 3\|organism:Danio rerio\|organism:Danio rerio\|ENA LAST UPDATE:2023 03 31\|scientific name:Danio rerio\|common name:zebrafish\|organism part:embryo\|age:24\|developmental stage:pharyngula prim 5\|genotype:rbm8a d5/d5\|ENA FIRST PUBLIC:2023 03 31\|ENA LAST UPDATE:2023 03 31	Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling	E MTAB 12503:Sample 3 p	Sample 3 p	RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling	Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined pooled embryos by Trizol LS extraction as per manufacturerâ€™s guidelines Invitrogen with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.	Experimental Factor: developmental stage:pharyngula prim 5\|Experimental Factor: genotype:rbm8a d5/d5	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	RANDOM	PAIRED	ILLUMINA	Illumina HiSeq 4000		ERP144048	Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling	ENA FIRST PUBLIC:2023 03 31\|ENA LAST UPDATE:2023 03 31	20170530.A-3_R1.fastq.gz 20170530.A-3_R2.fastq.gz	fastq fastq	13839085674.0	45824787.0	E MTAB 12503:20170530.A 3 R	0:151 1:151	A:3812423011;C:3120168590;G:3163957945;T:3729983766;N:12552362	151	151	3812423011	3120168590	3163957945	3729983766	12552362	ERX10233126	ERS14439191	ERA20162442	University of Zurich\|European Nucleotide Archive	University of Zurich\|European Nucleotide Archive	2	0.88987	0.74432	0.33651	0.27875	0.69229	0.72934	0.46981	0.46116	151	151	B	B	biological fallback assumption	illumina	hiseq_era	unknown	random_priming	trueseq	sc	unknown	unknown	Switzerland	2023-03-31	Pharyngula	Embryo	Whole Organism	All anatomical structures
11747	11747	ERR11608177	ERX11010308	ERS15939662	ERP148707	PRJEB63561	RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors	E-MTAB-13116	Transcriptome Analysis	Transcriptomic differences of gata1+ erythrocytes between the kdm4b / mutants and the WT embryos at 48 hpf were analyzed by RNA sequencing.	ENA FIRST PUBLIC:2024 07 01\|ENA LAST UPDATE:2024 07 01	Protocols: The 48 hpf gata1+ erythrocytes were sorted FACSAria BD Bioscience CA USA Two independent groups of RNA from wt and kdm4b / erythrocytes were extracted using TRIzol® Reagent Life Technologies each group contains three biological repeats. post adenylation of three prime ends of double strand cDNA fragments Adaptor with hairpin loop structure were ligated to prepare for hybridization. The library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then PCR was performed with Phusion High Fidelity DNA polymerase. At last PCR products were purified and the library quality was assessed on the Agilent Bioanalyzer 2100 system.	MU2	SAMEA113945412	Shanghai Institute of Nutrition and Diseases, Chinese Academy of Sciences	ENA first public:2024 07 01\|External Id:SAMEA113945412\|INSDC center name:Shanghai Institute of Nutrition and Diseases Chinese Academy of Sciences\|INSDC last update:2023 06 27T11:19:32Z\|INSDC status:public\|Submitter Id:E MTAB 13116:MU2\|age:48\|broker name:ArrayExpress\|cell type:erythrocyte\|collection date:not collected\|common name:zebrafish\|developmental stage:embryo stage\|disease:normal\|genotype:kdm4b / \|genotype:wild type genotype\|geographic location country and/or sea:not collected\|immunophenotype:gata1 positive\|individual:mixed pool of 200 individuals\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13116:MU2\|scientific name:Danio rerio\|sex:mixed\|strain:Tubingen	RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors	E MTAB 13116:MU2 p	MU2 p	RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors	The 48 hpf gata1+ erythrocytes were sorted FACSAria BD Bioscience CA USA Two independent groups of RNA from wt and kdm4b / erythrocytes were extracted using TRIzol® Reagent Life Technologies each group contains three biological repeats. post adenylation of three prime ends of double strand cDNA fragments Adaptor with hairpin loop structure were ligated to prepare for hybridization. The library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then PCR was performed with Phusion High Fidelity DNA polymerase. At last PCR products were purified and the library quality was assessed on the Agilent Bioanalyzer 2100 system.		RNA-Seq	TRANSCRIPTOMIC	RANDOM	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP148707	Illumina NovaSeq 6000 paired end sequencing; RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors	ENA FIRST PUBLIC:2024 07 01\|ENA LAST UPDATE:2024 07 01	MU2_R1.fastq.gz MU2_R2.fastq.gz	fastq fastq	8373912900.0	27913043.0	E MTAB 13116:MU2 R	0:150 1:150	A:2149105370;C:2028251580;G:2055193482;T:2141168979;N:193489	150	150	2149105370	2028251580	2055193482	2141168979	193489	ERX11010308	ERS15939662	ERA24542523	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive												B	B	biological fallback assumption	illumina	novaseq_era	3prime	random_priming	unknown	bulk	unknown	unknown	United Kingdom	2023-06-27	Hatching	Embryo	Whole Organism	All anatomical structures
11748	11748	ERR11608179	ERX11010310	ERS15939664	ERP148707	PRJEB63561	RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors	E-MTAB-13116	Transcriptome Analysis	Transcriptomic differences of gata1+ erythrocytes between the kdm4b / mutants and the WT embryos at 48 hpf were analyzed by RNA sequencing.	ENA FIRST PUBLIC:2024 07 01\|ENA LAST UPDATE:2024 07 01	Protocols: The 48 hpf gata1+ erythrocytes were sorted FACSAria BD Bioscience CA USA Two independent groups of RNA from wt and kdm4b / erythrocytes were extracted using TRIzol® Reagent Life Technologies each group contains three biological repeats. post adenylation of three prime ends of double strand cDNA fragments Adaptor with hairpin loop structure were ligated to prepare for hybridization. The library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then PCR was performed with Phusion High Fidelity DNA polymerase. At last PCR products were purified and the library quality was assessed on the Agilent Bioanalyzer 2100 system.	WT1	SAMEA113945414	Shanghai Institute of Nutrition and Diseases, Chinese Academy of Sciences	ENA first public:2024 07 01\|External Id:SAMEA113945414\|INSDC center name:Shanghai Institute of Nutrition and Diseases Chinese Academy of Sciences\|INSDC last update:2023 06 27T11:19:32Z\|INSDC status:public\|Submitter Id:E MTAB 13116:WT1\|age:48\|broker name:ArrayExpress\|cell type:erythrocyte\|collection date:not collected\|common name:zebrafish\|developmental stage:embryo stage\|disease:normal\|genotype:wild type genotype\|geographic location country and/or sea:not collected\|immunophenotype:gata1 positive\|individual:mixed pool of 200 individuals\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13116:WT1\|scientific name:Danio rerio\|sex:mixed\|strain:Tubingen	RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors	E MTAB 13116:WT1 p	WT1 p	RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors	The 48 hpf gata1+ erythrocytes were sorted FACSAria BD Bioscience CA USA Two independent groups of RNA from wt and kdm4b / erythrocytes were extracted using TRIzol® Reagent Life Technologies each group contains three biological repeats. post adenylation of three prime ends of double strand cDNA fragments Adaptor with hairpin loop structure were ligated to prepare for hybridization. The library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then PCR was performed with Phusion High Fidelity DNA polymerase. At last PCR products were purified and the library quality was assessed on the Agilent Bioanalyzer 2100 system.		RNA-Seq	TRANSCRIPTOMIC	RANDOM	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP148707	Illumina NovaSeq 6000 paired end sequencing; RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors	ENA FIRST PUBLIC:2024 07 01\|ENA LAST UPDATE:2024 07 01	WT1_R1.fastq.gz WT1_R2.fastq.gz	fastq fastq	6729388500.0	22431295.0	E MTAB 13116:WT1 R	0:150 1:150	A:1730015872;C:1621295817;G:1657133586;T:1720858352;N:84873	150	150	1730015872	1621295817	1657133586	1720858352	84873	ERX11010310	ERS15939664	ERA24542523	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive												B	B	biological fallback assumption	illumina	novaseq_era	3prime	random_priming	unknown	bulk	unknown	unknown	United Kingdom	2023-06-27	Hatching	Embryo	Whole Organism	All anatomical structures
11749	11749	ERR11608176	ERX11010307	ERS15939661	ERP148707	PRJEB63561	RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors	E-MTAB-13116	Transcriptome Analysis	Transcriptomic differences of gata1+ erythrocytes between the kdm4b / mutants and the WT embryos at 48 hpf were analyzed by RNA sequencing.	ENA FIRST PUBLIC:2024 07 01\|ENA LAST UPDATE:2024 07 01	Protocols: The 48 hpf gata1+ erythrocytes were sorted FACSAria BD Bioscience CA USA Two independent groups of RNA from wt and kdm4b / erythrocytes were extracted using TRIzol® Reagent Life Technologies each group contains three biological repeats. post adenylation of three prime ends of double strand cDNA fragments Adaptor with hairpin loop structure were ligated to prepare for hybridization. The library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then PCR was performed with Phusion High Fidelity DNA polymerase. At last PCR products were purified and the library quality was assessed on the Agilent Bioanalyzer 2100 system.	MU1	SAMEA113945411	Shanghai Institute of Nutrition and Diseases, Chinese Academy of Sciences	ENA first public:2024 07 01\|External Id:SAMEA113945411\|INSDC center name:Shanghai Institute of Nutrition and Diseases Chinese Academy of Sciences\|INSDC last update:2023 06 27T11:19:32Z\|INSDC status:public\|Submitter Id:E MTAB 13116:MU1\|age:48\|broker name:ArrayExpress\|cell type:erythrocyte\|collection date:not collected\|common name:zebrafish\|developmental stage:embryo stage\|disease:normal\|genotype:kdm4b / \|genotype:wild type genotype\|geographic location country and/or sea:not collected\|immunophenotype:gata1 positive\|individual:mixed pool of 200 individuals\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13116:MU1\|scientific name:Danio rerio\|sex:mixed\|strain:Tubingen	RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors	E MTAB 13116:MU1 p	MU1 p	RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors	The 48 hpf gata1+ erythrocytes were sorted FACSAria BD Bioscience CA USA Two independent groups of RNA from wt and kdm4b / erythrocytes were extracted using TRIzol® Reagent Life Technologies each group contains three biological repeats. post adenylation of three prime ends of double strand cDNA fragments Adaptor with hairpin loop structure were ligated to prepare for hybridization. The library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then PCR was performed with Phusion High Fidelity DNA polymerase. At last PCR products were purified and the library quality was assessed on the Agilent Bioanalyzer 2100 system.		RNA-Seq	TRANSCRIPTOMIC	RANDOM	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP148707	Illumina NovaSeq 6000 paired end sequencing; RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors	ENA FIRST PUBLIC:2024 07 01\|ENA LAST UPDATE:2024 07 01	MU1_R1.fastq.gz MU1_R2.fastq.gz	fastq fastq	7310352000.0	24367840.0	E MTAB 13116:MU1 R	0:150 1:150	A:1888660247;C:1748082353;G:1788562372;T:1884958596;N:88432	150	150	1888660247	1748082353	1788562372	1884958596	88432	ERX11010307	ERS15939661	ERA24542523	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive												B	B	biological fallback assumption	illumina	novaseq_era	3prime	random_priming	unknown	bulk	unknown	unknown	United Kingdom	2023-06-27	Hatching	Embryo	Whole Organism	All anatomical structures
11750	11750	ERR11608178	ERX11010309	ERS15939663	ERP148707	PRJEB63561	RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors	E-MTAB-13116	Transcriptome Analysis	Transcriptomic differences of gata1+ erythrocytes between the kdm4b / mutants and the WT embryos at 48 hpf were analyzed by RNA sequencing.	ENA FIRST PUBLIC:2024 07 01\|ENA LAST UPDATE:2024 07 01	Protocols: The 48 hpf gata1+ erythrocytes were sorted FACSAria BD Bioscience CA USA Two independent groups of RNA from wt and kdm4b / erythrocytes were extracted using TRIzol® Reagent Life Technologies each group contains three biological repeats. post adenylation of three prime ends of double strand cDNA fragments Adaptor with hairpin loop structure were ligated to prepare for hybridization. The library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then PCR was performed with Phusion High Fidelity DNA polymerase. At last PCR products were purified and the library quality was assessed on the Agilent Bioanalyzer 2100 system.	MU3	SAMEA113945413	Shanghai Institute of Nutrition and Diseases, Chinese Academy of Sciences	ENA first public:2024 07 01\|External Id:SAMEA113945413\|INSDC center name:Shanghai Institute of Nutrition and Diseases Chinese Academy of Sciences\|INSDC last update:2023 06 27T11:19:32Z\|INSDC status:public\|Submitter Id:E MTAB 13116:MU3\|age:48\|broker name:ArrayExpress\|cell type:erythrocyte\|collection date:not collected\|common name:zebrafish\|developmental stage:embryo stage\|disease:normal\|genotype:kdm4b / \|genotype:wild type genotype\|geographic location country and/or sea:not collected\|immunophenotype:gata1 positive\|individual:mixed pool of 200 individuals\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13116:MU3\|scientific name:Danio rerio\|sex:mixed\|strain:Tubingen	RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors	E MTAB 13116:MU3 p	MU3 p	RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors	The 48 hpf gata1+ erythrocytes were sorted FACSAria BD Bioscience CA USA Two independent groups of RNA from wt and kdm4b / erythrocytes were extracted using TRIzol® Reagent Life Technologies each group contains three biological repeats. post adenylation of three prime ends of double strand cDNA fragments Adaptor with hairpin loop structure were ligated to prepare for hybridization. The library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then PCR was performed with Phusion High Fidelity DNA polymerase. At last PCR products were purified and the library quality was assessed on the Agilent Bioanalyzer 2100 system.		RNA-Seq	TRANSCRIPTOMIC	RANDOM	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP148707	Illumina NovaSeq 6000 paired end sequencing; RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors	ENA FIRST PUBLIC:2024 07 01\|ENA LAST UPDATE:2024 07 01	MU3_R1.fastq.gz MU3_R2.fastq.gz	fastq fastq	8826207900.0	29420693.0	E MTAB 13116:MU3 R	0:150 1:150	A:2298326835;C:2100185951;G:2130807919;T:2296678033;N:209162	150	150	2298326835	2100185951	2130807919	2296678033	209162	ERX11010309	ERS15939663	ERA24542523	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive												B	B	biological fallback assumption	illumina	novaseq_era	3prime	random_priming	unknown	bulk	unknown	unknown	United Kingdom	2023-06-27	Hatching	Embryo	Whole Organism	All anatomical structures
11751	11751	ERR11608180	ERX11010311	ERS15939665	ERP148707	PRJEB63561	RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors	E-MTAB-13116	Transcriptome Analysis	Transcriptomic differences of gata1+ erythrocytes between the kdm4b / mutants and the WT embryos at 48 hpf were analyzed by RNA sequencing.	ENA FIRST PUBLIC:2024 07 01\|ENA LAST UPDATE:2024 07 01	Protocols: The 48 hpf gata1+ erythrocytes were sorted FACSAria BD Bioscience CA USA Two independent groups of RNA from wt and kdm4b / erythrocytes were extracted using TRIzol® Reagent Life Technologies each group contains three biological repeats. post adenylation of three prime ends of double strand cDNA fragments Adaptor with hairpin loop structure were ligated to prepare for hybridization. The library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then PCR was performed with Phusion High Fidelity DNA polymerase. At last PCR products were purified and the library quality was assessed on the Agilent Bioanalyzer 2100 system.	WT2	E MTAB 13116:WT2		strain:Tubingen\|disease:normal\|individual:mixed pool of 200 individuals\|organism:Danio rerio\|organism:Danio rerio\|collection date:not collected\|sex:mixed\|scientific name:Danio rerio\|common name:zebrafish\|organism part:embryo\|developmental stage:embryo stage\|genotype:wild type genotype\|isolate:not applicable\|immunophenotype:gata1 positive\|cell type:erythrocyte\|age:48\|geographic location country and/or sea:not collected\|ENA LAST UPDATE:2023 06 27	RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors	E MTAB 13116:WT2 p	WT2 p	RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors	The 48 hpf gata1+ erythrocytes were sorted FACSAria BD Bioscience CA USA Two independent groups of RNA from wt and kdm4b / erythrocytes were extracted using TRIzol® Reagent Life Technologies each group contains three biological repeats. post adenylation of three prime ends of double strand cDNA fragments Adaptor with hairpin loop structure were ligated to prepare for hybridization. The library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then PCR was performed with Phusion High Fidelity DNA polymerase. At last PCR products were purified and the library quality was assessed on the Agilent Bioanalyzer 2100 system.		RNA-Seq	TRANSCRIPTOMIC	RANDOM	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP148707	Illumina NovaSeq 6000 paired end sequencing; RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors	ENA FIRST PUBLIC:2024 07 01\|ENA LAST UPDATE:2024 07 01	WT2_R1.fastq.gz WT2_R2.fastq.gz	fastq fastq	8368621500.0	27895405.0	E MTAB 13116:WT2 R	0:150 1:150	A:2126734187;C:2050458346;G:2078646608;T:2112586140;N:196219	150	150	2126734187	2050458346	2078646608	2112586140	196219	ERX11010311	ERS15939665	ERA24542523	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive												B	B	biological fallback assumption	illumina	novaseq_era	3prime	random_priming	unknown	bulk	unknown	unknown	United Kingdom	2023-06-27	Hatching	Embryo	Whole Organism	All anatomical structures
11752	11752	ERR11608181	ERX11010312	ERS15939666	ERP148707	PRJEB63561	RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors	E-MTAB-13116	Transcriptome Analysis	Transcriptomic differences of gata1+ erythrocytes between the kdm4b / mutants and the WT embryos at 48 hpf were analyzed by RNA sequencing.	ENA FIRST PUBLIC:2024 07 01\|ENA LAST UPDATE:2024 07 01	Protocols: The 48 hpf gata1+ erythrocytes were sorted FACSAria BD Bioscience CA USA Two independent groups of RNA from wt and kdm4b / erythrocytes were extracted using TRIzol® Reagent Life Technologies each group contains three biological repeats. post adenylation of three prime ends of double strand cDNA fragments Adaptor with hairpin loop structure were ligated to prepare for hybridization. The library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then PCR was performed with Phusion High Fidelity DNA polymerase. At last PCR products were purified and the library quality was assessed on the Agilent Bioanalyzer 2100 system.	WT3	E MTAB 13116:WT3		strain:Tubingen\|disease:normal\|individual:mixed pool of 200 individuals\|organism:Danio rerio\|organism:Danio rerio\|collection date:not collected\|sex:mixed\|scientific name:Danio rerio\|common name:zebrafish\|organism part:embryo\|developmental stage:embryo stage\|genotype:wild type genotype\|isolate:not applicable\|immunophenotype:gata1 positive\|cell type:erythrocyte\|age:48\|geographic location country and/or sea:not collected\|ENA LAST UPDATE:2023 06 27	RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors	E MTAB 13116:WT3 p	WT3 p	RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors	The 48 hpf gata1+ erythrocytes were sorted FACSAria BD Bioscience CA USA Two independent groups of RNA from wt and kdm4b / erythrocytes were extracted using TRIzol® Reagent Life Technologies each group contains three biological repeats. post adenylation of three prime ends of double strand cDNA fragments Adaptor with hairpin loop structure were ligated to prepare for hybridization. The library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then PCR was performed with Phusion High Fidelity DNA polymerase. At last PCR products were purified and the library quality was assessed on the Agilent Bioanalyzer 2100 system.		RNA-Seq	TRANSCRIPTOMIC	RANDOM	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP148707	Illumina NovaSeq 6000 paired end sequencing; RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors	ENA FIRST PUBLIC:2024 07 01\|ENA LAST UPDATE:2024 07 01	WT3_R1.fastq.gz WT3_R2.fastq.gz	fastq fastq	8718445500.0	29061485.0	E MTAB 13116:WT3 R	0:150 1:150	A:2244668655;C:2103611849;G:2135345835;T:2234609621;N:209540	150	150	2244668655	2103611849	2135345835	2234609621	209540	ERX11010312	ERS15939666	ERA24542523	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive												B	B	biological fallback assumption	illumina	novaseq_era	3prime	random_priming	unknown	bulk	unknown	unknown	United Kingdom	2023-06-27	Hatching	Embryo	Whole Organism	All anatomical structures
19087	19087	ERR13834862	ERX13237628	ERS21098715	ERP164534	PRJEB80557	RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf	e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed	Other	This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol.	ENA FIRST PUBLIC:2025 01 01\|ENA LAST UPDATE:2025 01 01	retinal neurons	48HC1 S20 R1 001.fastq.gz	SAMEA116100635	GIMM	ENA first public:2024 01 01\|INSDC center name:GIMM\|INSDC status:public\|Submitter Id:48 HC1\|collected by:Jaakko Lehtimaki\|collection date:2021 11 24\|common name:zebrafish\|dev stage:48 hpf location country and/or sea:Portugal\|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP\|sample name:48 HC1\|scientific name:Danio rerio\|tissue type:retina	Raw reads: 48 HC1	webin reads 48 HC1					RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	Illumina HiSeq X		ERP164534	Raw reads: 48 HC1	ENA FIRST PUBLIC:2025 01 01\|ENA LAST UPDATE:2025 01 01	48HC1_S20_R1_001.fastq.gz	fastq	3768442091.0	38065677.0	webin reads 48 HC1	0:99.00	A:1055463738;C:792073627;G:817607736;T:1103223790;N:73200	99		1055463738	792073627	817607736	1103223790	73200	ERX13237628	ERS21098715	ERA30883416	Gulbenkian Institute for Molecular Medicine\|European Nucleotide Archive	Gulbenkian Institute for Molecular Medicine												B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Belgium	2024-01-01	Hatching	Embryo	Eye	Sensory System
19088	19088	ERR13834951	ERX13237717	ERS21098721	ERP164534	PRJEB80557	RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf	e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed	Other	This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol.	ENA FIRST PUBLIC:2025 01 01\|ENA LAST UPDATE:2025 01 01	retinal neurons	58PR3 S26 R1 001.fastq.gz	58 PR3		organism:Danio rerio\|collection date:2021 12 02\|scientific name:Danio rerio\|collected by:Jaakko Lehtimaki\|common name:zebrafish\|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP\|dev stage:58 hpf type:retina\|geographic location country and/or sea:Portugal	Raw reads: 58 PR3	webin reads 58 PR3					RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	Illumina HiSeq X		ERP164534	Raw reads: 58 PR3	ENA FIRST PUBLIC:2025 01 01\|ENA LAST UPDATE:2025 01 01	58PR3_S26_R1_001.fastq.gz	fastq	3869469736.0	38850717.0	webin reads 58 PR3	0:99.60	A:1103909449;C:804146524;G:827344036;T:1134036010;N:33717	99		1103909449	804146524	827344036	1134036010	33717	ERX13237717	ERS21098721	ERA30883529	Gulbenkian Institute for Molecular Medicine\|European Nucleotide Archive	Gulbenkian Institute for Molecular Medicine												B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Belgium	2025-01-01	Hatching	Embryo	Eye	Sensory System
19089	19089	ERR13835010	ERX13237776	ERS21098726	ERP164534	PRJEB80557	RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf	e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed	Other	This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol.	ENA FIRST PUBLIC:2025 01 01\|ENA LAST UPDATE:2025 01 01	retinal neurons	58AC4 S31 R1 001.fastq.gz	SAMEA116100646	GIMM	ENA first public:2024 01 01\|INSDC center name:GIMM\|INSDC status:public\|Submitter Id:58 AC4\|collected by:Jaakko Lehtimaki\|collection date:2021 12 02\|common name:zebrafish\|dev stage:58 hpf location country and/or sea:Portugal\|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP\|sample name:58 AC4\|scientific name:Danio rerio\|tissue type:retina	Raw reads: 58 AC4	webin reads 58 AC4					RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	Illumina HiSeq X		ERP164534	Raw reads: 58 AC4	ENA FIRST PUBLIC:2025 01 01\|ENA LAST UPDATE:2025 01 01	58AC4_S31_R1_001.fastq.gz	fastq	3607648651.0	36331933.0	webin reads 58 AC4	0:99.30	A:1038047870;C:736262498;G:759315202;T:1073962987;N:60094	99		1038047870	736262498	759315202	1073962987	60094	ERX13237776	ERS21098726	ERA30883721	Gulbenkian Institute for Molecular Medicine\|European Nucleotide Archive	Gulbenkian Institute for Molecular Medicine												B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Belgium	2024-01-01	Hatching	Embryo	Eye	Sensory System
19090	19090	ERR13822794	ERX13225546	ERS21098708	ERP164534	PRJEB80557	RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf	e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed	Other	This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol.	ENA FIRST PUBLIC:2025 01 01\|ENA LAST UPDATE:2025 01 01	retinal neurons	48PR2 S13 R1 001.fastq.gz	48 PR2		organism:Danio rerio\|collection date:2021 11 24\|scientific name:Danio rerio\|collected by:Jaakko Lehtimaki\|common name:zebrafish\|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP\|dev stage:48 hpf type:retina\|geographic location country and/or sea:Portugal	Raw reads: 48 PR2	webin reads 48 PR2					RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	Illumina HiSeq X		ERP164534	Raw reads: 48 PR2	ENA FIRST PUBLIC:2025 01 01\|ENA LAST UPDATE:2025 01 01	48PR2_S13_R1_001.fastq.gz	fastq	3809299607.0	38404185.0	webin reads 48 PR2	0:99.19	A:1067728192;C:802585802;G:828435932;T:1110435904;N:113777	99		1067728192	802585802	828435932	1110435904	113777	ERX13225546	ERS21098708	ERA30879682	Gulbenkian Institute for Molecular Medicine\|European Nucleotide Archive	Gulbenkian Institute for Molecular Medicine												B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Belgium	2025-01-01	Hatching	Embryo	Eye	Sensory System
19091	19091	ERR13834854	ERX13237620	ERS21098714	ERP164534	PRJEB80557	RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf	e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed	Other	This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol.	ENA FIRST PUBLIC:2025 01 01\|ENA LAST UPDATE:2025 01 01	retinal neurons	48AC4 S19 R1 001.fastq.gz	48 AC4		organism:Danio rerio\|collection date:2021 11 24\|scientific name:Danio rerio\|collected by:Jaakko Lehtimaki\|common name:zebrafish\|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP\|dev stage:48 hpf type:retina\|geographic location country and/or sea:Portugal	Raw reads: 48 AC4	webin reads 48 AC4					RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	Illumina HiSeq X		ERP164534	Raw reads: 48 AC4	ENA FIRST PUBLIC:2025 01 01\|ENA LAST UPDATE:2025 01 01	48AC4_S19_R1_001.fastq.gz	fastq	3410801894.0	34443068.0	webin reads 48 AC4	0:99.03	A:966160063;C:707754156;G:733039262;T:1003772756;N:75657	99		966160063	707754156	733039262	1003772756	75657	ERX13237620	ERS21098714	ERA30883390	Gulbenkian Institute for Molecular Medicine\|European Nucleotide Archive	Gulbenkian Institute for Molecular Medicine												B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Belgium	2025-01-01	Hatching	Embryo	Eye	Sensory System
19092	19092	ERR13828824	ERX13231590	ERS21098710	ERP164534	PRJEB80557	RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf	e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed	Other	This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol.	ENA FIRST PUBLIC:2025 01 01\|ENA LAST UPDATE:2025 01 01	retinal neurons	48PR4 S15 R1 001.fastq.gz	48 PR4		organism:Danio rerio\|collection date:2021 11 24\|scientific name:Danio rerio\|collected by:Jaakko Lehtimaki\|common name:zebrafish\|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP\|dev stage:48 hpf type:retina\|geographic location country and/or sea:Portugal	Raw reads: 48 PR4	webin reads 48 PR4					RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	Illumina HiSeq X		ERP164534	Raw reads: 48 PR4	ENA FIRST PUBLIC:2025 01 01\|ENA LAST UPDATE:2025 01 01	48PR4_S15_R1_001.fastq.gz	fastq	4365943927.0	44278278.0	webin reads 48 PR4	0:98.60	A:1214448497;C:927512154;G:957491418;T:1266385355;N:106503	98		1214448497	927512154	957491418	1266385355	106503	ERX13231590	ERS21098710	ERA30883309	Gulbenkian Institute for Molecular Medicine\|European Nucleotide Archive	Gulbenkian Institute for Molecular Medicine												B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Belgium	2025-01-01	Hatching	Embryo	Eye	Sensory System
19093	19093	ERR13834993	ERX13237759	ERS21098723	ERP164534	PRJEB80557	RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf	e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed	Other	This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol.	ENA FIRST PUBLIC:2025 01 01\|ENA LAST UPDATE:2025 01 01	retinal neurons	58AC1 S28 R1 001.fastq.gz	58 AC1		organism:Danio rerio\|collection date:2021 12 02\|scientific name:Danio rerio\|collected by:Jaakko Lehtimaki\|common name:zebrafish\|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP\|dev stage:58 hpf type:retina\|geographic location country and/or sea:Portugal	Raw reads: 58 AC1	webin reads 58 AC1					RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	Illumina HiSeq X		ERP164534	Raw reads: 58 AC1	ENA FIRST PUBLIC:2025 01 01\|ENA LAST UPDATE:2025 01 01	58AC1_S28_R1_001.fastq.gz	fastq	3710768269.0	37364763.0	webin reads 58 AC1	0:99.31	A:1060419097;C:761984557;G:786533722;T:1101603428;N:227465	99		1060419097	761984557	786533722	1101603428	227465	ERX13237759	ERS21098723	ERA30883659	Gulbenkian Institute for Molecular Medicine\|European Nucleotide Archive	Gulbenkian Institute for Molecular Medicine												B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Belgium	2025-01-01	Hatching	Embryo	Eye	Sensory System
19094	19094	ERR13834875	ERX13237641	ERS21098717	ERP164534	PRJEB80557	RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf	e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed	Other	This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol.	ENA FIRST PUBLIC:2025 01 01\|ENA LAST UPDATE:2025 01 01	retinal neurons	48HC3 S22 R1 001.fastq.gz	48 HC3		organism:Danio rerio\|collection date:2021 11 24\|scientific name:Danio rerio\|collected by:Jaakko Lehtimaki\|common name:zebrafish\|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP\|dev stage:48 hpf type:retina\|geographic location country and/or sea:Portugal	Raw reads: 48 HC3	webin reads 48 HC3					RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	Illumina HiSeq X		ERP164534	Raw reads: 48 HC3	ENA FIRST PUBLIC:2025 01 01\|ENA LAST UPDATE:2025 01 01	48HC3_S22_R1_001.fastq.gz	fastq	3083078586.0	31073491.0	webin reads 48 HC3	0:99.22	A:856250957;C:655140994;G:677078911;T:894558582;N:49142	99		856250957	655140994	677078911	894558582	49142	ERX13237641	ERS21098717	ERA30883447	Gulbenkian Institute for Molecular Medicine\|European Nucleotide Archive	Gulbenkian Institute for Molecular Medicine												B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Belgium	2025-01-01	Hatching	Embryo	Eye	Sensory System
19095	19095	ERR13834899	ERX13237665	ERS21098720	ERP164534	PRJEB80557	RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf	e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed	Other	This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol.	ENA FIRST PUBLIC:2025 01 01\|ENA LAST UPDATE:2025 01 01	retinal neurons	58PR2 S25 R1 001.fastq.gz	58 PR2		organism:Danio rerio\|collection date:2021 12 02\|scientific name:Danio rerio\|collected by:Jaakko Lehtimaki\|common name:zebrafish\|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP\|dev stage:58 hpf type:retina\|geographic location country and/or sea:Portugal	Raw reads: 58 PR2	webin reads 58 PR2					RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	Illumina HiSeq X		ERP164534	Raw reads: 58 PR2	ENA FIRST PUBLIC:2025 01 01\|ENA LAST UPDATE:2025 01 01	58PR2_S25_R1_001.fastq.gz	fastq	3849571818.0	38706841.0	webin reads 58 PR2	0:99.45	A:1089593011;C:803322469;G:827777017;T:1128836774;N:42547	99		1089593011	803322469	827777017	1128836774	42547	ERX13237665	ERS21098720	ERA30883518	Gulbenkian Institute for Molecular Medicine\|European Nucleotide Archive	Gulbenkian Institute for Molecular Medicine												B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Belgium	2025-01-01	Hatching	Embryo	Eye	Sensory System
19096	19096	ERR13834889	ERX13237655	ERS21098719	ERP164534	PRJEB80557	RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf	e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed	Other	This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol.	ENA FIRST PUBLIC:2025 01 01\|ENA LAST UPDATE:2025 01 01	retinal neurons	58PR1 S24 R1 001.fastq.gz	58 PR1		organism:Danio rerio\|collection date:2021 12 02\|scientific name:Danio rerio\|collected by:Jaakko Lehtimaki\|common name:zebrafish\|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP\|dev stage:58 hpf type:retina\|geographic location country and/or sea:Portugal	Raw reads: 58 PR1	webin reads 58 PR1					RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	Illumina HiSeq X		ERP164534	Raw reads: 58 PR1	ENA FIRST PUBLIC:2025 01 01\|ENA LAST UPDATE:2025 01 01	58PR1_S24_R1_001.fastq.gz	fastq	3945671240.0	39514922.0	webin reads 58 PR1	0:99.85	A:1135075173;C:807489123;G:827964380;T:1175109762;N:32802	99		1135075173	807489123	827964380	1175109762	32802	ERX13237655	ERS21098719	ERA30883497	Gulbenkian Institute for Molecular Medicine\|European Nucleotide Archive	Gulbenkian Institute for Molecular Medicine												B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Belgium	2025-01-01	Hatching	Embryo	Eye	Sensory System
19097	19097	ERR13835019	ERX13237785	ERS21098728	ERP164534	PRJEB80557	RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf	e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed	Other	This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol.	ENA FIRST PUBLIC:2025 01 01\|ENA LAST UPDATE:2025 01 01	retinal neurons	58HC2 S33 R1 001.fastq.gz	SAMEA116100648	GIMM	ENA first public:2024 01 01\|INSDC center name:GIMM\|INSDC status:public\|Submitter Id:58 HC2\|collected by:Jaakko Lehtimaki\|collection date:2021 12 02\|common name:zebrafish\|dev stage:58 hpf location country and/or sea:Portugal\|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP\|sample name:58 HC2\|scientific name:Danio rerio\|tissue type:retina	Raw reads: 58 HC2	webin reads 58 HC2					RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	Illumina HiSeq X		ERP164534	Raw reads: 58 HC2	ENA FIRST PUBLIC:2025 01 01\|ENA LAST UPDATE:2025 01 01	58HC2_S33_R1_001.fastq.gz	fastq	3711237069.0	37217240.0	webin reads 58 HC2	0:99.72	A:1070592288;C:757099665;G:780689044;T:1102575310;N:280762	99		1070592288	757099665	780689044	1102575310	280762	ERX13237785	ERS21098728	ERA30883748	Gulbenkian Institute for Molecular Medicine\|European Nucleotide Archive	Gulbenkian Institute for Molecular Medicine												B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Belgium	2024-01-01	Hatching	Embryo	Eye	Sensory System
19098	19098	ERR13822110	ERX13224862	ERS21098697	ERP164534	PRJEB80557	RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf	e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed	Other	This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol.	ENA FIRST PUBLIC:2025 01 01\|ENA LAST UPDATE:2025 01 01	retinal neurons	38PR2 S2 R1 001.fastq.gz	38 PR2		organism:Danio rerio\|collection date:2021 11 30\|scientific name:Danio rerio\|collected by:Jaakko Lehtimaki\|common name:zebrafish\|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP\|dev stage:38 hpf type:retina\|geographic location country and/or sea:Portugal	Raw reads: 38 PR2	webin reads 38 PR2					RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	Illumina HiSeq X		ERP164534	Raw reads: 38 PR2	ENA FIRST PUBLIC:2025 01 01\|ENA LAST UPDATE:2025 01 01	38PR2_S2_R1_001.fastq.gz	fastq	3463281109.0	34821985.0	webin reads 38 PR2	0:99.46	A:969862466;C:733798241;G:755135957;T:1004440555;N:43890	99		969862466	733798241	755135957	1004440555	43890	ERX13224862	ERS21098697	ERA30879238	Gulbenkian Institute for Molecular Medicine\|European Nucleotide Archive	Gulbenkian Institute for Molecular Medicine												B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Belgium	2025-01-01	Pharyngula	Embryo	Eye	Sensory System
19099	19099	ERR13822784	ERX13225536	ERS21098706	ERP164534	PRJEB80557	RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf	e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed	Other	This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol.	ENA FIRST PUBLIC:2025 01 01\|ENA LAST UPDATE:2025 01 01	retinal neurons	38HC3 S11 R1 001.fastq.gz	38 HC3		organism:Danio rerio\|collection date:2021 12 07\|scientific name:Danio rerio\|collected by:Jaakko Lehtimaki\|common name:zebrafish\|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP\|dev stage:38 hpf type:retina\|geographic location country and/or sea:Portugal	Raw reads: 38 HC3	webin reads 38 HC3					RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	Illumina HiSeq X		ERP164534	Raw reads: 38 HC3	ENA FIRST PUBLIC:2025 01 01\|ENA LAST UPDATE:2025 01 01	38HC3_S11_R1_001.fastq.gz	fastq	4360921873.0	44107486.0	webin reads 38 HC3	0:98.87	A:1222778761;C:918257887;G:948838973;T:1270939370;N:106882	98		1222778761	918257887	948838973	1270939370	106882	ERX13225536	ERS21098706	ERA30879613	Gulbenkian Institute for Molecular Medicine\|European Nucleotide Archive	Gulbenkian Institute for Molecular Medicine												B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Belgium	2025-01-01	Pharyngula	Embryo	Eye	Sensory System
19100	19100	ERR13828836	ERX13231602	ERS21098712	ERP164534	PRJEB80557	RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf	e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed	Other	This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol.	ENA FIRST PUBLIC:2025 01 01\|ENA LAST UPDATE:2025 01 01	retinal neurons	48AC2 S17 R1 001.fastq.gz	48 AC2		organism:Danio rerio\|collection date:2021 11 24\|scientific name:Danio rerio\|collected by:Jaakko Lehtimaki\|common name:zebrafish\|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP\|dev stage:48 hpf type:retina\|geographic location country and/or sea:Portugal	Raw reads: 48 AC2	webin reads 48 AC2					RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	Illumina HiSeq X		ERP164534	Raw reads: 48 AC2	ENA FIRST PUBLIC:2025 01 01\|ENA LAST UPDATE:2025 01 01	48AC2_S17_R1_001.fastq.gz	fastq	3205206588.0	32424632.0	webin reads 48 AC2	0:98.85	A:902438127;C:672433401;G:694813369;T:935445436;N:76255	98		902438127	672433401	694813369	935445436	76255	ERX13231602	ERS21098712	ERA30883343	Gulbenkian Institute for Molecular Medicine\|European Nucleotide Archive	Gulbenkian Institute for Molecular Medicine												B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Belgium	2025-01-01	Hatching	Embryo	Eye	Sensory System
19101	19101	ERR13835004	ERX13237770	ERS21098725	ERP164534	PRJEB80557	RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf	e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed	Other	This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol.	ENA FIRST PUBLIC:2025 01 01\|ENA LAST UPDATE:2025 01 01	retinal neurons	58AC3 S30 R1 001.fastq.gz	58 AC3		organism:Danio rerio\|collection date:2021 12 02\|scientific name:Danio rerio\|collected by:Jaakko Lehtimaki\|common name:zebrafish\|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP\|dev stage:58 hpf type:retina\|geographic location country and/or sea:Portugal	Raw reads: 58 AC3	webin reads 58 AC3					RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	Illumina HiSeq X		ERP164534	Raw reads: 58 AC3	ENA FIRST PUBLIC:2025 01 01\|ENA LAST UPDATE:2025 01 01	58AC3_S30_R1_001.fastq.gz	fastq	3782993133.0	38295959.0	webin reads 58 AC3	0:98.78	A:1080745150;C:779903026;G:803258485;T:1118994941;N:91531	98		1080745150	779903026	803258485	1118994941	91531	ERX13237770	ERS21098725	ERA30883697	Gulbenkian Institute for Molecular Medicine\|European Nucleotide Archive	Gulbenkian Institute for Molecular Medicine												B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Belgium	2025-01-01	Hatching	Embryo	Eye	Sensory System
19102	19102	ERR13834868	ERX13237634	ERS21098716	ERP164534	PRJEB80557	RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf	e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed	Other	This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol.	ENA FIRST PUBLIC:2025 01 01\|ENA LAST UPDATE:2025 01 01	retinal neurons	48HC2 S21 R1 001.fastq.gz	SAMEA116100636	GIMM	ENA first public:2024 01 01\|INSDC center name:GIMM\|INSDC status:public\|Submitter Id:48 HC2\|collected by:Jaakko Lehtimaki\|collection date:2021 11 24\|common name:zebrafish\|dev stage:48 hpf location country and/or sea:Portugal\|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP\|sample name:48 HC2\|scientific name:Danio rerio\|tissue type:retina	Raw reads: 48 HC2	webin reads 48 HC2					RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	Illumina HiSeq X		ERP164534	Raw reads: 48 HC2	ENA FIRST PUBLIC:2025 01 01\|ENA LAST UPDATE:2025 01 01	48HC2_S21_R1_001.fastq.gz	fastq	3424347865.0	34510204.0	webin reads 48 HC2	0:99.23	A:959488173;C:721171249;G:745705870;T:997922014;N:60559	99		959488173	721171249	745705870	997922014	60559	ERX13237634	ERS21098716	ERA30883434	Gulbenkian Institute for Molecular Medicine\|European Nucleotide Archive	Gulbenkian Institute for Molecular Medicine												B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Belgium	2024-01-01	Hatching	Embryo	Eye	Sensory System
19103	19103	ERR13822197	ERX13224949	ERS21098704	ERP164534	PRJEB80557	RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf	e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed	Other	This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol.	ENA FIRST PUBLIC:2025 01 01\|ENA LAST UPDATE:2025 01 01	retinal neurons	38HC1 S9 R1 001.fastq.gz	SAMEA116100624	GIMM	ENA first public:2024 01 01\|INSDC center name:GIMM\|INSDC status:public\|Submitter Id:38 HC1\|collected by:Jaakko Lehtimaki\|collection date:2021 11 30\|common name:zebrafish\|dev stage:38 hpf location country and/or sea:Portugal\|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP\|sample name:38 HC1\|scientific name:Danio rerio\|tissue type:retina	Raw reads: 38 HC1	webin reads 38 HC1					RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	Illumina HiSeq X		ERP164534	Raw reads: 38 HC1	ENA FIRST PUBLIC:2025 01 01\|ENA LAST UPDATE:2025 01 01	38HC1_S9_R1_001.fastq.gz	fastq	3784641498.0	38331162.0	webin reads 38 HC1	0:98.74	A:1064199311;C:791310791;G:818910597;T:1110118632;N:102167	98		1064199311	791310791	818910597	1110118632	102167	ERX13224949	ERS21098704	ERA30879548	Gulbenkian Institute for Molecular Medicine\|European Nucleotide Archive	Gulbenkian Institute for Molecular Medicine												B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Belgium	2024-01-01	Pharyngula	Embryo	Eye	Sensory System
19104	19104	ERR13834880	ERX13237646	ERS21098718	ERP164534	PRJEB80557	RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf	e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed	Other	This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol.	ENA FIRST PUBLIC:2025 01 01\|ENA LAST UPDATE:2025 01 01	retinal neurons	48HC4 S23 R1 001.fastq.gz	48 HC4		organism:Danio rerio\|collection date:2021 11 24\|scientific name:Danio rerio\|collected by:Jaakko Lehtimaki\|common name:zebrafish\|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP\|dev stage:48 hpf type:retina\|geographic location country and/or sea:Portugal	Raw reads: 48 HC4	webin reads 48 HC4					RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	Illumina HiSeq X		ERP164534	Raw reads: 48 HC4	ENA FIRST PUBLIC:2025 01 01\|ENA LAST UPDATE:2025 01 01	48HC4_S23_R1_001.fastq.gz	fastq	3660674315.0	36821474.0	webin reads 48 HC4	0:99.42	A:1035049987;C:763030378;G:788062167;T:1074303516;N:228267	99		1035049987	763030378	788062167	1074303516	228267	ERX13237646	ERS21098718	ERA30883470	Gulbenkian Institute for Molecular Medicine\|European Nucleotide Archive	Gulbenkian Institute for Molecular Medicine												B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Belgium	2025-01-01	Hatching	Embryo	Eye	Sensory System
19105	19105	ERR13822867	ERX13225633	ERS21098709	ERP164534	PRJEB80557	RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf	e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed	Other	This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol.	ENA FIRST PUBLIC:2025 01 01\|ENA LAST UPDATE:2025 01 01	retinal neurons	48PR3 S14 R1 001.fastq.gz	48 PR3		organism:Danio rerio\|collection date:2021 11 24\|scientific name:Danio rerio\|collected by:Jaakko Lehtimaki\|common name:zebrafish\|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP\|dev stage:48 hpf type:retina\|geographic location country and/or sea:Portugal	Raw reads: 48 PR3	webin reads 48 PR3					RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	Illumina HiSeq X		ERP164534	Raw reads: 48 PR3	ENA FIRST PUBLIC:2025 01 01\|ENA LAST UPDATE:2025 01 01	48PR3_S14_R1_001.fastq.gz	fastq	4232170464.0	42534853.0	webin reads 48 PR3	0:99.50	A:1195251409;C:889346003;G:917240118;T:1230272855;N:60079	99		1195251409	889346003	917240118	1230272855	60079	ERX13225633	ERS21098709	ERA30879704	Gulbenkian Institute for Molecular Medicine\|European Nucleotide Archive	Gulbenkian Institute for Molecular Medicine												B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Belgium	2025-01-01	Hatching	Embryo	Eye	Sensory System
19106	19106	ERR13822131	ERX13224883	ERS21098700	ERP164534	PRJEB80557	RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf	e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed	Other	This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol.	ENA FIRST PUBLIC:2025 01 01\|ENA LAST UPDATE:2025 01 01	retinal neurons	38AC1 S5 R1 001.fastq.gz	SAMEA116100620	GIMM	ENA first public:2024 01 01\|INSDC center name:GIMM\|INSDC status:public\|Submitter Id:38 AC1\|collected by:Jaakko Lehtimaki\|collection date:2021 11 30\|common name:zebrafish\|dev stage:38 hpf location country and/or sea:Portugal\|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP\|sample name:38 AC1\|scientific name:Danio rerio\|tissue type:retina	Raw reads: 38 AC1	webin reads 38 AC1					RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	Illumina HiSeq X		ERP164534	Raw reads: 38 AC1	ENA FIRST PUBLIC:2025 01 01\|ENA LAST UPDATE:2025 01 01	38AC1_S5_R1_001.fastq.gz	fastq	3836921113.0	38702139.0	webin reads 38 AC1	0:99.14	A:1066720805;C:818958589;G:843762182;T:1107403844;N:75693	99		1066720805	818958589	843762182	1107403844	75693	ERX13224883	ERS21098700	ERA30879356	Gulbenkian Institute for Molecular Medicine\|European Nucleotide Archive	Gulbenkian Institute for Molecular Medicine												B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Belgium	2024-01-01	Pharyngula	Embryo	Eye	Sensory System
19107	19107	ERR13822143	ERX13224895	ERS21098702	ERP164534	PRJEB80557	RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf	e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed	Other	This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol.	ENA FIRST PUBLIC:2025 01 01\|ENA LAST UPDATE:2025 01 01	retinal neurons	38AC3 S7 R1 001.fastq.gz	38 AC3		organism:Danio rerio\|collection date:2021 12 07\|scientific name:Danio rerio\|collected by:Jaakko Lehtimaki\|common name:zebrafish\|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP\|dev stage:38 hpf type:retina\|geographic location country and/or sea:Portugal	Raw reads: 38 AC3	webin reads 38 AC3					RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	Illumina HiSeq X		ERP164534	Raw reads: 38 AC3	ENA FIRST PUBLIC:2025 01 01\|ENA LAST UPDATE:2025 01 01	38AC3_S7_R1_001.fastq.gz	fastq	3452707377.0	34902410.0	webin reads 38 AC3	0:98.92	A:970868997;C:726795179;G:750560378;T:1004408693;N:74130	98		970868997	726795179	750560378	1004408693	74130	ERX13224895	ERS21098702	ERA30879451	Gulbenkian Institute for Molecular Medicine\|European Nucleotide Archive	Gulbenkian Institute for Molecular Medicine												B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Belgium	2025-01-01	Pharyngula	Embryo	Eye	Sensory System
19108	19108	ERR13828843	ERX13234350	ERS21098713	ERP164534	PRJEB80557	RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf	e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed	Other	This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol.	ENA FIRST PUBLIC:2025 01 01\|ENA LAST UPDATE:2025 01 01	retinal neurons	48AC3 S18 R1 001.fastq.gz	48 AC3		organism:Danio rerio\|collection date:2021 11 24\|scientific name:Danio rerio\|collected by:Jaakko Lehtimaki\|common name:zebrafish\|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP\|dev stage:48 hpf type:retina\|geographic location country and/or sea:Portugal	Raw reads: 48 AC3	webin reads 48 AC3					RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	Illumina HiSeq X		ERP164534	Raw reads: 48 AC3	ENA FIRST PUBLIC:2025 01 01\|ENA LAST UPDATE:2025 01 01	48AC3_S18_R1_001.fastq.gz	fastq	3733628911.0	37779462.0	webin reads 48 AC3	0:98.83	A:1047204450;C:786943605;G:812327274;T:1086893109;N:260473	98		1047204450	786943605	812327274	1086893109	260473	ERX13234350	ERS21098713	ERA30883366	Gulbenkian Institute for Molecular Medicine\|European Nucleotide Archive	Gulbenkian Institute for Molecular Medicine												B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Belgium	2025-01-01	Hatching	Embryo	Eye	Sensory System
19109	19109	ERR13822153	ERX13224905	ERS21098703	ERP164534	PRJEB80557	RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf	e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed	Other	This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol.	ENA FIRST PUBLIC:2025 01 01\|ENA LAST UPDATE:2025 01 01	retinal neurons	38AC4 S8 R1 001.fastq.gz	38 AC4		organism:Danio rerio\|collection date:2021 12 07\|scientific name:Danio rerio\|collected by:Jaakko Lehtimaki\|common name:zebrafish\|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP\|dev stage:38 hpf type:retina\|geographic location country and/or sea:Portugal	Raw reads: 38 AC4	webin reads 38 AC4					RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	Illumina HiSeq X		ERP164534	Raw reads: 38 AC4	ENA FIRST PUBLIC:2025 01 01\|ENA LAST UPDATE:2025 01 01	38AC4_S8_R1_001.fastq.gz	fastq	4130629624.0	41794865.0	webin reads 38 AC4	0:98.83	A:1156746387;C:877063962;G:905379690;T:1191264308;N:175277	98		1156746387	877063962	905379690	1191264308	175277	ERX13224905	ERS21098703	ERA30879532	Gulbenkian Institute for Molecular Medicine\|European Nucleotide Archive	Gulbenkian Institute for Molecular Medicine												B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Belgium	2025-01-01	Pharyngula	Embryo	Eye	Sensory System
19110	19110	ERR13822201	ERX13224953	ERS21098705	ERP164534	PRJEB80557	RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf	e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed	Other	This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol.	ENA FIRST PUBLIC:2025 01 01\|ENA LAST UPDATE:2025 01 01	retinal neurons	38HC2 S10 R1 001.fastq.gz	38 HC2		organism:Danio rerio\|collection date:2021 11 30\|scientific name:Danio rerio\|collected by:Jaakko Lehtimaki\|common name:zebrafish\|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP\|dev stage:38 hpf type:retina\|geographic location country and/or sea:Portugal	Raw reads: 38 HC2	webin reads 38 HC2					RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	Illumina HiSeq X		ERP164534	Raw reads: 38 HC2	ENA FIRST PUBLIC:2025 01 01\|ENA LAST UPDATE:2025 01 01	38HC2_S10_R1_001.fastq.gz	fastq	4221340137.0	42584743.0	webin reads 38 HC2	0:99.13	A:1195817135;C:879958039;G:908085464;T:1237394738;N:84761	99		1195817135	879958039	908085464	1237394738	84761	ERX13224953	ERS21098705	ERA30879582	Gulbenkian Institute for Molecular Medicine\|European Nucleotide Archive	Gulbenkian Institute for Molecular Medicine												B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Belgium	2025-01-01	Pharyngula	Embryo	Eye	Sensory System
19111	19111	ERR13822114	ERX13224866	ERS21098698	ERP164534	PRJEB80557	RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf	e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed	Other	This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol.	ENA FIRST PUBLIC:2025 01 01\|ENA LAST UPDATE:2025 01 01	retinal neurons	38PR3 S3 R1 001.fastq.gz	SAMEA116100618	GIMM	ENA first public:2024 01 01\|INSDC center name:GIMM\|INSDC status:public\|Submitter Id:38 PR3\|collected by:Jaakko Lehtimaki\|collection date:2021 12 07\|common name:zebrafish\|dev stage:38 hpf location country and/or sea:Portugal\|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP\|sample name:38 PR3\|scientific name:Danio rerio\|tissue type:retina	Raw reads: 38 PR3	webin reads 38 PR3					RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	Illumina HiSeq X		ERP164534	Raw reads: 38 PR3	ENA FIRST PUBLIC:2025 01 01\|ENA LAST UPDATE:2025 01 01	38PR3_S3_R1_001.fastq.gz	fastq	3894010106.0	39196855.0	webin reads 38 PR3	0:99.34	A:1093221995;C:818047738;G:843661747;T:1138957138;N:121488	99		1093221995	818047738	843661747	1138957138	121488	ERX13224866	ERS21098698	ERA30879273	Gulbenkian Institute for Molecular Medicine\|European Nucleotide Archive	Gulbenkian Institute for Molecular Medicine												B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Belgium	2024-01-01	Pharyngula	Embryo	Eye	Sensory System
19112	19112	ERR13822135	ERX13224887	ERS21098701	ERP164534	PRJEB80557	RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf	e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed	Other	This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol.	ENA FIRST PUBLIC:2025 01 01\|ENA LAST UPDATE:2025 01 01	retinal neurons	38AC2 S6 R1 001.fastq.gz	38 AC2		organism:Danio rerio\|collection date:2021 11 30\|scientific name:Danio rerio\|collected by:Jaakko Lehtimaki\|common name:zebrafish\|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP\|dev stage:38 hpf type:retina\|geographic location country and/or sea:Portugal	Raw reads: 38 AC2	webin reads 38 AC2					RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	Illumina HiSeq X		ERP164534	Raw reads: 38 AC2	ENA FIRST PUBLIC:2025 01 01\|ENA LAST UPDATE:2025 01 01	38AC2_S6_R1_001.fastq.gz	fastq	3913343007.0	39682834.0	webin reads 38 AC2	0:98.62	A:1089960083;C:827936673;G:855955684;T:1139372607;N:117960	98		1089960083	827936673	855955684	1139372607	117960	ERX13224887	ERS21098701	ERA30879382	Gulbenkian Institute for Molecular Medicine\|European Nucleotide Archive	Gulbenkian Institute for Molecular Medicine												B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Belgium	2025-01-01	Pharyngula	Embryo	Eye	Sensory System
19113	19113	ERR13835032	ERX13237798	ERS21098730	ERP164534	PRJEB80557	RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf	e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed	Other	This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol.	ENA FIRST PUBLIC:2025 01 01\|ENA LAST UPDATE:2025 01 01	retinal neurons	58HC4 S35 R1 001.fastq.gz	58 HC4		organism:Danio rerio\|collection date:2021 12 02\|scientific name:Danio rerio\|collected by:Jaakko Lehtimaki\|common name:zebrafish\|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP\|dev stage:58 hpf type:retina\|geographic location country and/or sea:Portugal	Raw reads: 58 HC4	webin reads 58 HC4					RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	Illumina HiSeq X		ERP164534	Raw reads: 58 HC4	ENA FIRST PUBLIC:2025 01 01\|ENA LAST UPDATE:2025 01 01	58HC4_S35_R1_001.fastq.gz	fastq	4418556015.0	44331835.0	webin reads 58 HC4	0:99.67	A:1255080581;C:916490847;G:946212615;T:1300735054;N:36918	99		1255080581	916490847	946212615	1300735054	36918	ERX13237798	ERS21098730	ERA30883773	Gulbenkian Institute for Molecular Medicine\|European Nucleotide Archive	Gulbenkian Institute for Molecular Medicine												B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Belgium	2025-01-01	Hatching	Embryo	Eye	Sensory System
19114	19114	ERR13828829	ERX13231595	ERS21098711	ERP164534	PRJEB80557	RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf	e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed	Other	This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol.	ENA FIRST PUBLIC:2025 01 01\|ENA LAST UPDATE:2025 01 01	retinal neurons	48AC1 S16 R1 001.fastq.gz	48 AC1		organism:Danio rerio\|collection date:2021 11 24\|scientific name:Danio rerio\|collected by:Jaakko Lehtimaki\|common name:zebrafish\|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP\|dev stage:48 hpf type:retina\|geographic location country and/or sea:Portugal	Raw reads: 48 AC1	webin reads 48 AC1					RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	Illumina HiSeq X		ERP164534	Raw reads: 48 AC1	ENA FIRST PUBLIC:2025 01 01\|ENA LAST UPDATE:2025 01 01	48AC1_S16_R1_001.fastq.gz	fastq	3933669121.0	39695406.0	webin reads 48 AC1	0:99.10	A:1105258159;C:824538054;G:854253688;T:1149538152;N:81068	99		1105258159	824538054	854253688	1149538152	81068	ERX13231595	ERS21098711	ERA30883326	Gulbenkian Institute for Molecular Medicine\|European Nucleotide Archive	Gulbenkian Institute for Molecular Medicine												B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Belgium	2025-01-01	Hatching	Embryo	Eye	Sensory System
19115	19115	ERR13822099	ERX13224851	ERS21098696	ERP164534	PRJEB80557	RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf	e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed	Other	This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol.	ENA FIRST PUBLIC:2025 01 01\|ENA LAST UPDATE:2025 01 01	retinal neurons	38PR1 S1 R1 001.fastq.gz	38 PR1		organism:Danio rerio\|collection date:2021 11 30\|scientific name:Danio rerio\|collected by:Jaakko Lehtimaki\|common name:zebrafish\|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP\|dev stage:38 hpf type:retina\|geographic location country and/or sea:Portugal	Raw reads: 38 PR1	webin reads 38 PR1					RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	Illumina HiSeq X		ERP164534	Raw reads: 38 PR1	ENA FIRST PUBLIC:2025 01 01\|ENA LAST UPDATE:2025 01 01	38PR1_S1_R1_001.fastq.gz	fastq	4256158288.0	42658127.0	webin reads 38 PR1	0:99.77	A:1193880575;C:899261652;G:926114030;T:1236860186;N:41845	99		1193880575	899261652	926114030	1236860186	41845	ERX13224851	ERS21098696	ERA30879152	Gulbenkian Institute for Molecular Medicine\|European Nucleotide Archive	Gulbenkian Institute for Molecular Medicine												B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Belgium	2025-01-01	Pharyngula	Embryo	Eye	Sensory System
19116	19116	ERR13822119	ERX13224871	ERS21098699	ERP164534	PRJEB80557	RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf	e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed	Other	This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol.	ENA FIRST PUBLIC:2025 01 01\|ENA LAST UPDATE:2025 01 01	retinal neurons	38PR4 S4 R1 001.fastq.gz	38 PR4		organism:Danio rerio\|collection date:2021 12 07\|scientific name:Danio rerio\|collected by:Jaakko Lehtimaki\|common name:zebrafish\|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP\|dev stage:38 hpf type:retina\|geographic location country and/or sea:Portugal	Raw reads: 38 PR4	webin reads 38 PR4					RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	Illumina HiSeq X		ERP164534	Raw reads: 38 PR4	ENA FIRST PUBLIC:2025 01 01\|ENA LAST UPDATE:2025 01 01	38PR4_S4_R1_001.fastq.gz	fastq	3726308046.0	37591038.0	webin reads 38 PR4	0:99.13	A:1043231302;C:789255840;G:812957881;T:1080801843;N:61180	99		1043231302	789255840	812957881	1080801843	61180	ERX13224871	ERS21098699	ERA30879302	Gulbenkian Institute for Molecular Medicine\|European Nucleotide Archive	Gulbenkian Institute for Molecular Medicine												B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Belgium	2025-01-01	Pharyngula	Embryo	Eye	Sensory System
19117	19117	ERR13835025	ERX13237791	ERS21098729	ERP164534	PRJEB80557	RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf	e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed	Other	This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol.	ENA FIRST PUBLIC:2025 01 01\|ENA LAST UPDATE:2025 01 01	retinal neurons	58HC3 S34 R1 001.fastq.gz	58 HC3		organism:Danio rerio\|collection date:2021 12 02\|scientific name:Danio rerio\|collected by:Jaakko Lehtimaki\|common name:zebrafish\|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP\|dev stage:58 hpf type:retina\|geographic location country and/or sea:Portugal	Raw reads: 58 HC3	webin reads 58 HC3					RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	Illumina HiSeq X		ERP164534	Raw reads: 58 HC3	ENA FIRST PUBLIC:2025 01 01\|ENA LAST UPDATE:2025 01 01	58HC3_S34_R1_001.fastq.gz	fastq	3523899212.0	35292613.0	webin reads 58 HC3	0:99.85	A:1012516999;C:723225071;G:745152410;T:1042976092;N:28640	99		1012516999	723225071	745152410	1042976092	28640	ERX13237791	ERS21098729	ERA30883757	Gulbenkian Institute for Molecular Medicine\|European Nucleotide Archive	Gulbenkian Institute for Molecular Medicine												B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Belgium	2025-01-01	Hatching	Embryo	Eye	Sensory System
19118	19118	ERR13835014	ERX13237780	ERS21098727	ERP164534	PRJEB80557	RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf	e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed	Other	This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol.	ENA FIRST PUBLIC:2025 01 01\|ENA LAST UPDATE:2025 01 01	retinal neurons	58HC1 S32 R1 001.fastq.gz	58 HC1		organism:Danio rerio\|collection date:2021 12 02\|scientific name:Danio rerio\|collected by:Jaakko Lehtimaki\|common name:zebrafish\|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP\|dev stage:58 hpf type:retina\|geographic location country and/or sea:Portugal	Raw reads: 58 HC1	webin reads 58 HC1					RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	Illumina HiSeq X		ERP164534	Raw reads: 58 HC1	ENA FIRST PUBLIC:2025 01 01\|ENA LAST UPDATE:2025 01 01	58HC1_S32_R1_001.fastq.gz	fastq	3436493821.0	34597887.0	webin reads 58 HC1	0:99.33	A:980894291;C:707196785;G:729948858;T:1018400124;N:53763	99		980894291	707196785	729948858	1018400124	53763	ERX13237780	ERS21098727	ERA30883731	Gulbenkian Institute for Molecular Medicine\|European Nucleotide Archive	Gulbenkian Institute for Molecular Medicine												B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Belgium	2025-01-01	Hatching	Embryo	Eye	Sensory System
19119	19119	ERR13834987	ERX13237753	ERS21098722	ERP164534	PRJEB80557	RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf	e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed	Other	This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol.	ENA FIRST PUBLIC:2025 01 01\|ENA LAST UPDATE:2025 01 01	retinal neurons	58PR4 S27 R1 001.fastq.gz	58 PR4		organism:Danio rerio\|collection date:2021 12 02\|scientific name:Danio rerio\|collected by:Jaakko Lehtimaki\|common name:zebrafish\|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP\|dev stage:58 hpf type:retina\|geographic location country and/or sea:Portugal	Raw reads: 58 PR4	webin reads 58 PR4					RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	Illumina HiSeq X		ERP164534	Raw reads: 58 PR4	ENA FIRST PUBLIC:2025 01 01\|ENA LAST UPDATE:2025 01 01	58PR4_S27_R1_001.fastq.gz	fastq	3069040814.0	30923422.0	webin reads 58 PR4	0:99.25	A:875776938;C:633951750;G:653308475;T:905949639;N:54012	99		875776938	633951750	653308475	905949639	54012	ERX13237753	ERS21098722	ERA30883641	Gulbenkian Institute for Molecular Medicine\|European Nucleotide Archive	Gulbenkian Institute for Molecular Medicine												B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Belgium	2025-01-01	Hatching	Embryo	Eye	Sensory System
19120	19120	ERR13822788	ERX13225540	ERS21098707	ERP164534	PRJEB80557	RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf	e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed	Other	This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol.	ENA FIRST PUBLIC:2025 01 01\|ENA LAST UPDATE:2025 01 01	retinal neurons	38HC4 S12 R1 001.fastq.gz	38 HC4		organism:Danio rerio\|collection date:2021 12 07\|scientific name:Danio rerio\|collected by:Jaakko Lehtimaki\|common name:zebrafish\|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP\|dev stage:38 hpf type:retina\|geographic location country and/or sea:Portugal	Raw reads: 38 HC4	webin reads 38 HC4					RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	Illumina HiSeq X		ERP164534	Raw reads: 38 HC4	ENA FIRST PUBLIC:2025 01 01\|ENA LAST UPDATE:2025 01 01	38HC4_S12_R1_001.fastq.gz	fastq	3353994440.0	33744828.0	webin reads 38 HC4	0:99.39	A:939537209;C:709367668;G:731849729;T:973193819;N:46015	99		939537209	709367668	731849729	973193819	46015	ERX13225540	ERS21098707	ERA30879650	Gulbenkian Institute for Molecular Medicine\|European Nucleotide Archive	Gulbenkian Institute for Molecular Medicine												B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Belgium	2025-01-01	Pharyngula	Embryo	Eye	Sensory System
19121	19121	ERR13834997	ERX13237763	ERS21098724	ERP164534	PRJEB80557	RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf	e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed	Other	This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol.	ENA FIRST PUBLIC:2025 01 01\|ENA LAST UPDATE:2025 01 01	retinal neurons	58AC2 S29 R1 001.fastq.gz	58 AC2		organism:Danio rerio\|collection date:2021 12 02\|scientific name:Danio rerio\|collected by:Jaakko Lehtimaki\|common name:zebrafish\|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP\|dev stage:58 hpf type:retina\|geographic location country and/or sea:Portugal	Raw reads: 58 AC2	webin reads 58 AC2					RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	Illumina HiSeq X		ERP164534	Raw reads: 58 AC2	ENA FIRST PUBLIC:2025 01 01\|ENA LAST UPDATE:2025 01 01	58AC2_S29_R1_001.fastq.gz	fastq	3872162091.0	38898173.0	webin reads 58 AC2	0:99.55	A:1111663794;C:793747086;G:817730996;T:1148980297;N:39918	99		1111663794	793747086	817730996	1148980297	39918	ERX13237763	ERS21098724	ERA30883678	Gulbenkian Institute for Molecular Medicine\|European Nucleotide Archive	Gulbenkian Institute for Molecular Medicine												B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_plate	smartseq	Belgium	2025-01-01	Hatching	Embryo	Eye	Sensory System
32370	32370	SRR29180530	SRX24700714	SRS21428245	SRP509851	PRJNA1116337	Ioxynil and diethylstilbestrol disrupt vascular and heart development in zebrafish	PRJNA1116337	Other	Endocrine disruption is one of the consequences of industrialization and chemicals released into theenvironment have a profound impact on organisms. Waterborne micromolar concentrations of ioxynil IOX and diethylstilbestrol DES in fish affect the development of the heart vasculature and thyroid gland.				DES		isolate:exposure to DES\|age:48 hpf\|dev stage:embryos\|collection date:2018 06\|geo loc name:Portugal\|sex:pooled male and female\|tissue:embryos\|treatment:exposure to DES\|BioSampleModel:Model organism or animal	RNA seq of DES treated	DES	DES	Sequencing the transcriptomes of zebrafish embryos of DES treated			RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	Illumina HiSeq 4000		SRP509851			DES_TAAGGC_L001_R1_001.fastq.gz DES_TAAGGC_L001_R2_001.fastq.gz	fastq fastq	9169560000.0	30565200.0	DES TAAGGC L001 R1 001.fastq.gz	0:150 1:150	A:2545096687;C:2037322055;G:2024787099;T:2562124529;N:229630	150	150	2545096687	2037322055	2024787099	2562124529	229630	SRX24700714	SRS21428245	SRA1878028	Shanghai Ocean University\|College of Fisheries and Life Science	Shanghai Ocean University												B	B	biological fallback assumption	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	China	2024-05-25	Hatching	Embryo	Embryo Imprecise	All anatomical structures
32371	32371	SRR29180531	SRX24700713	SRS21428246	SRP509851	PRJNA1116337	Ioxynil and diethylstilbestrol disrupt vascular and heart development in zebrafish	PRJNA1116337	Other	Endocrine disruption is one of the consequences of industrialization and chemicals released into theenvironment have a profound impact on organisms. Waterborne micromolar concentrations of ioxynil IOX and diethylstilbestrol DES in fish affect the development of the heart vasculature and thyroid gland.				IOX		isolate:exposure to IOX\|age:48 hpf\|dev stage:embryos\|collection date:2018 06\|geo loc name:Portugal\|sex:pooled male and female\|tissue:embryos\|treatment:exposure to IOX\|BioSampleModel:Model organism or animal	RNA seq of IOX treated	IOX	IOX	Sequencing the transcriptomes of zebrafish embryos of IOX treated			RNA-Seq	TRANSCRIPTOMIC	RANDOM	PAIRED	ILLUMINA	Illumina HiSeq 4000		SRP509851			IOX_CGTACT_L001_R1_001.fastq.gz IOX_CGTACT_L001_R2_001.fastq.gz	fastq fastq	9547157100.0	31823857.0	IOX CGTACT L001 R1 001.fastq.gz	0:150 1:150	A:2631030736;C:2146265744;G:2124421595;T:2645201596;N:237429	150	150	2631030736	2146265744	2124421595	2645201596	237429	SRX24700713	SRS21428246	SRA1878028	Shanghai Ocean University\|College of Fisheries and Life Science	Shanghai Ocean University												B	B	biological fallback assumption	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	China	2024-05-25	Hatching	Embryo	Embryo Imprecise	All anatomical structures
32372	32372	SRR29180532	SRX24700712	SRS21428244	SRP509851	PRJNA1116337	Ioxynil and diethylstilbestrol disrupt vascular and heart development in zebrafish	PRJNA1116337	Other	Endocrine disruption is one of the consequences of industrialization and chemicals released into theenvironment have a profound impact on organisms. Waterborne micromolar concentrations of ioxynil IOX and diethylstilbestrol DES in fish affect the development of the heart vasculature and thyroid gland.				CTR		isolate:control\|age:48 hpf\|dev stage:embryos\|collection date:2018 06\|geo loc name:Portugal\|sex:pooled male and female\|tissue:embryos\|treatment:control\|BioSampleModel:Model organism or animal	RNA seq of CTR treated	CTR	CTR	Sequencing the transcriptomes of zebrafish embryos of control			RNA-Seq	TRANSCRIPTOMIC	RANDOM	PAIRED	ILLUMINA	Illumina HiSeq 4000		SRP509851			CTR_AGGCAG_L001_R1_001.fastq.gz CTR_AGGCAG_L001_R2_001.fastq.gz	fastq fastq	9602954100.0	32009847.0	CTR AGGCAG L001 R1 001.fastq.gz	0:150 1:150	A:2637866848;C:2169057233;G:2152906664;T:2642882530;N:240825	150	150	2637866848	2169057233	2152906664	2642882530	240825	SRX24700712	SRS21428244	SRA1878028	Shanghai Ocean University\|College of Fisheries and Life Science	Shanghai Ocean University												B	B	biological fallback assumption	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	China	2024-05-25	Hatching	Embryo	Embryo Imprecise	All anatomical structures
39827	39827	SRR2441454	SRX1321833	SRS1109642	SRP062493	PRJNA293106	Danio rerio Raw sequence reads	PRJNA293106	Metagenomics	Zebrafish Hypoxia RNAseq		RNAseq at 24hpf following hypoxia		24hpf hypoxia		strain:TU\|age:24hpf\|sex:not determined\|tissue:brain\|treatment:hypoxia\|BioSampleModel:Model organism or animal	Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample 24hpf hypoxia	24hpf.hypoxia.3.10329X21	24hpf.hypoxia.3.10329X21	We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition. For hypoxia we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected. We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages. At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation. RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer. The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides single end stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.			RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	Illumina HiSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</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>	SRP062493			10329X21_130822_SN141_0719_AD2CK5ACXX_7.txt.gz	fastq	1205447950.0	24108959.0	24hpf.hypoxia.3.10329X21	0:50	A:299680333;C:267717935;G:264833481;T:357936794;N:15279407	50		299680333	267717935	264833481	357936794	15279407	SRX1321833	SRS1109642	SRA289450	University of Utah\|Bonkowsky	University of Utah	1	0.87455		0.24266		0.74121		0.57777		50		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	trueseq	bulk	unknown	unknown	United States	2015-10-10	Pharyngula	Embryo	Brain	Nervous System
39828	39828	SRR2437828	SRX1321832	SRS1109643	SRP062493	PRJNA293106	Danio rerio Raw sequence reads	PRJNA293106	Metagenomics	Zebrafish Hypoxia RNAseq		RNAseq at 48hpf following normoxia		48hpf normoxia		strain:TU\|age:48hpf\|sex:not determined\|tissue:brain\|treatment:normoxia\|BioSampleModel:Model organism or animal	Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample 48hpf normoxia	48hpf.normoxia.3.10329X16	48hpf.normoxia.3.10329X16	We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition. For hypoxia we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected. We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages. At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation. RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer. The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides single end stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.			RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	Illumina HiSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</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>	SRP062493			10329X16_130822_SN141_0719_AD2CK5ACXX_6.txt.gz	fastq	985942500.0	19718850.0	48hpf.normoxia.3.10329X16	0:50	A:251856100;C:223081125;G:216430606;T:294554748;N:19921	50		251856100	223081125	216430606	294554748	19921	SRX1321832	SRS1109643	SRA289450	University of Utah\|Bonkowsky	University of Utah	1	0.94791		0.26704		0.68708		0.54445		50		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	trueseq	bulk	unknown	unknown	United States	2015-10-10	Hatching	Embryo	Brain	Nervous System
39829	39829	SRR2434699	SRX1321831	SRS1109642	SRP062493	PRJNA293106	Danio rerio Raw sequence reads	PRJNA293106	Metagenomics	Zebrafish Hypoxia RNAseq		RNAseq at 24hpf following hypoxia		24hpf hypoxia		strain:TU\|age:24hpf\|sex:not determined\|tissue:brain\|treatment:hypoxia\|BioSampleModel:Model organism or animal	Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample 24hpf hypoxia	24hpf.hypoxia.2.10329X11	24hpf.hypoxia.2.10329X11	We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition. For hypoxia we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected. We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages. At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation. RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer. The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides single end stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.			RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	Illumina HiSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</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>	SRP062493			10329X11_130822_SN141_0719_AD2CK5ACXX_5.txt.gz	fastq	1227682750.0	24553655.0	24hpf.hypoxia.2.10329X11	0:50	A:299759613;C:292757497;G:281904026;T:353193075;N:68539	50		299759613	292757497	281904026	353193075	68539	SRX1321831	SRS1109642	SRA289450	University of Utah\|Bonkowsky	University of Utah	1	0.94855		0.27579		0.73298		0.58307		50		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	trueseq	bulk	unknown	unknown	United States	2015-10-07	Pharyngula	Embryo	Brain	Nervous System
39830	39830	SRR2433795	SRX1321830	SRS1109644	SRP062493	PRJNA293106	Danio rerio Raw sequence reads	PRJNA293106	Metagenomics	Zebrafish Hypoxia RNAseq		RNAseq at 60hpf following normoxia		60hpf Normoxia		strain:TU\|age:60hpf\|sex:not determined\|tissue:brain\|treatment:normoxia\|BioSampleModel:Model organism or animal	Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample 60hpf Normoxia	60hpf.normoxia.3.	60hpf.normoxia.3.	We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition. For hypoxia we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected. We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages. At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation. RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer. The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides single end stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.			RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	Illumina HiSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</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>	SRP062493			10329X8_130822_SN141_0719_AD2CK5ACXX_5.txt.gz	fastq	1112799950.0	22255999.0	60hpf.normoxia.3.	0:50	A:294304558;C:248234752;G:238088577;T:332109252;N:62811	50		294304558	248234752	238088577	332109252	62811	SRX1321830	SRS1109644	SRA289450	University of Utah\|Bonkowsky	University of Utah	1	0.94922		0.34314		0.67838		0.51455		50		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	trueseq	bulk	unknown	unknown	United States	2015-10-10	Hatching	Embryo	Brain	Nervous System
39831	39831	SRR2426760	SRX1321829	SRS1109645	SRP062493	PRJNA293106	Danio rerio Raw sequence reads	PRJNA293106	Metagenomics	Zebrafish Hypoxia RNAseq		RNAseq at 36hpf following hypoxia		36hpf hypoxia		strain:TU\|age:36hpf\|sex:not determined\|tissue:brain\|treatment:hypoxia\|BioSampleModel:Model organism or animal	Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample 36hpf hypoxia	36hpf.hypoxia.1.10329X4	36hpf.hypoxia.1.10329X4	We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition. For hypoxia we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected. We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages. At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation. RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer. The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides single end stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.			RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	Illumina HiSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</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>	SRP062493			10329X4_130822_SN141_0719_AD2CK5ACXX_4.txt.gz	fastq	1604107450.0	32082149.0	36hpf.hypoxia.1.10329X4	0:50	A:395786409;C:358263833;G:358391489;T:491601452;N:64267	50		395786409	358263833	358391489	491601452	64267	SRX1321829	SRS1109645	SRA289450	University of Utah\|Bonkowsky	University of Utah	1	0.95408		0.28965		0.69593		0.54826		50		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	trueseq	bulk	unknown	unknown	United States	2015-10-10	Pharyngula	Embryo	Brain	Nervous System
39832	39832	SRR2417497	SRX1321828	SRS1109646	SRP062493	PRJNA293106	Danio rerio Raw sequence reads	PRJNA293106	Metagenomics	Zebrafish Hypoxia RNAseq		RNAseq at 48hpf following hypoxia		48hpf hypoxia		strain:TU\|age:48hpf\|sex:not determined\|tissue:brain\|treatment:hypoxia\|BioSampleModel:Model organism or animal	Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample 48hpf hypoxia	48hpf.hypoxia.3.10329X25	48hpf.hypoxia.3.10329X25	We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition. For hypoxia we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected. We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages. At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation. RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer. The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides single end stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.			RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	Illumina HiSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</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>	SRP062493			10329X25_130822_SN141_0719_AD2CK5ACXX_8.txt.gz	fastq	1234710500.0	24694210.0	48hpf.hypoxia.3.10329X25	0:50	A:309392529;C:284311489;G:275471070;T:365515358;N:20054	50		309392529	284311489	275471070	365515358	20054	SRX1321828	SRS1109646	SRA289450	University of Utah\|Bonkowsky	University of Utah	1	0.94675		0.25877		0.71453		0.5239		50		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	trueseq	bulk	unknown	unknown	United States	2015-09-16	Hatching	Embryo	Brain	Nervous System
39833	39833	SRR2417496	SRX1321827	SRS1109644	SRP062493	PRJNA293106	Danio rerio Raw sequence reads	PRJNA293106	Metagenomics	Zebrafish Hypoxia RNAseq		RNAseq at 60hpf following normoxia		60hpf Normoxia		strain:TU\|age:60hpf\|sex:not determined\|tissue:brain\|treatment:normoxia\|BioSampleModel:Model organism or animal	Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample 60hpf Normoxia	60hpf.normoxia.2.10329X28	60hpf.normoxia.2.10329X28	We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition. For hypoxia we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected. We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages. At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation. RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer. The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides single end stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.			RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	Illumina HiSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</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>	SRP062493			10329X28_130822_SN141_0719_AD2CK5ACXX_8.txt.gz	fastq	1015786750.0	20315735.0	60hpf.normoxia.2.10329X28	0:50	A:259102784;C:230364456;G:226008843;T:300294199;N:16468	50		259102784	230364456	226008843	300294199	16468	SRX1321827	SRS1109644	SRA289450	University of Utah\|Bonkowsky	University of Utah	1	0.95197		0.30503		0.68333		0.52243		50		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	trueseq	bulk	unknown	unknown	United States	2015-09-16	Hatching	Embryo	Brain	Nervous System
39834	39834	SRR2400601	SRX1321826	SRS1109642	SRP062493	PRJNA293106	Danio rerio Raw sequence reads	PRJNA293106	Metagenomics	Zebrafish Hypoxia RNAseq		RNAseq at 24hpf following hypoxia		24hpf hypoxia		strain:TU\|age:24hpf\|sex:not determined\|tissue:brain\|treatment:hypoxia\|BioSampleModel:Model organism or animal	Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample 24hpf hypoxia	24hpf.hypoxia.1.10329X2	24hpf.hypoxia.1.10329X2	We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition. For hypoxia we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected. We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages. At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation. RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer. The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides single end stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.			RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	Illumina HiSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</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>	SRP062493			10329X2_130822_SN141_0719_AD2CK5ACXX_4.txt.gz	fastq	1249046350.0	24980927.0	24hpf.hypoxia.1.10329X2	0:50	A:309098695;C:281875016;G:278706888;T:379315616;N:50135	50		309098695	281875016	278706888	379315616	50135	SRX1321826	SRS1109642	SRA289450	University of Utah\|Bonkowsky	University of Utah	1	0.95443		0.27405		0.69747		0.40987		50		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	trueseq	bulk	unknown	unknown	United States	2015-10-10	Pharyngula	Embryo	Brain	Nervous System
39837	39837	SRR2342161	SRX1321823	SRS1109648	SRP062493	PRJNA293106	Danio rerio Raw sequence reads	PRJNA293106	Metagenomics	Zebrafish Hypoxia RNAseq		RNAseq at 60hpf following hypoxia		60hpf hypoxia		strain:TU\|age:60hpf\|sex:not determined\|tissue:brain\|treatment:hypoxia\|BioSampleModel:Model organism or animal	Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample 60hpf hypoxia	60hpf.hypoxia.3.10329X27	60hpf.hypoxia.3.10329X27	We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition. For hypoxia we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected. We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages. At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation. RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer. The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides single end stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.			RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	Illumina HiSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</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>	SRP062493			10329X27_130822_SN141_0719_AD2CK5ACXX_8.txt.gz	fastq	1073269500.0	21465390.0	60hpf.hypoxia.3.10329X27	0:50	A:280500644;C:237758835;G:234061287;T:320931292;N:17442	50		280500644	237758835	234061287	320931292	17442	SRX1321823	SRS1109648	SRA289450	University of Utah\|Bonkowsky	University of Utah	1	0.94774		0.36354		0.70065		0.51075		50		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	trueseq	bulk	unknown	unknown	United States	2015-10-10	Hatching	Embryo	Brain	Nervous System
39838	39838	SRR2341509	SRX1321822	SRS1109643	SRP062493	PRJNA293106	Danio rerio Raw sequence reads	PRJNA293106	Metagenomics	Zebrafish Hypoxia RNAseq		RNAseq at 48hpf following normoxia		48hpf normoxia		strain:TU\|age:48hpf\|sex:not determined\|tissue:brain\|treatment:normoxia\|BioSampleModel:Model organism or animal	Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample 48hpf normoxia	48hpf.normoxia.210329X26	48hpf.normoxia.210329X26	We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition. For hypoxia we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected. We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages. At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation. RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer. The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides single end stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.			RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	Illumina HiSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</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>	SRP062493			10329X26_130822_SN141_0719_AD2CK5ACXX_8.txt.gz	fastq	1075868850.0	21517377.0	48hpf.normoxia.210329X26	0:50	A:271795722;C:246789566;G:240496674;T:316769688;N:17200	50		271795722	246789566	240496674	316769688	17200	SRX1321822	SRS1109643	SRA289450	University of Utah\|Bonkowsky	University of Utah	1	0.94644		0.26805		0.68745		0.53833		50		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	trueseq	bulk	unknown	unknown	United States	2015-10-10	Hatching	Embryo	Brain	Nervous System
39839	39839	SRR2340149	SRX1321821	SRS1109650	SRP062493	PRJNA293106	Danio rerio Raw sequence reads	PRJNA293106	Metagenomics	Zebrafish Hypoxia RNAseq		RNAseq at 36hpf following normoxia		36hpf normoxia		strain:TU\|age:36hpf\|sex:not determined\|tissue:brain\|treatment:normoxia\|BioSampleModel:Model organism or animal	Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample 36hpf normoxia	36hpf.normoxia.3.10329X24	36hpf.normoxia.3.10329X24	We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition. For hypoxia we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected. We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages. At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation. RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer. The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides single end stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.			RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	Illumina HiSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</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>	SRP062493			10329X24_130822_SN141_0719_AD2CK5ACXX_7.txt.gz	fastq	1588630750.0	31772615.0	36hpf.normoxia.3.10329X24	0:50	A:404319446;C:349459823;G:346545846;T:468209953;N:20095682	50		404319446	349459823	346545846	468209953	20095682	SRX1321821	SRS1109650	SRA289450	University of Utah\|Bonkowsky	University of Utah	1	0.8739		0.32489		0.71701		0.51646		50		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	trueseq	bulk	unknown	unknown	United States	2015-10-10	Pharyngula	Embryo	Brain	Nervous System
39840	39840	SRR2245887	SRX1321820	SRS1109645	SRP062493	PRJNA293106	Danio rerio Raw sequence reads	PRJNA293106	Metagenomics	Zebrafish Hypoxia RNAseq		RNAseq at 36hpf following hypoxia		36hpf hypoxia		strain:TU\|age:36hpf\|sex:not determined\|tissue:brain\|treatment:hypoxia\|BioSampleModel:Model organism or animal	Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample 36hpf hypoxia	36hpf.hypoxia.3.10329X23	36hpf.hypoxia.3.10329X23	We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition. For hypoxia we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected. We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages. At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation. RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer. The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides single end stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.			RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	Illumina HiSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</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>	SRP062493			10329X23_130822_SN141_0719_AD2CK5ACXX_7.txt.gz	fastq	1207331350.0	24146627.0	36hpf.hypoxia.3.10329X23	0:50	A:305628501;C:266059461;G:259888045;T:360487730;N:15267613	50		305628501	266059461	259888045	360487730	15267613	SRX1321820	SRS1109645	SRA289450	University of Utah\|Bonkowsky	University of Utah	1	0.87814		0.27249		0.72853		0.53527		50		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	trueseq	bulk	unknown	unknown	United States	2015-10-10	Pharyngula	Embryo	Brain	Nervous System
39841	39841	SRR2245257	SRX1321819	SRS1109651	SRP062493	PRJNA293106	Danio rerio Raw sequence reads	PRJNA293106	Metagenomics	Zebrafish Hypoxia RNAseq		RNAseq at 24hpf following normoxia		24hpf normoxia		strain:TU\|age:24hpf\|sex:not determined\|tissue:brain\|treatment:normoxia\|BioSampleModel:Model organism or animal	Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample 24hpf normoxia	24hpf.normoxia.3.10329X22	24hpf.normoxia.3.10329X22	We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition. For hypoxia we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected. We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages. At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation. RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer. The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides single end stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.			RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	Illumina HiSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</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>	SRP062493			10329X22_130822_SN141_0719_AD2CK5ACXX_7.txt.gz	fastq	1257159050.0	25143181.0	24hpf.normoxia.3.10329X22	0:50	A:320558638;C:275312235;G:271710647;T:373637690;N:15939840	50		320558638	275312235	271710647	373637690	15939840	SRX1321819	SRS1109651	SRA289450	University of Utah\|Bonkowsky	University of Utah	1	0.87634		0.30298		0.71356		0.54673		50		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	trueseq	bulk	unknown	unknown	United States	2015-10-10	Pharyngula	Embryo	Brain	Nervous System
39844	39844	SRR2241311	SRX1321816	SRS1109644	SRP062493	PRJNA293106	Danio rerio Raw sequence reads	PRJNA293106	Metagenomics	Zebrafish Hypoxia RNAseq		RNAseq at 60hpf following normoxia		60hpf Normoxia		strain:TU\|age:60hpf\|sex:not determined\|tissue:brain\|treatment:normoxia\|BioSampleModel:Model organism or animal	Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample 60hpf Normoxia	60hpf.normoxia.1.10329X18	60hpf.normoxia.1.10329X18	We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition. For hypoxia we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected. We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages. At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation. RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer. The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides single end stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.			RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	Illumina HiSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</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>	SRP062493			10329X18_130822_SN141_0719_AD2CK5ACXX_6.txt.gz	fastq	1118115050.0	22362301.0	60hpf.normoxia.1.10329X18	0:50	A:287072563;C:255244675;G:248573701;T:327203388;N:20723	50		287072563	255244675	248573701	327203388	20723	SRX1321816	SRS1109644	SRA289450	University of Utah\|Bonkowsky	University of Utah	1	0.93238		0.30064		0.68574		0.51934		50		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	trueseq	bulk	unknown	unknown	United States	2015-10-10	Hatching	Embryo	Brain	Nervous System
39845	39845	SRR2240748	SRX1321815	SRS1109648	SRP062493	PRJNA293106	Danio rerio Raw sequence reads	PRJNA293106	Metagenomics	Zebrafish Hypoxia RNAseq		RNAseq at 60hpf following hypoxia		60hpf hypoxia		strain:TU\|age:60hpf\|sex:not determined\|tissue:brain\|treatment:hypoxia\|BioSampleModel:Model organism or animal	Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample 60hpf hypoxia	60hpf.hypoxia.2.10329X17	60hpf.hypoxia.2.10329X17	We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition. For hypoxia we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected. We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages. At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation. RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer. The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides single end stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.			RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	Illumina HiSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</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>	SRP062493			10329X17_130822_SN141_0719_AD2CK5ACXX_6.txt.gz	fastq	1074686900.0	21493738.0	60hpf.hypoxia.2.10329X17	0:50	A:276432361;C:244039609;G:234638386;T:319556004;N:20540	50		276432361	244039609	234638386	319556004	20540	SRX1321815	SRS1109648	SRA289450	University of Utah\|Bonkowsky	University of Utah	1	0.9502		0.3077		0.6899		0.50645		50		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	trueseq	bulk	unknown	unknown	United States	2015-09-03	Hatching	Embryo	Brain	Nervous System
39846	39846	SRR2239869	SRX1321814	SRS1109646	SRP062493	PRJNA293106	Danio rerio Raw sequence reads	PRJNA293106	Metagenomics	Zebrafish Hypoxia RNAseq		RNAseq at 48hpf following hypoxia		48hpf hypoxia		strain:TU\|age:48hpf\|sex:not determined\|tissue:brain\|treatment:hypoxia\|BioSampleModel:Model organism or animal	Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample 48hpf hypoxia	48hpf.hypoxia.2.10329X15	48hpf.hypoxia.2.10329X15	We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition. For hypoxia we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected. We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages. At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation. RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer. The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides single end stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.			RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	Illumina HiSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</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>	SRP062493			10329X15_130822_SN141_0719_AD2CK5ACXX_6.txt.gz	fastq	1111913550.0	22238271.0	48hpf.hypoxia.2.10329X15	0:50	A:288023952;C:248947169;G:243195362;T:331723738;N:23329	50		288023952	248947169	243195362	331723738	23329	SRX1321814	SRS1109646	SRA289450	University of Utah\|Bonkowsky	University of Utah	1	0.93753		0.34521		0.70246		0.51535		50		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	trueseq	bulk	unknown	unknown	United States	2015-10-10	Hatching	Embryo	Brain	Nervous System
39847	39847	SRR2239772	SRX1321813	SRS1109650	SRP062493	PRJNA293106	Danio rerio Raw sequence reads	PRJNA293106	Metagenomics	Zebrafish Hypoxia RNAseq		RNAseq at 36hpf following normoxia		36hpf normoxia		strain:TU\|age:36hpf\|sex:not determined\|tissue:brain\|treatment:normoxia\|BioSampleModel:Model organism or animal	Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample 36hpf normoxia	36hpf.normoxia.2.10329X14	36hpf.normoxia.2.10329X14	We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition. For hypoxia we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected. We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages. At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation. RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer. The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides single end stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.			RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	Illumina HiSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</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>	SRP062493			10329X14_130822_SN141_0719_AD2CK5ACXX_6.txt.gz	fastq	1533885200.0	30677704.0	36hpf.normoxia.2.10329X14	0:50	A:392813056;C:354469675;G:348871622;T:437692730;N:38117	50		392813056	354469675	348871622	437692730	38117	SRX1321813	SRS1109650	SRA289450	University of Utah\|Bonkowsky	University of Utah	1	0.91439		0.31812		0.70863		0.51667		50		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	trueseq	bulk	unknown	unknown	United States	2015-10-10	Pharyngula	Embryo	Brain	Nervous System
39848	39848	SRR2232685	SRX1321812	SRS1109645	SRP062493	PRJNA293106	Danio rerio Raw sequence reads	PRJNA293106	Metagenomics	Zebrafish Hypoxia RNAseq		RNAseq at 36hpf following hypoxia		36hpf hypoxia		strain:TU\|age:36hpf\|sex:not determined\|tissue:brain\|treatment:hypoxia\|BioSampleModel:Model organism or animal	Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample 36hpf hypoxia	36hpf.hypoxia.2.10329X13	36hpf.hypoxia.2.10329X13	We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition. For hypoxia we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected. We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages. At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation. RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer. The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides single end stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.			RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	Illumina HiSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</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>	SRP062493			10329X13_130822_SN141_0719_AD2CK5ACXX_6.txt.gz	fastq	1112846200.0	22256924.0	36hpf.hypoxia.2.10329X13	0:50	A:279147206;C:259582122;G:249642505;T:324452965;N:21402	50		279147206	259582122	249642505	324452965	21402	SRX1321812	SRS1109645	SRA289450	University of Utah\|Bonkowsky	University of Utah	1	0.94469		0.25952		0.72243		0.52701		50		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	trueseq	bulk	unknown	unknown	United States	2015-10-10	Pharyngula	Embryo	Brain	Nervous System
39849	39849	SRR2227658	SRX1321811	SRS1109651	SRP062493	PRJNA293106	Danio rerio Raw sequence reads	PRJNA293106	Metagenomics	Zebrafish Hypoxia RNAseq		RNAseq at 24hpf following normoxia		24hpf normoxia		strain:TU\|age:24hpf\|sex:not determined\|tissue:brain\|treatment:normoxia\|BioSampleModel:Model organism or animal	Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample 24hpf normoxia	24hpf.normoxia.2.10329X12	24hpf.normoxia.2.10329X12	We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition. For hypoxia we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected. We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages. At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation. RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer. The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides single end stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.			RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	Illumina HiSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</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>	SRP062493			10329X12_130822_SN141_0719_AD2CK5ACXX_5.txt.gz	fastq	1243623750.0	24872475.0	24hpf.normoxia.2.10329X12	0:50	A:317179221;C:285081899;G:274648790;T:366643275;N:70565	50		317179221	285081899	274648790	366643275	70565	SRX1321811	SRS1109651	SRA289450	University of Utah\|Bonkowsky	University of Utah	1	0.95045		0.27525		0.69688		0.53555		50		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	trueseq	bulk	unknown	unknown	United States	2015-09-01	Pharyngula	Embryo	Brain	Nervous System
39852	39852	SRR2225888	SRX1321808	SRS1109648	SRP062493	PRJNA293106	Danio rerio Raw sequence reads	PRJNA293106	Metagenomics	Zebrafish Hypoxia RNAseq		RNAseq at 60hpf following hypoxia		60hpf hypoxia		strain:TU\|age:60hpf\|sex:not determined\|tissue:brain\|treatment:hypoxia\|BioSampleModel:Model organism or animal	Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample 60hpf hypoxia	60hpf.hypoxia.1.10329X7	60hpf.hypoxia.1.10329X7	We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition. For hypoxia we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected. We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages. At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation. RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer. The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides single end stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.			RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	Illumina HiSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</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>	SRP062493			10329X7_130822_SN141_0719_AD2CK5ACXX_5.txt.gz	fastq	1102232350.0	22044647.0	60hpf.hypoxia.1.10329X7	0:50	A:288570352;C:247978180;G:238128703;T:327492563;N:62552	50		288570352	247978180	238128703	327492563	62552	SRX1321808	SRS1109648	SRA289450	University of Utah\|Bonkowsky	University of Utah	1	0.94824		0.31808		0.69244		0.51505		50		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	trueseq	bulk	unknown	unknown	United States	2015-10-10	Hatching	Embryo	Brain	Nervous System
39853	39853	SRR2225789	SRX1321807	SRS1109646	SRP062493	PRJNA293106	Danio rerio Raw sequence reads	PRJNA293106	Metagenomics	Zebrafish Hypoxia RNAseq		RNAseq at 48hpf following hypoxia		48hpf hypoxia		strain:TU\|age:48hpf\|sex:not determined\|tissue:brain\|treatment:hypoxia\|BioSampleModel:Model organism or animal	Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample 48hpf hypoxia	48hpf.hypoxia.1.10329X6	48hpf.hypoxia.1.10329X6	We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition. For hypoxia we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected. We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages. At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation. RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer. The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides single end stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.			RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	Illumina HiSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</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>	SRP062493			10329X6_130822_SN141_0719_AD2CK5ACXX_4.txt.gz	fastq	1250042950.0	25000859.0	48hpf.hypoxia.1.10329X6	0:50	A:312511165;C:283310381;G:277279378;T:376891744;N:50282	50		312511165	283310381	277279378	376891744	50282	SRX1321807	SRS1109646	SRA289450	University of Utah\|Bonkowsky	University of Utah	1	0.94959		0.28331		0.68757		0.53976		50		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	trueseq	bulk	unknown	unknown	United States	2015-09-01	Hatching	Embryo	Brain	Nervous System
39854	39854	SRR2225675	SRX1321806	SRS1109650	SRP062493	PRJNA293106	Danio rerio Raw sequence reads	PRJNA293106	Metagenomics	Zebrafish Hypoxia RNAseq		RNAseq at 36hpf following normoxia		36hpf normoxia		strain:TU\|age:36hpf\|sex:not determined\|tissue:brain\|treatment:normoxia\|BioSampleModel:Model organism or animal	Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample 36hpf normoxia	36hpf.normoxia.1.10329X5	36hpf.normoxia.1.10329X5	We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition. For hypoxia we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected. We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages. At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation. RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer. The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides single end stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.			RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	Illumina HiSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</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>	SRP062493			10329X5_130822_SN141_0719_AD2CK5ACXX_4.txt.gz	fastq	1244744700.0	24894894.0	36hpf.normoxia.1.10329X5	0:50	A:301597123;C:287750990;G:281194881;T:374152417;N:49289	50		301597123	287750990	281194881	374152417	49289	SRX1321806	SRS1109650	SRA289450	University of Utah\|Bonkowsky	University of Utah	1	0.95571		0.22791		0.71177		0.53801		50		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	trueseq	bulk	unknown	unknown	United States	2015-10-10	Pharyngula	Embryo	Brain	Nervous System
39855	39855	SRR2225572	SRX1321805	SRS1109651	SRP062493	PRJNA293106	Danio rerio Raw sequence reads	PRJNA293106	Metagenomics	Zebrafish Hypoxia RNAseq		RNAseq at 24hpf following normoxia		24hpf normoxia		strain:TU\|age:24hpf\|sex:not determined\|tissue:brain\|treatment:normoxia\|BioSampleModel:Model organism or animal	Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample 24hpf normoxia	24hpf.normoxia.1.10329X3	24hpf.normoxia.1.10329X3	We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition. For hypoxia we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected. We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages. At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation. RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer. The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides single end stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.			RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	Illumina HiSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</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>	SRP062493			10329X3_130822_SN141_0719_AD2CK5ACXX_4.txt.gz	fastq	1293605500.0	25872110.0	24hpf.normoxia.1.10329X3	0:50	A:310265067;C:296406990;G:295054246;T:391826687;N:52510	50		310265067	296406990	295054246	391826687	52510	SRX1321805	SRS1109651	SRA289450	University of Utah\|Bonkowsky	University of Utah	1	0.95596		0.21907		0.71512		0.39029		50		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	trueseq	bulk	unknown	unknown	United States	2015-09-01	Pharyngula	Embryo	Brain	Nervous System
39856	39856	SRR2222835	SRX1321804	SRS1109643	SRP062493	PRJNA293106	Danio rerio Raw sequence reads	PRJNA293106	Metagenomics	Zebrafish Hypoxia RNAseq		RNAseq at 48hpf following normoxia		48hpf normoxia		strain:TU\|age:48hpf\|sex:not determined\|tissue:brain\|treatment:normoxia\|BioSampleModel:Model organism or animal	Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample 48hpf normoxia	48hpf.1.10329X1	48hpf.1.10329X1	We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition. For hypoxia we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected. We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages. At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation. RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer. The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides single end stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.			RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	Illumina HiSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</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>	SRP062493			10329X1_130822_SN141_0719_AD2CK5ACXX_4.txt.gz	fastq	1215136450.0	24302729.0	48hpf.1.10329X1	0:50	A:291802893;C:276442849;G:277217342;T:369624915;N:48451	50		291802893	276442849	277217342	369624915	48451	SRX1321804	SRS1109643	SRA289450	University of Utah\|Bonkowsky	University of Utah	1	0.95575		0.23021		0.72679		0.60296		50		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	trueseq	bulk	unknown	unknown	United States	2015-09-01	Hatching	Embryo	Brain	Nervous System
42097	42097	SRR5483549	SRX2766898	SRS2151000	SRP105338	PRJNA381309	Danio rerio strain:AB Raw sequence reads	PRJNA381309	Whole Genome Sequencing	RNA seq data from control and MCT8 morphant zebrafish embryos at 25hpf			C1 CGATGT L001 R1 001	C1		strain:AB\|dev stage:25hpf\|sex:not applicable\|tissue:Whole embryo\|death date:25 hpf type:ReplicateC1L1R1\|treatment:CTR morpholino\|BioSampleModel:Model organism or animal	Pair end L1R1	C1 CGATGT L001	C1 CGATGT L001	Total RNA was extrated from pools of 50 embryos using EZNA total RNA extraction kit I and Dnased with Ambion turbo Dnase kit.Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries following Illumina's standard procedures			RNA-Seq	TRANSCRIPTOMIC	RANDOM	PAIRED	ILLUMINA	Illumina HiSeq 1000		SRP105338		loader:fastq load.py	C1_CGATGT_L001_R1_001.fastq C1_CGATGT_L001_R2_001.fastq C1_CGATGT_L002_R1_001.fastq C1_CGATGT_L002_R2_001.fastq	fastq fastq fastq fastq	1411679200.0	14356543.0	C1 CGATGT L001 R2 001.fastq		A:371472311;C:327400140;G:335224751;T:377147836;N:434162			371472311	327400140	335224751	377147836	434162	SRX2766898	SRS2151000	SRA557338	Centro Ciencias do Mar\|Comparative Endocrinology and Integrative Biology	Centro Ciencias do Mar	2	0.93533	0.94243	0.07183	0.07215	0.72111	0.72251	0.46894	0.47065	50	50	B	B	biological fallback assumption	illumina	hiseq_era	unknown	random_priming	trueseq	bulk	unknown	unknown	Portugal	2017-09-19	Pharyngula	Embryo	Whole Organism	All anatomical structures

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;