{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where devstage_curation_coarse = \"Embryo\" and tissue_curation = \"Brain\"", "rows": [[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. 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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", null, "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", null, null, null, null, null, null, null, null, "Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17\u03b1 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 17\u03b1 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", null, "ERP018188", "Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17\u00ce\u00b1 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, null, null, null, 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, null, 0.31904, null, 0.74905, null, 0.47154, null, 122, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "full_length", "random_priming", "ribozero", "bulk", "unknown", "unknown", null, "Sweden", "2016-10-19", "Pharyngula", "Embryo", "Brain", "Nervous System"], [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", null, "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", null, null, null, null, null, null, null, null, "Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17\u03b1 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 17\u03b1 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", null, "ERP018188", "Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17\u00ce\u00b1 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, null, null, null, 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, null, 0.25542, null, 0.76481, null, 0.4886, null, 12, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "full_length", "random_priming", "ribozero", "bulk", "unknown", "unknown", null, "Sweden", "2016-10-19", "Pharyngula", "Embryo", "Brain", "Nervous System"], [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", null, "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", null, null, null, null, null, null, null, null, "Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17\u03b1 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 17\u03b1 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", null, "ERP018188", "Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17\u00ce\u00b1 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, null, null, null, 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, null, 0.32503, null, 0.74241, null, 0.4815, null, 128, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "full_length", "random_priming", "ribozero", "bulk", "unknown", "unknown", null, "Sweden", "2016-10-19", "Pharyngula", "Embryo", "Brain", "Nervous System"], [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", null, "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", null, null, null, null, null, null, null, null, "Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17\u03b1 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 17\u03b1 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", null, "ERP018188", "Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17\u00ce\u00b1 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, null, null, null, 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, null, 0.22334, null, 0.76353, null, 0.49163, null, 93, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "full_length", "random_priming", "ribozero", "bulk", "unknown", "unknown", null, "Sweden", "2016-10-19", "Pharyngula", "Embryo", "Brain", "Nervous System"], [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", null, "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", null, null, null, null, null, null, null, null, "Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17\u03b1 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 17\u03b1 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", null, "ERP018188", "Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17\u00ce\u00b1 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, null, null, null, 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, null, 0.18649, null, 0.81178, null, 0.52885, null, 116, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "full_length", "random_priming", "ribozero", "bulk", "unknown", "unknown", null, "Sweden", "2016-10-19", "Pharyngula", "Embryo", "Brain", "Nervous System"], [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", null, "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", null, null, null, null, null, null, null, null, "Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17\u03b1 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 17\u03b1 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", null, "ERP018188", "Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17\u00ce\u00b1 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, null, null, null, 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, null, 0.33159, null, 0.76619, null, 0.514, null, 56, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "full_length", "random_priming", "ribozero", "bulk", "unknown", "unknown", null, "Sweden", "2016-10-19", "Pharyngula", "Embryo", "Brain", "Nervous System"], [28692, "SRR26535343", "SRX22238470", "SRS19292731", "SRP468564", "PRJNA1032461", "A syngeneic spontaneous zebrafish model oftp53 deficient EGFRviii and PI3KCAH1047R driven glioblastoma reveals inhibitory roles for inflammation during tumor initiation and relapsein vivo", "GSE246295", "Transcriptome Analysis", "To build a patient relevantin vivomodel of human glioblastoma we expressed common oncogenic variants including activated human EGFRviii or KRAS and PI3KCAH1047Runder the control of the radial glial specific promoterher4.1in syngeneictp53loss of function mutant zebrafish.Robust tumor formation was observed prior to 45 days of life with a gene expression signature similar to human glioblastoma of the mesenchymal subtype along with a strong inflammatory component. Within early stage tumor lesions and in an intact and endogenous tumor microenvironment we visualized infiltration of phagocytic cells as well as internalization of tumor cells bympeg1.1:GFP+ microglia/macrophages suggesting negative regulatory pressure by pro inflammatory cell types on tumor growth at early stages of glioblastoma initiationin vivo. Furthermore CRISPR/Cas9 mediated gene targeting of master inflammatory transcription factorsirf7andirf8led to increased tumor formation in the primary context while suppression of microglial/macrophage activity led to enhanced tumor cell engraftment following transplantation into otherwise immune competent zebrafish hosts. Altogether we developed a genetically relevant model of aggressive human glioblastoma and harnessed the unique advantages of zebrafish including live imaging high throughput genetic and chemical manipulations to highlight important tumor suppressive roles for the innate immune system on glioblastoma initiation with important future significance for therapeutic discovery and optimizations. Overall design: To capture broad transcriptomic differences in tumor burdened brains versus normal brains we performed bulk RNA sequencing and gene expression analysis of whole brains and sorted cells. EGFRviii derived tumors were induced by microinjection of EGFRviii PI3KCAH1047R and mScarlet constructs defined as EPS. KRAS derived tumors were induced by microinjection of KRAS PI3KCAH1047R GFP constructs defined as KPG. Three whole brains positive for fluorescent tumors EPS 1 3 KPG 1 3 alongside three control brains from injected siblings who did not develop tumors CTRL 1 3 were dissected for each condition for bulk RNA sequencing. We also performed fluorescent activated cell sorting on pooled dissociated brains from the EPS condition resulting in enrichment for mScarlet postive tumor cells CS Pos and mScarlet negative cells CS Neg for comparative analysis.", null, "pubmed:39052000", null, "EGFRviii PI3KCAH1047R mScarlet tumor negative control brain 2", "GSM7866394", null, "source name:Whole Brain|strain:CG1 p53null|tissue:Whole Brain|geo loc name:missing|collection date:missing", "EGFRviii PI3KCAH1047R mScarlet tumor negative control brain 2", "Raw .fastq data was processed using Salmon quantification of transcripts for each sample. A \u201cdecoy aware\u201d index was built with the Danio rerio transcriptome and genome using the GRCz11 assembly with a k mers length of 23 with entries manually added for GFP mScarlet EGFRviii KRAS and PI3KCAH1047R transcripts. Samples were then quantified with the following arguments: r seqBias mp 3 validateMappings rangeFactorizationBins 4. Differential gene expression was compared utilizing DESeq2 and GSEA. Assembly: GRCz11 Supplementary files format and content: Tab delimited .csv file including raw counts for all conditions.", "Whole Brain", "Fertilized embryos injected with either EPS or KPG construct mix", "Dissected brains or sorted cells were immediately put into Trizol. RNA was then extracted and purified utilizing Monarch RNA Cleanup Kit following manufacturer's recommendations Sequence ready polyA enriched libraries were prepared using the NEB Ultra II Directional mRNA prep kit for Illumina according to manufacturer\u2019s recommendations", "Zebrafish were housed and reared following approved animal use protocol", "strain:CG1 p53null|tissue:Whole Brain", "GSM7866394", "GSM7866394: EGFRviii PI3KCAH1047R mScarlet tumor negative control brain 2; Danio rerio; RNA Seq", "GSM7866394 r1", "GSM7866394", "1", "Dissected brains or sorted cells were immediately put into Trizol. RNA was then extracted and purified utilizing Monarch RNA Cleanup Kit following manufacturer's recommendations Sequence ready polyA enriched libraries were prepared using the NEB Ultra II Directional mRNA prep kit for Illumina according to manufacturer's recommendations", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP468564", null, "loader:fastq load.py", "CTRL_3.fastq.gz", "fastq", 7081948098.0, 70118298.0, "GSM7866394 r1", "0:101", "A:1894557984;C:1627945034;G:1550203852;T:2009224463;N:16765", 101, null, null, null, 1894557984, 1627945034, 1550203852, 2009224463, 16765, "SRX22238470", "SRS19292731", "SRA1740017", "Hayes Lab, DSCB, Sickkids Research", "Hayes Lab, DSCB, Sickkids Research", 1, 0.94543, null, 0.14646, null, 0.68883, null, 0.49451, null, 101, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "Canada", "2023-10-26", "Undetermined", "Embryo", "Brain", "Nervous System"], [28693, "SRR26535344", "SRX22238469", "SRS19292730", "SRP468564", "PRJNA1032461", "A syngeneic spontaneous zebrafish model oftp53 deficient EGFRviii and PI3KCAH1047R driven glioblastoma reveals inhibitory roles for inflammation during tumor initiation and relapsein vivo", "GSE246295", "Transcriptome Analysis", "To build a patient relevantin vivomodel of human glioblastoma we expressed common oncogenic variants including activated human EGFRviii or KRAS and PI3KCAH1047Runder the control of the radial glial specific promoterher4.1in syngeneictp53loss of function mutant zebrafish.Robust tumor formation was observed prior to 45 days of life with a gene expression signature similar to human glioblastoma of the mesenchymal subtype along with a strong inflammatory component. Within early stage tumor lesions and in an intact and endogenous tumor microenvironment we visualized infiltration of phagocytic cells as well as internalization of tumor cells bympeg1.1:GFP+ microglia/macrophages suggesting negative regulatory pressure by pro inflammatory cell types on tumor growth at early stages of glioblastoma initiationin vivo. Furthermore CRISPR/Cas9 mediated gene targeting of master inflammatory transcription factorsirf7andirf8led to increased tumor formation in the primary context while suppression of microglial/macrophage activity led to enhanced tumor cell engraftment following transplantation into otherwise immune competent zebrafish hosts. Altogether we developed a genetically relevant model of aggressive human glioblastoma and harnessed the unique advantages of zebrafish including live imaging high throughput genetic and chemical manipulations to highlight important tumor suppressive roles for the innate immune system on glioblastoma initiation with important future significance for therapeutic discovery and optimizations. Overall design: To capture broad transcriptomic differences in tumor burdened brains versus normal brains we performed bulk RNA sequencing and gene expression analysis of whole brains and sorted cells. EGFRviii derived tumors were induced by microinjection of EGFRviii PI3KCAH1047R and mScarlet constructs defined as EPS. KRAS derived tumors were induced by microinjection of KRAS PI3KCAH1047R GFP constructs defined as KPG. Three whole brains positive for fluorescent tumors EPS 1 3 KPG 1 3 alongside three control brains from injected siblings who did not develop tumors CTRL 1 3 were dissected for each condition for bulk RNA sequencing. We also performed fluorescent activated cell sorting on pooled dissociated brains from the EPS condition resulting in enrichment for mScarlet postive tumor cells CS Pos and mScarlet negative cells CS Neg for comparative analysis.", null, "pubmed:39052000", null, "EGFRviii PI3KCAH1047R mScarlet tumor negative control brain 1", "GSM7866393", null, "source name:Whole Brain|strain:CG1 p53null|tissue:Whole Brain|geo loc name:missing|collection date:missing", "EGFRviii PI3KCAH1047R mScarlet tumor negative control brain 1", "Raw .fastq data was processed using Salmon quantification of transcripts for each sample. A \u201cdecoy aware\u201d index was built with the Danio rerio transcriptome and genome using the GRCz11 assembly with a k mers length of 23 with entries manually added for GFP mScarlet EGFRviii KRAS and PI3KCAH1047R transcripts. Samples were then quantified with the following arguments: r seqBias mp 3 validateMappings rangeFactorizationBins 4. Differential gene expression was compared utilizing DESeq2 and GSEA. Assembly: GRCz11 Supplementary files format and content: Tab delimited .csv file including raw counts for all conditions.", "Whole Brain", "Fertilized embryos injected with either EPS or KPG construct mix", "Dissected brains or sorted cells were immediately put into Trizol. RNA was then extracted and purified utilizing Monarch RNA Cleanup Kit following manufacturer's recommendations Sequence ready polyA enriched libraries were prepared using the NEB Ultra II Directional mRNA prep kit for Illumina according to manufacturer\u2019s recommendations", "Zebrafish were housed and reared following approved animal use protocol", "strain:CG1 p53null|tissue:Whole Brain", "GSM7866393", "GSM7866393: EGFRviii PI3KCAH1047R mScarlet tumor negative control brain 1; Danio rerio; RNA Seq", "GSM7866393 r1", "GSM7866393", "1", "Dissected brains or sorted cells were immediately put into Trizol. RNA was then extracted and purified utilizing Monarch RNA Cleanup Kit following manufacturer's recommendations Sequence ready polyA enriched libraries were prepared using the NEB Ultra II Directional mRNA prep kit for Illumina according to manufacturer's recommendations", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP468564", null, "loader:fastq load.py", "CTRL_2.fastq.gz", "fastq", 7840572329.0, 77629429.0, "GSM7866393 r1", "0:101", "A:2099360211;C:1783653297;G:1717681461;T:2239858766;N:18594", 101, null, null, null, 2099360211, 1783653297, 1717681461, 2239858766, 18594, "SRX22238469", "SRS19292730", "SRA1740017", "Hayes Lab, DSCB, Sickkids Research", "Hayes Lab, DSCB, Sickkids Research", 1, 0.93984, null, 0.1663, null, 0.69033, null, 0.484, null, 101, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "Canada", "2023-10-26", "Undetermined", "Embryo", "Brain", "Nervous System"], [28694, "SRR26535345", "SRX22238468", "SRS19292729", "SRP468564", "PRJNA1032461", "A syngeneic spontaneous zebrafish model oftp53 deficient EGFRviii and PI3KCAH1047R driven glioblastoma reveals inhibitory roles for inflammation during tumor initiation and relapsein vivo", "GSE246295", "Transcriptome Analysis", "To build a patient relevantin vivomodel of human glioblastoma we expressed common oncogenic variants including activated human EGFRviii or KRAS and PI3KCAH1047Runder the control of the radial glial specific promoterher4.1in syngeneictp53loss of function mutant zebrafish.Robust tumor formation was observed prior to 45 days of life with a gene expression signature similar to human glioblastoma of the mesenchymal subtype along with a strong inflammatory component. Within early stage tumor lesions and in an intact and endogenous tumor microenvironment we visualized infiltration of phagocytic cells as well as internalization of tumor cells bympeg1.1:GFP+ microglia/macrophages suggesting negative regulatory pressure by pro inflammatory cell types on tumor growth at early stages of glioblastoma initiationin vivo. Furthermore CRISPR/Cas9 mediated gene targeting of master inflammatory transcription factorsirf7andirf8led to increased tumor formation in the primary context while suppression of microglial/macrophage activity led to enhanced tumor cell engraftment following transplantation into otherwise immune competent zebrafish hosts. Altogether we developed a genetically relevant model of aggressive human glioblastoma and harnessed the unique advantages of zebrafish including live imaging high throughput genetic and chemical manipulations to highlight important tumor suppressive roles for the innate immune system on glioblastoma initiation with important future significance for therapeutic discovery and optimizations. Overall design: To capture broad transcriptomic differences in tumor burdened brains versus normal brains we performed bulk RNA sequencing and gene expression analysis of whole brains and sorted cells. EGFRviii derived tumors were induced by microinjection of EGFRviii PI3KCAH1047R and mScarlet constructs defined as EPS. KRAS derived tumors were induced by microinjection of KRAS PI3KCAH1047R GFP constructs defined as KPG. Three whole brains positive for fluorescent tumors EPS 1 3 KPG 1 3 alongside three control brains from injected siblings who did not develop tumors CTRL 1 3 were dissected for each condition for bulk RNA sequencing. We also performed fluorescent activated cell sorting on pooled dissociated brains from the EPS condition resulting in enrichment for mScarlet postive tumor cells CS Pos and mScarlet negative cells CS Neg for comparative analysis.", null, "pubmed:39052000", null, "KRAS PI3KCAH1047R GFP tumor negative control brain", "GSM7866392", null, "source name:Whole Brain|strain:CG1 p53null|tissue:Whole Brain|geo loc name:missing|collection date:missing", "KRAS PI3KCAH1047R GFP tumor negative control brain", "Raw .fastq data was processed using Salmon quantification of transcripts for each sample. A \u201cdecoy aware\u201d index was built with the Danio rerio transcriptome and genome using the GRCz11 assembly with a k mers length of 23 with entries manually added for GFP mScarlet EGFRviii KRAS and PI3KCAH1047R transcripts. Samples were then quantified with the following arguments: r seqBias mp 3 validateMappings rangeFactorizationBins 4. Differential gene expression was compared utilizing DESeq2 and GSEA. Assembly: GRCz11 Supplementary files format and content: Tab delimited .csv file including raw counts for all conditions.", "Whole Brain", "Fertilized embryos injected with either EPS or KPG construct mix", "Dissected brains or sorted cells were immediately put into Trizol. RNA was then extracted and purified utilizing Monarch RNA Cleanup Kit following manufacturer's recommendations Sequence ready polyA enriched libraries were prepared using the NEB Ultra II Directional mRNA prep kit for Illumina according to manufacturer\u2019s recommendations", "Zebrafish were housed and reared following approved animal use protocol", "strain:CG1 p53null|tissue:Whole Brain", "GSM7866392", "GSM7866392: KRAS PI3KCAH1047R GFP tumor negative control brain; Danio rerio; RNA Seq", "GSM7866392 r1", "GSM7866392", "1", "Dissected brains or sorted cells were immediately put into Trizol. RNA was then extracted and purified utilizing Monarch RNA Cleanup Kit following manufacturer's recommendations Sequence ready polyA enriched libraries were prepared using the NEB Ultra II Directional mRNA prep kit for Illumina according to manufacturer's recommendations", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP468564", null, "loader:fastq load.py", "CTRL_1.fastq.gz", "fastq", 10164914720.0, 100642720.0, "GSM7866392 r1", "0:101", "A:2650336113;C:2354113843;G:2276252979;T:2884188285;N:23500", 101, null, null, null, 2650336113, 2354113843, 2276252979, 2884188285, 23500, "SRX22238468", "SRS19292729", "SRA1740017", "Hayes Lab, DSCB, Sickkids Research", "Hayes Lab, DSCB, Sickkids Research", 1, 0.94271, null, 0.10831, null, 0.68527, null, 0.50207, null, 101, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "Canada", "2023-10-26", "Undetermined", "Embryo", "Brain", "Nervous System"], [28695, "SRR26535346", "SRX22238467", "SRS19292728", "SRP468564", "PRJNA1032461", "A syngeneic spontaneous zebrafish model oftp53 deficient EGFRviii and PI3KCAH1047R driven glioblastoma reveals inhibitory roles for inflammation during tumor initiation and relapsein vivo", "GSE246295", "Transcriptome Analysis", "To build a patient relevantin vivomodel of human glioblastoma we expressed common oncogenic variants including activated human EGFRviii or KRAS and PI3KCAH1047Runder the control of the radial glial specific promoterher4.1in syngeneictp53loss of function mutant zebrafish.Robust tumor formation was observed prior to 45 days of life with a gene expression signature similar to human glioblastoma of the mesenchymal subtype along with a strong inflammatory component. Within early stage tumor lesions and in an intact and endogenous tumor microenvironment we visualized infiltration of phagocytic cells as well as internalization of tumor cells bympeg1.1:GFP+ microglia/macrophages suggesting negative regulatory pressure by pro inflammatory cell types on tumor growth at early stages of glioblastoma initiationin vivo. Furthermore CRISPR/Cas9 mediated gene targeting of master inflammatory transcription factorsirf7andirf8led to increased tumor formation in the primary context while suppression of microglial/macrophage activity led to enhanced tumor cell engraftment following transplantation into otherwise immune competent zebrafish hosts. Altogether we developed a genetically relevant model of aggressive human glioblastoma and harnessed the unique advantages of zebrafish including live imaging high throughput genetic and chemical manipulations to highlight important tumor suppressive roles for the innate immune system on glioblastoma initiation with important future significance for therapeutic discovery and optimizations. Overall design: To capture broad transcriptomic differences in tumor burdened brains versus normal brains we performed bulk RNA sequencing and gene expression analysis of whole brains and sorted cells. EGFRviii derived tumors were induced by microinjection of EGFRviii PI3KCAH1047R and mScarlet constructs defined as EPS. KRAS derived tumors were induced by microinjection of KRAS PI3KCAH1047R GFP constructs defined as KPG. Three whole brains positive for fluorescent tumors EPS 1 3 KPG 1 3 alongside three control brains from injected siblings who did not develop tumors CTRL 1 3 were dissected for each condition for bulk RNA sequencing. We also performed fluorescent activated cell sorting on pooled dissociated brains from the EPS condition resulting in enrichment for mScarlet postive tumor cells CS Pos and mScarlet negative cells CS Neg for comparative analysis.", null, "pubmed:39052000", null, "EGFRviii PI3KCAH1047R mScarlet tumor positive whole brain 3", "GSM7866391", null, "source name:Whole Brain|strain:CG1 p53null|tissue:Whole Brain|geo loc name:missing|collection date:missing", "EGFRviii PI3KCAH1047R mScarlet tumor positive whole brain 3", "Raw .fastq data was processed using Salmon quantification of transcripts for each sample. A \u201cdecoy aware\u201d index was built with the Danio rerio transcriptome and genome using the GRCz11 assembly with a k mers length of 23 with entries manually added for GFP mScarlet EGFRviii KRAS and PI3KCAH1047R transcripts. Samples were then quantified with the following arguments: r seqBias mp 3 validateMappings rangeFactorizationBins 4. Differential gene expression was compared utilizing DESeq2 and GSEA. Assembly: GRCz11 Supplementary files format and content: Tab delimited .csv file including raw counts for all conditions.", "Whole Brain", "Fertilized embryos injected with either EPS or KPG construct mix", "Dissected brains or sorted cells were immediately put into Trizol. RNA was then extracted and purified utilizing Monarch RNA Cleanup Kit following manufacturer's recommendations Sequence ready polyA enriched libraries were prepared using the NEB Ultra II Directional mRNA prep kit for Illumina according to manufacturer\u2019s recommendations", "Zebrafish were housed and reared following approved animal use protocol", "strain:CG1 p53null|tissue:Whole Brain", "GSM7866391", "GSM7866391: EGFRviii PI3KCAH1047R mScarlet tumor positive whole brain 3; Danio rerio; RNA Seq", "GSM7866391 r1", "GSM7866391", "1", "Dissected brains or sorted cells were immediately put into Trizol. RNA was then extracted and purified utilizing Monarch RNA Cleanup Kit following manufacturer's recommendations Sequence ready polyA enriched libraries were prepared using the NEB Ultra II Directional mRNA prep kit for Illumina according to manufacturer's recommendations", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP468564", null, "loader:fastq load.py", "EPS_3.fastq.gz", "fastq", 9796714170.0, 96997170.0, "GSM7866391 r1", "0:101", "A:2627522717;C:2223655583;G:2134761894;T:2810751194;N:22782", 101, null, null, null, 2627522717, 2223655583, 2134761894, 2810751194, 22782, "SRX22238467", "SRS19292728", "SRA1740017", "Hayes Lab, DSCB, Sickkids Research", "Hayes Lab, DSCB, Sickkids Research", 1, 0.92543, null, 0.1876, null, 0.67308, null, 0.4886, null, 101, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "Canada", "2023-10-26", "Undetermined", "Embryo", "Brain", "Nervous System"], [28696, "SRR26535347", "SRX22238466", "SRS19292727", "SRP468564", "PRJNA1032461", "A syngeneic spontaneous zebrafish model oftp53 deficient EGFRviii and PI3KCAH1047R driven glioblastoma reveals inhibitory roles for inflammation during tumor initiation and relapsein vivo", "GSE246295", "Transcriptome Analysis", "To build a patient relevantin vivomodel of human glioblastoma we expressed common oncogenic variants including activated human EGFRviii or KRAS and PI3KCAH1047Runder the control of the radial glial specific promoterher4.1in syngeneictp53loss of function mutant zebrafish.Robust tumor formation was observed prior to 45 days of life with a gene expression signature similar to human glioblastoma of the mesenchymal subtype along with a strong inflammatory component. Within early stage tumor lesions and in an intact and endogenous tumor microenvironment we visualized infiltration of phagocytic cells as well as internalization of tumor cells bympeg1.1:GFP+ microglia/macrophages suggesting negative regulatory pressure by pro inflammatory cell types on tumor growth at early stages of glioblastoma initiationin vivo. Furthermore CRISPR/Cas9 mediated gene targeting of master inflammatory transcription factorsirf7andirf8led to increased tumor formation in the primary context while suppression of microglial/macrophage activity led to enhanced tumor cell engraftment following transplantation into otherwise immune competent zebrafish hosts. Altogether we developed a genetically relevant model of aggressive human glioblastoma and harnessed the unique advantages of zebrafish including live imaging high throughput genetic and chemical manipulations to highlight important tumor suppressive roles for the innate immune system on glioblastoma initiation with important future significance for therapeutic discovery and optimizations. Overall design: To capture broad transcriptomic differences in tumor burdened brains versus normal brains we performed bulk RNA sequencing and gene expression analysis of whole brains and sorted cells. EGFRviii derived tumors were induced by microinjection of EGFRviii PI3KCAH1047R and mScarlet constructs defined as EPS. KRAS derived tumors were induced by microinjection of KRAS PI3KCAH1047R GFP constructs defined as KPG. Three whole brains positive for fluorescent tumors EPS 1 3 KPG 1 3 alongside three control brains from injected siblings who did not develop tumors CTRL 1 3 were dissected for each condition for bulk RNA sequencing. We also performed fluorescent activated cell sorting on pooled dissociated brains from the EPS condition resulting in enrichment for mScarlet postive tumor cells CS Pos and mScarlet negative cells CS Neg for comparative analysis.", null, "pubmed:39052000", null, "EGFRviii PI3KCAH1047R mScarlet tumor positive whole brain 2", "GSM7866390", null, "source name:Whole Brain|strain:CG1 p53null|tissue:Whole Brain|geo loc name:missing|collection date:missing", "EGFRviii PI3KCAH1047R mScarlet tumor positive whole brain 2", "Raw .fastq data was processed using Salmon quantification of transcripts for each sample. A \u201cdecoy aware\u201d index was built with the Danio rerio transcriptome and genome using the GRCz11 assembly with a k mers length of 23 with entries manually added for GFP mScarlet EGFRviii KRAS and PI3KCAH1047R transcripts. Samples were then quantified with the following arguments: r seqBias mp 3 validateMappings rangeFactorizationBins 4. Differential gene expression was compared utilizing DESeq2 and GSEA. Assembly: GRCz11 Supplementary files format and content: Tab delimited .csv file including raw counts for all conditions.", "Whole Brain", "Fertilized embryos injected with either EPS or KPG construct mix", "Dissected brains or sorted cells were immediately put into Trizol. RNA was then extracted and purified utilizing Monarch RNA Cleanup Kit following manufacturer's recommendations Sequence ready polyA enriched libraries were prepared using the NEB Ultra II Directional mRNA prep kit for Illumina according to manufacturer\u2019s recommendations", "Zebrafish were housed and reared following approved animal use protocol", "strain:CG1 p53null|tissue:Whole Brain", "GSM7866390", "GSM7866390: EGFRviii PI3KCAH1047R mScarlet tumor positive whole brain 2; Danio rerio; RNA Seq", "GSM7866390 r1", "GSM7866390", "1", "Dissected brains or sorted cells were immediately put into Trizol. RNA was then extracted and purified utilizing Monarch RNA Cleanup Kit following manufacturer's recommendations Sequence ready polyA enriched libraries were prepared using the NEB Ultra II Directional mRNA prep kit for Illumina according to manufacturer's recommendations", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP468564", null, "loader:fastq load.py", "EPS_2.fastq.gz", "fastq", 7839595861.0, 77619761.0, "GSM7866390 r1", "0:101", "A:2093456023;C:1792947580;G:1718784421;T:2234389453;N:18384", 101, null, null, null, 2093456023, 1792947580, 1718784421, 2234389453, 18384, "SRX22238466", "SRS19292727", "SRA1740017", "Hayes Lab, DSCB, Sickkids Research", "Hayes Lab, DSCB, Sickkids Research", 1, 0.93807, null, 0.14978, null, 0.68854, null, 0.47786, null, 101, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "Canada", "2023-10-26", "Undetermined", "Embryo", "Brain", "Nervous System"], [28697, "SRR26535348", "SRX22238465", "SRS19292726", "SRP468564", "PRJNA1032461", "A syngeneic spontaneous zebrafish model oftp53 deficient EGFRviii and PI3KCAH1047R driven glioblastoma reveals inhibitory roles for inflammation during tumor initiation and relapsein vivo", "GSE246295", "Transcriptome Analysis", "To build a patient relevantin vivomodel of human glioblastoma we expressed common oncogenic variants including activated human EGFRviii or KRAS and PI3KCAH1047Runder the control of the radial glial specific promoterher4.1in syngeneictp53loss of function mutant zebrafish.Robust tumor formation was observed prior to 45 days of life with a gene expression signature similar to human glioblastoma of the mesenchymal subtype along with a strong inflammatory component. Within early stage tumor lesions and in an intact and endogenous tumor microenvironment we visualized infiltration of phagocytic cells as well as internalization of tumor cells bympeg1.1:GFP+ microglia/macrophages suggesting negative regulatory pressure by pro inflammatory cell types on tumor growth at early stages of glioblastoma initiationin vivo. Furthermore CRISPR/Cas9 mediated gene targeting of master inflammatory transcription factorsirf7andirf8led to increased tumor formation in the primary context while suppression of microglial/macrophage activity led to enhanced tumor cell engraftment following transplantation into otherwise immune competent zebrafish hosts. Altogether we developed a genetically relevant model of aggressive human glioblastoma and harnessed the unique advantages of zebrafish including live imaging high throughput genetic and chemical manipulations to highlight important tumor suppressive roles for the innate immune system on glioblastoma initiation with important future significance for therapeutic discovery and optimizations. Overall design: To capture broad transcriptomic differences in tumor burdened brains versus normal brains we performed bulk RNA sequencing and gene expression analysis of whole brains and sorted cells. EGFRviii derived tumors were induced by microinjection of EGFRviii PI3KCAH1047R and mScarlet constructs defined as EPS. KRAS derived tumors were induced by microinjection of KRAS PI3KCAH1047R GFP constructs defined as KPG. Three whole brains positive for fluorescent tumors EPS 1 3 KPG 1 3 alongside three control brains from injected siblings who did not develop tumors CTRL 1 3 were dissected for each condition for bulk RNA sequencing. We also performed fluorescent activated cell sorting on pooled dissociated brains from the EPS condition resulting in enrichment for mScarlet postive tumor cells CS Pos and mScarlet negative cells CS Neg for comparative analysis.", null, "pubmed:39052000", null, "EGFRviii PI3KCAH1047R mScarlet tumor positive whole brain 1", "GSM7866389", null, "source name:Whole Brain|strain:CG1 p53null|tissue:Whole Brain|geo loc name:missing|collection date:missing", "EGFRviii PI3KCAH1047R mScarlet tumor positive whole brain 1", "Raw .fastq data was processed using Salmon quantification of transcripts for each sample. A \u201cdecoy aware\u201d index was built with the Danio rerio transcriptome and genome using the GRCz11 assembly with a k mers length of 23 with entries manually added for GFP mScarlet EGFRviii KRAS and PI3KCAH1047R transcripts. Samples were then quantified with the following arguments: r seqBias mp 3 validateMappings rangeFactorizationBins 4. Differential gene expression was compared utilizing DESeq2 and GSEA. Assembly: GRCz11 Supplementary files format and content: Tab delimited .csv file including raw counts for all conditions.", "Whole Brain", "Fertilized embryos injected with either EPS or KPG construct mix", "Dissected brains or sorted cells were immediately put into Trizol. RNA was then extracted and purified utilizing Monarch RNA Cleanup Kit following manufacturer's recommendations Sequence ready polyA enriched libraries were prepared using the NEB Ultra II Directional mRNA prep kit for Illumina according to manufacturer\u2019s recommendations", "Zebrafish were housed and reared following approved animal use protocol", "strain:CG1 p53null|tissue:Whole Brain", "GSM7866389", "GSM7866389: EGFRviii PI3KCAH1047R mScarlet tumor positive whole brain 1; Danio rerio; RNA Seq", "GSM7866389 r1", "GSM7866389", "1", "Dissected brains or sorted cells were immediately put into Trizol. RNA was then extracted and purified utilizing Monarch RNA Cleanup Kit following manufacturer's recommendations Sequence ready polyA enriched libraries were prepared using the NEB Ultra II Directional mRNA prep kit for Illumina according to manufacturer's recommendations", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP468564", null, "loader:fastq load.py", "EPS_1.fastq.gz", "fastq", 8403475528.0, 83202728.0, "GSM7866389 r1", "0:101", "A:2217465507;C:1940028683;G:1857031218;T:2388930530;N:19590", 101, null, null, null, 2217465507, 1940028683, 1857031218, 2388930530, 19590, "SRX22238465", "SRS19292726", "SRA1740017", "Hayes Lab, DSCB, Sickkids Research", "Hayes Lab, DSCB, Sickkids Research", 1, 0.94596, null, 0.12916, null, 0.68619, null, 0.4957, null, 101, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "Canada", "2023-10-26", "Undetermined", "Embryo", "Brain", "Nervous System"], [28698, "SRR26535349", "SRX22238464", "SRS19292725", "SRP468564", "PRJNA1032461", "A syngeneic spontaneous zebrafish model oftp53 deficient EGFRviii and PI3KCAH1047R driven glioblastoma reveals inhibitory roles for inflammation during tumor initiation and relapsein vivo", "GSE246295", "Transcriptome Analysis", "To build a patient relevantin vivomodel of human glioblastoma we expressed common oncogenic variants including activated human EGFRviii or KRAS and PI3KCAH1047Runder the control of the radial glial specific promoterher4.1in syngeneictp53loss of function mutant zebrafish.Robust tumor formation was observed prior to 45 days of life with a gene expression signature similar to human glioblastoma of the mesenchymal subtype along with a strong inflammatory component. Within early stage tumor lesions and in an intact and endogenous tumor microenvironment we visualized infiltration of phagocytic cells as well as internalization of tumor cells bympeg1.1:GFP+ microglia/macrophages suggesting negative regulatory pressure by pro inflammatory cell types on tumor growth at early stages of glioblastoma initiationin vivo. Furthermore CRISPR/Cas9 mediated gene targeting of master inflammatory transcription factorsirf7andirf8led to increased tumor formation in the primary context while suppression of microglial/macrophage activity led to enhanced tumor cell engraftment following transplantation into otherwise immune competent zebrafish hosts. Altogether we developed a genetically relevant model of aggressive human glioblastoma and harnessed the unique advantages of zebrafish including live imaging high throughput genetic and chemical manipulations to highlight important tumor suppressive roles for the innate immune system on glioblastoma initiation with important future significance for therapeutic discovery and optimizations. Overall design: To capture broad transcriptomic differences in tumor burdened brains versus normal brains we performed bulk RNA sequencing and gene expression analysis of whole brains and sorted cells. EGFRviii derived tumors were induced by microinjection of EGFRviii PI3KCAH1047R and mScarlet constructs defined as EPS. KRAS derived tumors were induced by microinjection of KRAS PI3KCAH1047R GFP constructs defined as KPG. Three whole brains positive for fluorescent tumors EPS 1 3 KPG 1 3 alongside three control brains from injected siblings who did not develop tumors CTRL 1 3 were dissected for each condition for bulk RNA sequencing. We also performed fluorescent activated cell sorting on pooled dissociated brains from the EPS condition resulting in enrichment for mScarlet postive tumor cells CS Pos and mScarlet negative cells CS Neg for comparative analysis.", null, "pubmed:39052000", null, "KRAS PI3KCAH1047R GFP tumor positive whole brain 3", "GSM7866388", null, "source name:Whole Brain|strain:CG1 p53null|tissue:Whole Brain|geo loc name:missing|collection date:missing", "KRAS PI3KCAH1047R GFP tumor positive whole brain 3", "Raw .fastq data was processed using Salmon quantification of transcripts for each sample. A \u201cdecoy aware\u201d index was built with the Danio rerio transcriptome and genome using the GRCz11 assembly with a k mers length of 23 with entries manually added for GFP mScarlet EGFRviii KRAS and PI3KCAH1047R transcripts. Samples were then quantified with the following arguments: r seqBias mp 3 validateMappings rangeFactorizationBins 4. Differential gene expression was compared utilizing DESeq2 and GSEA. Assembly: GRCz11 Supplementary files format and content: Tab delimited .csv file including raw counts for all conditions.", "Whole Brain", "Fertilized embryos injected with either EPS or KPG construct mix", "Dissected brains or sorted cells were immediately put into Trizol. RNA was then extracted and purified utilizing Monarch RNA Cleanup Kit following manufacturer's recommendations Sequence ready polyA enriched libraries were prepared using the NEB Ultra II Directional mRNA prep kit for Illumina according to manufacturer\u2019s recommendations", "Zebrafish were housed and reared following approved animal use protocol", "strain:CG1 p53null|tissue:Whole Brain", "GSM7866388", "GSM7866388: KRAS PI3KCAH1047R GFP tumor positive whole brain 3; Danio rerio; RNA Seq", "GSM7866388 r1", "GSM7866388", "1", "Dissected brains or sorted cells were immediately put into Trizol. RNA was then extracted and purified utilizing Monarch RNA Cleanup Kit following manufacturer's recommendations Sequence ready polyA enriched libraries were prepared using the NEB Ultra II Directional mRNA prep kit for Illumina according to manufacturer's recommendations", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP468564", null, "loader:fastq load.py", "KPG_3.fastq.gz", "fastq", 7609183450.0, 75338450.0, "GSM7866388 r1", "0:101", "A:2040241047;C:1721563382;G:1666400346;T:2180961056;N:17619", 101, null, null, null, 2040241047, 1721563382, 1666400346, 2180961056, 17619, "SRX22238464", "SRS19292725", "SRA1740017", "Hayes Lab, DSCB, Sickkids Research", "Hayes Lab, DSCB, Sickkids Research", 1, 0.93555, null, 0.16895, null, 0.68199, null, 0.50032, null, 101, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "Canada", "2023-10-26", "Undetermined", "Embryo", "Brain", "Nervous System"], [28699, "SRR26535350", "SRX22238463", "SRS19292724", "SRP468564", "PRJNA1032461", "A syngeneic spontaneous zebrafish model oftp53 deficient EGFRviii and PI3KCAH1047R driven glioblastoma reveals inhibitory roles for inflammation during tumor initiation and relapsein vivo", "GSE246295", "Transcriptome Analysis", "To build a patient relevantin vivomodel of human glioblastoma we expressed common oncogenic variants including activated human EGFRviii or KRAS and PI3KCAH1047Runder the control of the radial glial specific promoterher4.1in syngeneictp53loss of function mutant zebrafish.Robust tumor formation was observed prior to 45 days of life with a gene expression signature similar to human glioblastoma of the mesenchymal subtype along with a strong inflammatory component. Within early stage tumor lesions and in an intact and endogenous tumor microenvironment we visualized infiltration of phagocytic cells as well as internalization of tumor cells bympeg1.1:GFP+ microglia/macrophages suggesting negative regulatory pressure by pro inflammatory cell types on tumor growth at early stages of glioblastoma initiationin vivo. Furthermore CRISPR/Cas9 mediated gene targeting of master inflammatory transcription factorsirf7andirf8led to increased tumor formation in the primary context while suppression of microglial/macrophage activity led to enhanced tumor cell engraftment following transplantation into otherwise immune competent zebrafish hosts. Altogether we developed a genetically relevant model of aggressive human glioblastoma and harnessed the unique advantages of zebrafish including live imaging high throughput genetic and chemical manipulations to highlight important tumor suppressive roles for the innate immune system on glioblastoma initiation with important future significance for therapeutic discovery and optimizations. Overall design: To capture broad transcriptomic differences in tumor burdened brains versus normal brains we performed bulk RNA sequencing and gene expression analysis of whole brains and sorted cells. EGFRviii derived tumors were induced by microinjection of EGFRviii PI3KCAH1047R and mScarlet constructs defined as EPS. KRAS derived tumors were induced by microinjection of KRAS PI3KCAH1047R GFP constructs defined as KPG. Three whole brains positive for fluorescent tumors EPS 1 3 KPG 1 3 alongside three control brains from injected siblings who did not develop tumors CTRL 1 3 were dissected for each condition for bulk RNA sequencing. We also performed fluorescent activated cell sorting on pooled dissociated brains from the EPS condition resulting in enrichment for mScarlet postive tumor cells CS Pos and mScarlet negative cells CS Neg for comparative analysis.", null, "pubmed:39052000", null, "KRAS PI3KCAH1047R GFP tumor positive whole brain 2", "GSM7866387", null, "source name:Whole Brain|strain:CG1 p53null|tissue:Whole Brain|geo loc name:missing|collection date:missing", "KRAS PI3KCAH1047R GFP tumor positive whole brain 2", "Raw .fastq data was processed using Salmon quantification of transcripts for each sample. A \u201cdecoy aware\u201d index was built with the Danio rerio transcriptome and genome using the GRCz11 assembly with a k mers length of 23 with entries manually added for GFP mScarlet EGFRviii KRAS and PI3KCAH1047R transcripts. Samples were then quantified with the following arguments: r seqBias mp 3 validateMappings rangeFactorizationBins 4. Differential gene expression was compared utilizing DESeq2 and GSEA. Assembly: GRCz11 Supplementary files format and content: Tab delimited .csv file including raw counts for all conditions.", "Whole Brain", "Fertilized embryos injected with either EPS or KPG construct mix", "Dissected brains or sorted cells were immediately put into Trizol. RNA was then extracted and purified utilizing Monarch RNA Cleanup Kit following manufacturer's recommendations Sequence ready polyA enriched libraries were prepared using the NEB Ultra II Directional mRNA prep kit for Illumina according to manufacturer\u2019s recommendations", "Zebrafish were housed and reared following approved animal use protocol", "strain:CG1 p53null|tissue:Whole Brain", "GSM7866387", "GSM7866387: KRAS PI3KCAH1047R GFP tumor positive whole brain 2; Danio rerio; RNA Seq", "GSM7866387 r1", "GSM7866387", "1", "Dissected brains or sorted cells were immediately put into Trizol. RNA was then extracted and purified utilizing Monarch RNA Cleanup Kit following manufacturer's recommendations Sequence ready polyA enriched libraries were prepared using the NEB Ultra II Directional mRNA prep kit for Illumina according to manufacturer's recommendations", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP468564", null, "loader:fastq load.py", "KPG_2.fastq.gz", "fastq", 8446573339.0, 83629439.0, "GSM7866387 r1", "0:101", "A:2223763293;C:1944013929;G:1869828652;T:2408947564;N:19901", 101, null, null, null, 2223763293, 1944013929, 1869828652, 2408947564, 19901, "SRX22238463", "SRS19292724", "SRA1740017", "Hayes Lab, DSCB, Sickkids Research", "Hayes Lab, DSCB, Sickkids Research", 1, 0.94943, null, 0.11539, null, 0.68428, null, 0.51019, null, 101, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "Canada", "2023-10-26", "Undetermined", "Embryo", "Brain", "Nervous System"], [28700, "SRR26535351", "SRX22238462", "SRS19292723", "SRP468564", "PRJNA1032461", "A syngeneic spontaneous zebrafish model oftp53 deficient EGFRviii and PI3KCAH1047R driven glioblastoma reveals inhibitory roles for inflammation during tumor initiation and relapsein vivo", "GSE246295", "Transcriptome Analysis", "To build a patient relevantin vivomodel of human glioblastoma we expressed common oncogenic variants including activated human EGFRviii or KRAS and PI3KCAH1047Runder the control of the radial glial specific promoterher4.1in syngeneictp53loss of function mutant zebrafish.Robust tumor formation was observed prior to 45 days of life with a gene expression signature similar to human glioblastoma of the mesenchymal subtype along with a strong inflammatory component. Within early stage tumor lesions and in an intact and endogenous tumor microenvironment we visualized infiltration of phagocytic cells as well as internalization of tumor cells bympeg1.1:GFP+ microglia/macrophages suggesting negative regulatory pressure by pro inflammatory cell types on tumor growth at early stages of glioblastoma initiationin vivo. Furthermore CRISPR/Cas9 mediated gene targeting of master inflammatory transcription factorsirf7andirf8led to increased tumor formation in the primary context while suppression of microglial/macrophage activity led to enhanced tumor cell engraftment following transplantation into otherwise immune competent zebrafish hosts. Altogether we developed a genetically relevant model of aggressive human glioblastoma and harnessed the unique advantages of zebrafish including live imaging high throughput genetic and chemical manipulations to highlight important tumor suppressive roles for the innate immune system on glioblastoma initiation with important future significance for therapeutic discovery and optimizations. Overall design: To capture broad transcriptomic differences in tumor burdened brains versus normal brains we performed bulk RNA sequencing and gene expression analysis of whole brains and sorted cells. EGFRviii derived tumors were induced by microinjection of EGFRviii PI3KCAH1047R and mScarlet constructs defined as EPS. KRAS derived tumors were induced by microinjection of KRAS PI3KCAH1047R GFP constructs defined as KPG. Three whole brains positive for fluorescent tumors EPS 1 3 KPG 1 3 alongside three control brains from injected siblings who did not develop tumors CTRL 1 3 were dissected for each condition for bulk RNA sequencing. We also performed fluorescent activated cell sorting on pooled dissociated brains from the EPS condition resulting in enrichment for mScarlet postive tumor cells CS Pos and mScarlet negative cells CS Neg for comparative analysis.", null, "pubmed:39052000", null, "KRAS PI3KCAH1047R GFP tumor positive whole brain 1", "GSM7866386", null, "source name:Whole Brain|strain:CG1 p53null|tissue:Whole Brain|geo loc name:missing|collection date:missing", "KRAS PI3KCAH1047R GFP tumor positive whole brain 1", "Raw .fastq data was processed using Salmon quantification of transcripts for each sample. A \u201cdecoy aware\u201d index was built with the Danio rerio transcriptome and genome using the GRCz11 assembly with a k mers length of 23 with entries manually added for GFP mScarlet EGFRviii KRAS and PI3KCAH1047R transcripts. Samples were then quantified with the following arguments: r seqBias mp 3 validateMappings rangeFactorizationBins 4. Differential gene expression was compared utilizing DESeq2 and GSEA. Assembly: GRCz11 Supplementary files format and content: Tab delimited .csv file including raw counts for all conditions.", "Whole Brain", "Fertilized embryos injected with either EPS or KPG construct mix", "Dissected brains or sorted cells were immediately put into Trizol. RNA was then extracted and purified utilizing Monarch RNA Cleanup Kit following manufacturer's recommendations Sequence ready polyA enriched libraries were prepared using the NEB Ultra II Directional mRNA prep kit for Illumina according to manufacturer\u2019s recommendations", "Zebrafish were housed and reared following approved animal use protocol", "strain:CG1 p53null|tissue:Whole Brain", "GSM7866386", "GSM7866386: KRAS PI3KCAH1047R GFP tumor positive whole brain 1; Danio rerio; RNA Seq", "GSM7866386 r1", "GSM7866386", "1", "Dissected brains or sorted cells were immediately put into Trizol. RNA was then extracted and purified utilizing Monarch RNA Cleanup Kit following manufacturer's recommendations Sequence ready polyA enriched libraries were prepared using the NEB Ultra II Directional mRNA prep kit for Illumina according to manufacturer's recommendations", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP468564", null, "loader:fastq load.py", "KPG_1.fastq.gz", "fastq", 4326209053.0, 42833753.0, "GSM7866386 r1", "0:101", "A:1143856405;C:993993009;G:951829931;T:1236519669;N:10039", 101, null, null, null, 1143856405, 993993009, 951829931, 1236519669, 10039, "SRX22238462", "SRS19292723", "SRA1740017", "Hayes Lab, DSCB, Sickkids Research", "Hayes Lab, DSCB, Sickkids Research", 1, 0.94443, null, 0.13057, null, 0.68503, null, 0.50149, null, 101, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "Canada", "2023-10-26", "Undetermined", "Embryo", "Brain", "Nervous System"], [31871, "SRR33650039", "SRX28877239", "SRS25103945", "SRP502657", "PRJNA1101966", "Pioneer neurons are molecularly distinct and their axon targeting is regulated by retinoic acid signaling", "GSE264323", "Transcriptome Analysis", "During nervous system development pioneer neurons are the first to extend their axons into target tissues creating a scaffold for follower neurons. Despite years of study whether pioneer neurons are a molecularly distinct population is unknown. Analysis of zebrafish posterior lateral line pLL sensory neurons during axon growth using single cell RNA sequencing scRNA seq revealed that pioneer and follower neurons are transcriptionally distinct. Expression profiling of differentiating pLL progenitors defined follower as the ground state whereas \u201cpioneer\u201d is a later developmental state. The scRNA seq data revealed active retinoic acid RA signaling in followers but not in pioneers. Modulation of RA signaling within single pLL neurons showed that its downregulation in pioneers is necessary for expression of neurotrophic factor receptor ret which is required for correct targeting of pioneer axons. Our study provided insights into the molecular landscape of pioneer neurons and revealed the regulatory role of RA signaling in their development. Overall design: Fourteen hpf eighteen hpf twenty two hpf forty eight hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer's solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer's solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin 1 mM EDTA pH 8.0 PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28\u00b0 C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X 30% calf serum 6 mM CaCl2 PBS was added and samples were centrifuged 350xg 4\u00b0 C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS 0.8 mM CaCl2 50 U/mL penicillin 0.05 mg/mL streptomycin DMEM. Samples were centrifuged again 350g 4\u00b0 C for 5 minutes and supernatant was removed. 700 \u00b5l of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 \u00b5m cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 \u00b5l PBS/ 2% BSA in a siliconized 1.5mL tube.", null, null, null, "WT zebrafish neurons", "GSM8997253", null, "source name:neuron|tissue:neuron|genotype:mixed|geo loc name:missing|collection date:missing", "WT zebrafish neurons", "using Cell Ranger version 3.1.0; 10X Genomics Pleasanton CA. USA Assembly: ZebraFishGRCz11 Supplementary files format and content: Tab separated values files and matrix files", "neuron", null, "Twenty two old TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer\u2019s solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer\u2019s solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin 1 mM EDTA pH 8.0 PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28\u00b0 C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X 30% calf serum 6 mM CaCl2 PBS was added and samples were centrifuged 350xg 4\u00b0 C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS 0.8 mM CaCl2 50 U/mL penicillin 0.05 mg/mL streptomycin DMEM. Samples were centrifuged again 350g 4\u00b0 C for 5 minutes and supernatant was removed. 700 \u03bcl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 \u03bcm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 \u03bcl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter\u2019s instructions single cell 3\u2019 v3 protocol 10x Genomics.", null, "tissue:neuron|genotype:mixed", "GSM8997253", "GSM8997253: WT zebrafish neurons; Danio rerio; RNA Seq", "GSM8997253 r1", "GSM8997253", "1", "Twenty two old TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer's solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer's solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin 1 mM EDTA pH 8.0 PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28\u00b0 C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X 30% calf serum 6 mM CaCl2 PBS was added and samples were centrifuged 350xg 4\u00b0 C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS 0.8 mM CaCl2 50 U/mL penicillin 0.05 mg/mL streptomycin DMEM. Samples were centrifuged again 350g 4\u00b0 C for 5 minutes and supernatant was removed. 700 \u03bcl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 \u03bcm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 \u03bcl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter's instructions single cell three prime v3 protocol 10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP502657", null, null, "CEL221031AN_WT_18s_S3_L001_I1_001.fastq.gz CEL221031AN_WT_18s_S3_L001_I2_001.fastq.gz CEL221031AN_WT_18s_S3_L001_R1_001.fastq.gz CEL221031AN_WT_18s_S3_L001_R2_001.fastq.gz", "fastq fastq fastq fastq", 76460696208.0, 554063016.0, "GSM8997253 r1", "0:10 1:10 2:28 3:90", "A:15627919564;C:9793027889;G:11041478751;T:13400880335;N:2364901", 10, 10, 28, 90, 15627919564, 9793027889, 11041478751, 13400880335, 2364901, "SRX28877239", "SRS25103945", "SRA2133742", "Oregon Health and Science Univ", "Oregon Health and Science Univ", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2025-05-20", "Undetermined", "Embryo", "Brain", "Nervous System"], [34088, "SRR31047783", "SRX26432306", "SRS22949546", "SRP539617", "PRJNA1175041", "6PPD induces cerebrovascular defects by triggering oxidative stress and ferroptosis in zebrafish", "GSE279887", "Transcriptome Analysis", "N 1 3 dimethylbutyl N' phenyl p phenylenediamine 6PPD which is widely used as an antiozonant in rubber tires has recently got much attention for its acute aquatic toxicity. However the developmental toxicity of 6PPD in cerebrovascular network remains unknown. Here we investigated the effects of 6PPD exposure in cerebral vascular using the larvae of zebrafish. 6PPD would not affect the body length and shape of zebrafish larvae at the concentrations ranging from 20 \u00b5g/L to 1000 \u00b5g/L. 6PPD induced developmental defects in the brain in a concentration dependent manner. The trunk vascular development would not be affected while the cerebrovascular network was disrupted upon 6PPD exposure. 6PPD would trigger excessive Reactive Oxygen Species ROS in the brain indicating abnormal oxidative stress. Mechanistically brain specific transcriptome analysis showed that 6PPD could potentially cause the blockage of arachidonic acid AA metabolism related genes and the upregulation of ferroptosis related genes. Besides treatment with ferroptosis inhibitor N Acetyl L cysteine NAC attenuated oxidative damage and improved the construction of cerebrovascular network upon 6PPD exposure. Moreover using a human vascular endothelial cell line we further confirmed that 6PPD could trigger abnormal oxidative stress and defective expansion capacity implying the conserved toxicity cross species. These findings are useful for the elucidation of toxicity underlying 6PPD in cerebrovascular systems of both zebrafish and humans. Overall design: To investigate the effects of 6PPD on zebrafish development embryos were treated with 500 \u00b5g/L 6PPD from 10 hpf until 2 dpf dpf. For transcriptomic analysis three biological replicates were prepared for both the 6PPD treatment group and the DMSO control group. For each replicate the heads of 150 embryos at 2 dpf were dissected flash frozen in liquid nitrogen and sent for transcriptomic sequencing. The raw data analysis was performed to identify differentially expressed genes between the 6PPD treated and control groups.", null, null, null, "6PPD 3", "GSM8582553", null, "source name:Brain|tissue:Brain|treatment:6PPD|geo loc name:missing|collection date:missing", "6PPD 3", "Self house pipeline Sequence reads were trimmed for adaptor sequence/low quality seguence using fastp parameter Quality limit: 20 Trimmed sequence reads were mapped to GRCz11.109 use HISAT2 Read count extraction and normalization were performed using featureCounts and StringTie Assembly: GRCz11.109 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: tab delimited text files include FPKM values for each Sample", "Brain", "For transcriptomic analysis three biological replicates were prepared for both the 500 \u03bcg/L 6PPD treatment group and the DMSO control group. The embryos were treated from 10 hpf to 2dpf.For each replicate the heads of 150 embryos at 2 dpf were dissected flash frozen in liquid nitrogen.", "Total RNA was isolated and purified using TRIzol reagent Invitrogen Carlsbad CA USA following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND 1000 NanoDrop Wilmington DE USA. The RNA integrity was assessed by Bioanalyzer 2100 Agilent CA USA with RIN number >7.0 and confirmed by electrophoresis with denaturing agarose gel. Poly A RNA is purified from 1\u03bcg total RNA using Dynabeads Oligo dT25 61005 Thermo Fisher CA USA using two rounds of purification. Then the polyA RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module NEB cat.e6150 USA under 94\u2103 5 7min. Then the cleaved RNA fragments were reverse transcribed to create the cDNA by SuperScript\u2122 II Reverse Transcriptase Invitrogen cat. 1896649 USA which were next used to synthesise U labeled second stranded DNAs with E. coli DNA polymerase I NEB cat.m0209 USA RNase H NEB cat.m0297 USA and dUTP Solution Thermo Fisher cat.R0133 USA\uff09. An A base is then added to the blunt ends of each strand preparing them for ligation to the indexed adapters. Each adapter contains a T base overhang for ligating the adapter to the A tailed fragmented DNA. Single or dual index adapters are ligated to the fragments and size selection was performed with AMPureXP beads. post the heat labile UDG enzyme NEB cat.m0280 USA treatment of the U labeled second stranded DNAs the ligated products are amplified with PCR by the following conditions: initial denaturation at 95\u2103 for 3 min; 8 cycles of denaturation at 98\u2103 for 15 sec annealing at 60\u2103 for 15 sec and extension at 72\u2103 for 30 sec; and then final extension at 72\u2103 for 5 min. The average insert size for the final cDNA library was 300\u00b150 bp. At last we performed the 2\u00d7150bp paired end sequencing PE150 on an illumina Novaseq\u2122 6000 LC Bio Technology CO. Ltd. Hangzhou China following the vendor's recommended protocol.", "Embryos were collected and cultured in egg water 0.06 mg/mL sea salt 0.5 mg/L methylene blue and incubated before 24 hpf at 28\u00b0C. To inhibit pigmentation embryos were treated with 0.003% 1 phenyl 2 thiourea PTU Aladdin starting at 24 hpf.", "tissue:Brain|treatment:6PPD", "GSM8582553", "GSM8582553: 6PPD 3; Danio rerio; RNA Seq", "GSM8582553 r1", "GSM8582553", "1", "Total RNA was isolated and purified using TRIzol reagent Invitrogen Carlsbad CA USA following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND 1000 NanoDrop Wilmington DE USA. The RNA integrity was assessed by Bioanalyzer 2100 Agilent CA USA with RIN number >7.0 and confirmed by electrophoresis with denaturing agarose gel. Poly A RNA is purified from 1\u03bcg total RNA using Dynabeads Oligo dT25 61005 Thermo Fisher CA USA using two rounds of purification. Then the polyA RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module NEB cat.e6150 USA under 94\u2103 5 7min. Then the cleaved RNA fragments were reverse transcribed to create the cDNA by SuperScript\u2122 II Reverse Transcriptase Invitrogen cat. 1896649 USA which were next used to synthesise U labeled second stranded DNAs with E. coli DNA polymerase I NEB cat.m0209 USA RNase H NEB cat.m0297 USA and dUTP Solution Thermo Fisher cat.R0133 USA\uff09. An A base is then added to the blunt ends of each strand preparing them for ligation to the indexed adapters. Each adapter contains a T base overhang for ligating the adapter to the A tailed fragmented DNA. Single or dual index adapters are ligated to the fragments and size selection was performed with AMPureXP beads. post the heat labile UDG enzyme NEB cat.m0280 USA treatment of the U labeled second stranded DNAs the ligated products are amplified with PCR by the following conditions: initial denaturation at 95\u2103 for 3 min; 8 cycles of denaturation at 98\u2103 for 15 sec annealing at 60\u2103 for 15 sec and extension at 72\u2103 for 30 sec; and then final extension at 72\u2103 for 5 min. The average insert size for the final cDNA library was 300\u00b150 bp. At last we performed the 2\u00d7150bp paired end sequencing PE150 on an illumina Novaseq\u2122 6000 LC Bio Technology CO. Ltd. Hangzhou China following the vendor's recommended protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539617", null, null, "6PPD3head_Clean_Data1.fq.gz 6PPD3head_Clean_Data2.fq.gz", "fastq fastq", 5643201065.0, 19058349.0, "GSM8582553 r1", null, null, null, null, null, null, null, null, null, null, null, "SRX26432306", "SRS22949546", "SRA1994053", "Guizhou Medical University", "Guizhou Medical University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-10-19", "Multi-stage", "Embryo", "Brain", "Nervous System"], [34089, "SRR31047784", "SRX26432305", "SRS22949545", "SRP539617", "PRJNA1175041", "6PPD induces cerebrovascular defects by triggering oxidative stress and ferroptosis in zebrafish", "GSE279887", "Transcriptome Analysis", "N 1 3 dimethylbutyl N' phenyl p phenylenediamine 6PPD which is widely used as an antiozonant in rubber tires has recently got much attention for its acute aquatic toxicity. However the developmental toxicity of 6PPD in cerebrovascular network remains unknown. Here we investigated the effects of 6PPD exposure in cerebral vascular using the larvae of zebrafish. 6PPD would not affect the body length and shape of zebrafish larvae at the concentrations ranging from 20 \u00b5g/L to 1000 \u00b5g/L. 6PPD induced developmental defects in the brain in a concentration dependent manner. The trunk vascular development would not be affected while the cerebrovascular network was disrupted upon 6PPD exposure. 6PPD would trigger excessive Reactive Oxygen Species ROS in the brain indicating abnormal oxidative stress. Mechanistically brain specific transcriptome analysis showed that 6PPD could potentially cause the blockage of arachidonic acid AA metabolism related genes and the upregulation of ferroptosis related genes. Besides treatment with ferroptosis inhibitor N Acetyl L cysteine NAC attenuated oxidative damage and improved the construction of cerebrovascular network upon 6PPD exposure. Moreover using a human vascular endothelial cell line we further confirmed that 6PPD could trigger abnormal oxidative stress and defective expansion capacity implying the conserved toxicity cross species. These findings are useful for the elucidation of toxicity underlying 6PPD in cerebrovascular systems of both zebrafish and humans. Overall design: To investigate the effects of 6PPD on zebrafish development embryos were treated with 500 \u00b5g/L 6PPD from 10 hpf until 2 dpf dpf. For transcriptomic analysis three biological replicates were prepared for both the 6PPD treatment group and the DMSO control group. For each replicate the heads of 150 embryos at 2 dpf were dissected flash frozen in liquid nitrogen and sent for transcriptomic sequencing. The raw data analysis was performed to identify differentially expressed genes between the 6PPD treated and control groups.", null, null, null, "6PPD 2", "GSM8582552", null, "source name:Brain|tissue:Brain|treatment:6PPD|geo loc name:missing|collection date:missing", "6PPD 2", "Self house pipeline Sequence reads were trimmed for adaptor sequence/low quality seguence using fastp parameter Quality limit: 20 Trimmed sequence reads were mapped to GRCz11.109 use HISAT2 Read count extraction and normalization were performed using featureCounts and StringTie Assembly: GRCz11.109 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: tab delimited text files include FPKM values for each Sample", "Brain", "For transcriptomic analysis three biological replicates were prepared for both the 500 \u03bcg/L 6PPD treatment group and the DMSO control group. The embryos were treated from 10 hpf to 2dpf.For each replicate the heads of 150 embryos at 2 dpf were dissected flash frozen in liquid nitrogen.", "Total RNA was isolated and purified using TRIzol reagent Invitrogen Carlsbad CA USA following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND 1000 NanoDrop Wilmington DE USA. The RNA integrity was assessed by Bioanalyzer 2100 Agilent CA USA with RIN number >7.0 and confirmed by electrophoresis with denaturing agarose gel. Poly A RNA is purified from 1\u03bcg total RNA using Dynabeads Oligo dT25 61005 Thermo Fisher CA USA using two rounds of purification. Then the polyA RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module NEB cat.e6150 USA under 94\u2103 5 7min. Then the cleaved RNA fragments were reverse transcribed to create the cDNA by SuperScript\u2122 II Reverse Transcriptase Invitrogen cat. 1896649 USA which were next used to synthesise U labeled second stranded DNAs with E. coli DNA polymerase I NEB cat.m0209 USA RNase H NEB cat.m0297 USA and dUTP Solution Thermo Fisher cat.R0133 USA\uff09. An A base is then added to the blunt ends of each strand preparing them for ligation to the indexed adapters. Each adapter contains a T base overhang for ligating the adapter to the A tailed fragmented DNA. Single or dual index adapters are ligated to the fragments and size selection was performed with AMPureXP beads. post the heat labile UDG enzyme NEB cat.m0280 USA treatment of the U labeled second stranded DNAs the ligated products are amplified with PCR by the following conditions: initial denaturation at 95\u2103 for 3 min; 8 cycles of denaturation at 98\u2103 for 15 sec annealing at 60\u2103 for 15 sec and extension at 72\u2103 for 30 sec; and then final extension at 72\u2103 for 5 min. The average insert size for the final cDNA library was 300\u00b150 bp. At last we performed the 2\u00d7150bp paired end sequencing PE150 on an illumina Novaseq\u2122 6000 LC Bio Technology CO. Ltd. Hangzhou China following the vendor's recommended protocol.", "Embryos were collected and cultured in egg water 0.06 mg/mL sea salt 0.5 mg/L methylene blue and incubated before 24 hpf at 28\u00b0C. To inhibit pigmentation embryos were treated with 0.003% 1 phenyl 2 thiourea PTU Aladdin starting at 24 hpf.", "tissue:Brain|treatment:6PPD", "GSM8582552", "GSM8582552: 6PPD 2; Danio rerio; RNA Seq", "GSM8582552 r1", "GSM8582552", "1", "Total RNA was isolated and purified using TRIzol reagent Invitrogen Carlsbad CA USA following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND 1000 NanoDrop Wilmington DE USA. The RNA integrity was assessed by Bioanalyzer 2100 Agilent CA USA with RIN number >7.0 and confirmed by electrophoresis with denaturing agarose gel. Poly A RNA is purified from 1\u03bcg total RNA using Dynabeads Oligo dT25 61005 Thermo Fisher CA USA using two rounds of purification. Then the polyA RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module NEB cat.e6150 USA under 94\u2103 5 7min. Then the cleaved RNA fragments were reverse transcribed to create the cDNA by SuperScript\u2122 II Reverse Transcriptase Invitrogen cat. 1896649 USA which were next used to synthesise U labeled second stranded DNAs with E. coli DNA polymerase I NEB cat.m0209 USA RNase H NEB cat.m0297 USA and dUTP Solution Thermo Fisher cat.R0133 USA\uff09. An A base is then added to the blunt ends of each strand preparing them for ligation to the indexed adapters. Each adapter contains a T base overhang for ligating the adapter to the A tailed fragmented DNA. Single or dual index adapters are ligated to the fragments and size selection was performed with AMPureXP beads. post the heat labile UDG enzyme NEB cat.m0280 USA treatment of the U labeled second stranded DNAs the ligated products are amplified with PCR by the following conditions: initial denaturation at 95\u2103 for 3 min; 8 cycles of denaturation at 98\u2103 for 15 sec annealing at 60\u2103 for 15 sec and extension at 72\u2103 for 30 sec; and then final extension at 72\u2103 for 5 min. The average insert size for the final cDNA library was 300\u00b150 bp. At last we performed the 2\u00d7150bp paired end sequencing PE150 on an illumina Novaseq\u2122 6000 LC Bio Technology CO. Ltd. Hangzhou China following the vendor's recommended protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539617", null, null, "6PPD2head_Clean_Data1.fq.gz 6PPD2head_Clean_Data2.fq.gz", "fastq fastq", 6184525960.0, 20877930.0, "GSM8582552 r1", null, null, null, null, null, null, null, null, null, null, null, "SRX26432305", "SRS22949545", "SRA1994053", "Guizhou Medical University", "Guizhou Medical University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-10-19", "Multi-stage", "Embryo", "Brain", "Nervous System"], [34090, "SRR31047785", "SRX26432304", "SRS22949544", "SRP539617", "PRJNA1175041", "6PPD induces cerebrovascular defects by triggering oxidative stress and ferroptosis in zebrafish", "GSE279887", "Transcriptome Analysis", "N 1 3 dimethylbutyl N' phenyl p phenylenediamine 6PPD which is widely used as an antiozonant in rubber tires has recently got much attention for its acute aquatic toxicity. However the developmental toxicity of 6PPD in cerebrovascular network remains unknown. Here we investigated the effects of 6PPD exposure in cerebral vascular using the larvae of zebrafish. 6PPD would not affect the body length and shape of zebrafish larvae at the concentrations ranging from 20 \u00b5g/L to 1000 \u00b5g/L. 6PPD induced developmental defects in the brain in a concentration dependent manner. The trunk vascular development would not be affected while the cerebrovascular network was disrupted upon 6PPD exposure. 6PPD would trigger excessive Reactive Oxygen Species ROS in the brain indicating abnormal oxidative stress. Mechanistically brain specific transcriptome analysis showed that 6PPD could potentially cause the blockage of arachidonic acid AA metabolism related genes and the upregulation of ferroptosis related genes. Besides treatment with ferroptosis inhibitor N Acetyl L cysteine NAC attenuated oxidative damage and improved the construction of cerebrovascular network upon 6PPD exposure. Moreover using a human vascular endothelial cell line we further confirmed that 6PPD could trigger abnormal oxidative stress and defective expansion capacity implying the conserved toxicity cross species. These findings are useful for the elucidation of toxicity underlying 6PPD in cerebrovascular systems of both zebrafish and humans. Overall design: To investigate the effects of 6PPD on zebrafish development embryos were treated with 500 \u00b5g/L 6PPD from 10 hpf until 2 dpf dpf. For transcriptomic analysis three biological replicates were prepared for both the 6PPD treatment group and the DMSO control group. For each replicate the heads of 150 embryos at 2 dpf were dissected flash frozen in liquid nitrogen and sent for transcriptomic sequencing. The raw data analysis was performed to identify differentially expressed genes between the 6PPD treated and control groups.", null, null, null, "6PPD 1", "GSM8582551", null, "source name:Brain|tissue:Brain|treatment:6PPD|geo loc name:missing|collection date:missing", "6PPD 1", "Self house pipeline Sequence reads were trimmed for adaptor sequence/low quality seguence using fastp parameter Quality limit: 20 Trimmed sequence reads were mapped to GRCz11.109 use HISAT2 Read count extraction and normalization were performed using featureCounts and StringTie Assembly: GRCz11.109 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: tab delimited text files include FPKM values for each Sample", "Brain", "For transcriptomic analysis three biological replicates were prepared for both the 500 \u03bcg/L 6PPD treatment group and the DMSO control group. The embryos were treated from 10 hpf to 2dpf.For each replicate the heads of 150 embryos at 2 dpf were dissected flash frozen in liquid nitrogen.", "Total RNA was isolated and purified using TRIzol reagent Invitrogen Carlsbad CA USA following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND 1000 NanoDrop Wilmington DE USA. The RNA integrity was assessed by Bioanalyzer 2100 Agilent CA USA with RIN number >7.0 and confirmed by electrophoresis with denaturing agarose gel. Poly A RNA is purified from 1\u03bcg total RNA using Dynabeads Oligo dT25 61005 Thermo Fisher CA USA using two rounds of purification. Then the polyA RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module NEB cat.e6150 USA under 94\u2103 5 7min. Then the cleaved RNA fragments were reverse transcribed to create the cDNA by SuperScript\u2122 II Reverse Transcriptase Invitrogen cat. 1896649 USA which were next used to synthesise U labeled second stranded DNAs with E. coli DNA polymerase I NEB cat.m0209 USA RNase H NEB cat.m0297 USA and dUTP Solution Thermo Fisher cat.R0133 USA\uff09. An A base is then added to the blunt ends of each strand preparing them for ligation to the indexed adapters. Each adapter contains a T base overhang for ligating the adapter to the A tailed fragmented DNA. Single or dual index adapters are ligated to the fragments and size selection was performed with AMPureXP beads. post the heat labile UDG enzyme NEB cat.m0280 USA treatment of the U labeled second stranded DNAs the ligated products are amplified with PCR by the following conditions: initial denaturation at 95\u2103 for 3 min; 8 cycles of denaturation at 98\u2103 for 15 sec annealing at 60\u2103 for 15 sec and extension at 72\u2103 for 30 sec; and then final extension at 72\u2103 for 5 min. The average insert size for the final cDNA library was 300\u00b150 bp. At last we performed the 2\u00d7150bp paired end sequencing PE150 on an illumina Novaseq\u2122 6000 LC Bio Technology CO. Ltd. Hangzhou China following the vendor's recommended protocol.", "Embryos were collected and cultured in egg water 0.06 mg/mL sea salt 0.5 mg/L methylene blue and incubated before 24 hpf at 28\u00b0C. To inhibit pigmentation embryos were treated with 0.003% 1 phenyl 2 thiourea PTU Aladdin starting at 24 hpf.", "tissue:Brain|treatment:6PPD", "GSM8582551", "GSM8582551: 6PPD 1; Danio rerio; RNA Seq", "GSM8582551 r1", "GSM8582551", "1", "Total RNA was isolated and purified using TRIzol reagent Invitrogen Carlsbad CA USA following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND 1000 NanoDrop Wilmington DE USA. The RNA integrity was assessed by Bioanalyzer 2100 Agilent CA USA with RIN number >7.0 and confirmed by electrophoresis with denaturing agarose gel. Poly A RNA is purified from 1\u03bcg total RNA using Dynabeads Oligo dT25 61005 Thermo Fisher CA USA using two rounds of purification. Then the polyA RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module NEB cat.e6150 USA under 94\u2103 5 7min. Then the cleaved RNA fragments were reverse transcribed to create the cDNA by SuperScript\u2122 II Reverse Transcriptase Invitrogen cat. 1896649 USA which were next used to synthesise U labeled second stranded DNAs with E. coli DNA polymerase I NEB cat.m0209 USA RNase H NEB cat.m0297 USA and dUTP Solution Thermo Fisher cat.R0133 USA\uff09. An A base is then added to the blunt ends of each strand preparing them for ligation to the indexed adapters. Each adapter contains a T base overhang for ligating the adapter to the A tailed fragmented DNA. Single or dual index adapters are ligated to the fragments and size selection was performed with AMPureXP beads. post the heat labile UDG enzyme NEB cat.m0280 USA treatment of the U labeled second stranded DNAs the ligated products are amplified with PCR by the following conditions: initial denaturation at 95\u2103 for 3 min; 8 cycles of denaturation at 98\u2103 for 15 sec annealing at 60\u2103 for 15 sec and extension at 72\u2103 for 30 sec; and then final extension at 72\u2103 for 5 min. The average insert size for the final cDNA library was 300\u00b150 bp. At last we performed the 2\u00d7150bp paired end sequencing PE150 on an illumina Novaseq\u2122 6000 LC Bio Technology CO. Ltd. Hangzhou China following the vendor's recommended protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539617", null, null, "6PPD1head_Clean_Data1.fq.gz 6PPD1head_Clean_Data2.fq.gz", "fastq fastq", 5412472152.0, 18274114.0, "GSM8582551 r1", null, null, null, null, null, null, null, null, null, null, null, "SRX26432304", "SRS22949544", "SRA1994053", "Guizhou Medical University", "Guizhou Medical University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-10-19", "Multi-stage", "Embryo", "Brain", "Nervous System"], [34091, "SRR31047786", "SRX26432303", "SRS22949543", "SRP539617", "PRJNA1175041", "6PPD induces cerebrovascular defects by triggering oxidative stress and ferroptosis in zebrafish", "GSE279887", "Transcriptome Analysis", "N 1 3 dimethylbutyl N' phenyl p phenylenediamine 6PPD which is widely used as an antiozonant in rubber tires has recently got much attention for its acute aquatic toxicity. However the developmental toxicity of 6PPD in cerebrovascular network remains unknown. Here we investigated the effects of 6PPD exposure in cerebral vascular using the larvae of zebrafish. 6PPD would not affect the body length and shape of zebrafish larvae at the concentrations ranging from 20 \u00b5g/L to 1000 \u00b5g/L. 6PPD induced developmental defects in the brain in a concentration dependent manner. The trunk vascular development would not be affected while the cerebrovascular network was disrupted upon 6PPD exposure. 6PPD would trigger excessive Reactive Oxygen Species ROS in the brain indicating abnormal oxidative stress. Mechanistically brain specific transcriptome analysis showed that 6PPD could potentially cause the blockage of arachidonic acid AA metabolism related genes and the upregulation of ferroptosis related genes. Besides treatment with ferroptosis inhibitor N Acetyl L cysteine NAC attenuated oxidative damage and improved the construction of cerebrovascular network upon 6PPD exposure. Moreover using a human vascular endothelial cell line we further confirmed that 6PPD could trigger abnormal oxidative stress and defective expansion capacity implying the conserved toxicity cross species. These findings are useful for the elucidation of toxicity underlying 6PPD in cerebrovascular systems of both zebrafish and humans. Overall design: To investigate the effects of 6PPD on zebrafish development embryos were treated with 500 \u00b5g/L 6PPD from 10 hpf until 2 dpf dpf. For transcriptomic analysis three biological replicates were prepared for both the 6PPD treatment group and the DMSO control group. For each replicate the heads of 150 embryos at 2 dpf were dissected flash frozen in liquid nitrogen and sent for transcriptomic sequencing. The raw data analysis was performed to identify differentially expressed genes between the 6PPD treated and control groups.", null, null, null, "Con 3", "GSM8582550", null, "source name:Brain|tissue:Brain|treatment:DMSO|geo loc name:missing|collection date:missing", "Con 3", "Self house pipeline Sequence reads were trimmed for adaptor sequence/low quality seguence using fastp parameter Quality limit: 20 Trimmed sequence reads were mapped to GRCz11.109 use HISAT2 Read count extraction and normalization were performed using featureCounts and StringTie Assembly: GRCz11.109 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: tab delimited text files include FPKM values for each Sample", "Brain", "For transcriptomic analysis three biological replicates were prepared for both the 500 \u03bcg/L 6PPD treatment group and the DMSO control group. The embryos were treated from 10 hpf to 2dpf.For each replicate the heads of 150 embryos at 2 dpf were dissected flash frozen in liquid nitrogen.", "Total RNA was isolated and purified using TRIzol reagent Invitrogen Carlsbad CA USA following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND 1000 NanoDrop Wilmington DE USA. The RNA integrity was assessed by Bioanalyzer 2100 Agilent CA USA with RIN number >7.0 and confirmed by electrophoresis with denaturing agarose gel. Poly A RNA is purified from 1\u03bcg total RNA using Dynabeads Oligo dT25 61005 Thermo Fisher CA USA using two rounds of purification. Then the polyA RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module NEB cat.e6150 USA under 94\u2103 5 7min. Then the cleaved RNA fragments were reverse transcribed to create the cDNA by SuperScript\u2122 II Reverse Transcriptase Invitrogen cat. 1896649 USA which were next used to synthesise U labeled second stranded DNAs with E. coli DNA polymerase I NEB cat.m0209 USA RNase H NEB cat.m0297 USA and dUTP Solution Thermo Fisher cat.R0133 USA\uff09. An A base is then added to the blunt ends of each strand preparing them for ligation to the indexed adapters. Each adapter contains a T base overhang for ligating the adapter to the A tailed fragmented DNA. Single or dual index adapters are ligated to the fragments and size selection was performed with AMPureXP beads. post the heat labile UDG enzyme NEB cat.m0280 USA treatment of the U labeled second stranded DNAs the ligated products are amplified with PCR by the following conditions: initial denaturation at 95\u2103 for 3 min; 8 cycles of denaturation at 98\u2103 for 15 sec annealing at 60\u2103 for 15 sec and extension at 72\u2103 for 30 sec; and then final extension at 72\u2103 for 5 min. The average insert size for the final cDNA library was 300\u00b150 bp. At last we performed the 2\u00d7150bp paired end sequencing PE150 on an illumina Novaseq\u2122 6000 LC Bio Technology CO. Ltd. Hangzhou China following the vendor's recommended protocol.", "Embryos were collected and cultured in egg water 0.06 mg/mL sea salt 0.5 mg/L methylene blue and incubated before 24 hpf at 28\u00b0C. To inhibit pigmentation embryos were treated with 0.003% 1 phenyl 2 thiourea PTU Aladdin starting at 24 hpf.", "tissue:Brain|treatment:DMSO", "GSM8582550", "GSM8582550: Con 3; Danio rerio; RNA Seq", "GSM8582550 r1", "GSM8582550", "1", "Total RNA was isolated and purified using TRIzol reagent Invitrogen Carlsbad CA USA following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND 1000 NanoDrop Wilmington DE USA. The RNA integrity was assessed by Bioanalyzer 2100 Agilent CA USA with RIN number >7.0 and confirmed by electrophoresis with denaturing agarose gel. Poly A RNA is purified from 1\u03bcg total RNA using Dynabeads Oligo dT25 61005 Thermo Fisher CA USA using two rounds of purification. Then the polyA RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module NEB cat.e6150 USA under 94\u2103 5 7min. Then the cleaved RNA fragments were reverse transcribed to create the cDNA by SuperScript\u2122 II Reverse Transcriptase Invitrogen cat. 1896649 USA which were next used to synthesise U labeled second stranded DNAs with E. coli DNA polymerase I NEB cat.m0209 USA RNase H NEB cat.m0297 USA and dUTP Solution Thermo Fisher cat.R0133 USA\uff09. An A base is then added to the blunt ends of each strand preparing them for ligation to the indexed adapters. Each adapter contains a T base overhang for ligating the adapter to the A tailed fragmented DNA. Single or dual index adapters are ligated to the fragments and size selection was performed with AMPureXP beads. post the heat labile UDG enzyme NEB cat.m0280 USA treatment of the U labeled second stranded DNAs the ligated products are amplified with PCR by the following conditions: initial denaturation at 95\u2103 for 3 min; 8 cycles of denaturation at 98\u2103 for 15 sec annealing at 60\u2103 for 15 sec and extension at 72\u2103 for 30 sec; and then final extension at 72\u2103 for 5 min. The average insert size for the final cDNA library was 300\u00b150 bp. At last we performed the 2\u00d7150bp paired end sequencing PE150 on an illumina Novaseq\u2122 6000 LC Bio Technology CO. Ltd. Hangzhou China following the vendor's recommended protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539617", null, null, "Con3head_Clean_Data1.fq.gz Con3head_Clean_Data2.fq.gz", "fastq fastq", 6118959402.0, 20641047.0, "GSM8582550 r1", null, null, null, null, null, null, null, null, null, null, null, "SRX26432303", "SRS22949543", "SRA1994053", "Guizhou Medical University", "Guizhou Medical University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-10-19", "Multi-stage", "Embryo", "Brain", "Nervous System"], [34092, "SRR31047787", "SRX26432302", "SRS22949542", "SRP539617", "PRJNA1175041", "6PPD induces cerebrovascular defects by triggering oxidative stress and ferroptosis in zebrafish", "GSE279887", "Transcriptome Analysis", "N 1 3 dimethylbutyl N' phenyl p phenylenediamine 6PPD which is widely used as an antiozonant in rubber tires has recently got much attention for its acute aquatic toxicity. However the developmental toxicity of 6PPD in cerebrovascular network remains unknown. Here we investigated the effects of 6PPD exposure in cerebral vascular using the larvae of zebrafish. 6PPD would not affect the body length and shape of zebrafish larvae at the concentrations ranging from 20 \u00b5g/L to 1000 \u00b5g/L. 6PPD induced developmental defects in the brain in a concentration dependent manner. The trunk vascular development would not be affected while the cerebrovascular network was disrupted upon 6PPD exposure. 6PPD would trigger excessive Reactive Oxygen Species ROS in the brain indicating abnormal oxidative stress. Mechanistically brain specific transcriptome analysis showed that 6PPD could potentially cause the blockage of arachidonic acid AA metabolism related genes and the upregulation of ferroptosis related genes. Besides treatment with ferroptosis inhibitor N Acetyl L cysteine NAC attenuated oxidative damage and improved the construction of cerebrovascular network upon 6PPD exposure. Moreover using a human vascular endothelial cell line we further confirmed that 6PPD could trigger abnormal oxidative stress and defective expansion capacity implying the conserved toxicity cross species. These findings are useful for the elucidation of toxicity underlying 6PPD in cerebrovascular systems of both zebrafish and humans. Overall design: To investigate the effects of 6PPD on zebrafish development embryos were treated with 500 \u00b5g/L 6PPD from 10 hpf until 2 dpf dpf. For transcriptomic analysis three biological replicates were prepared for both the 6PPD treatment group and the DMSO control group. For each replicate the heads of 150 embryos at 2 dpf were dissected flash frozen in liquid nitrogen and sent for transcriptomic sequencing. The raw data analysis was performed to identify differentially expressed genes between the 6PPD treated and control groups.", null, null, null, "Con 2", "GSM8582549", null, "source name:Brain|tissue:Brain|treatment:DMSO|geo loc name:missing|collection date:missing", "Con 2", "Self house pipeline Sequence reads were trimmed for adaptor sequence/low quality seguence using fastp parameter Quality limit: 20 Trimmed sequence reads were mapped to GRCz11.109 use HISAT2 Read count extraction and normalization were performed using featureCounts and StringTie Assembly: GRCz11.109 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: tab delimited text files include FPKM values for each Sample", "Brain", "For transcriptomic analysis three biological replicates were prepared for both the 500 \u03bcg/L 6PPD treatment group and the DMSO control group. The embryos were treated from 10 hpf to 2dpf.For each replicate the heads of 150 embryos at 2 dpf were dissected flash frozen in liquid nitrogen.", "Total RNA was isolated and purified using TRIzol reagent Invitrogen Carlsbad CA USA following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND 1000 NanoDrop Wilmington DE USA. The RNA integrity was assessed by Bioanalyzer 2100 Agilent CA USA with RIN number >7.0 and confirmed by electrophoresis with denaturing agarose gel. Poly A RNA is purified from 1\u03bcg total RNA using Dynabeads Oligo dT25 61005 Thermo Fisher CA USA using two rounds of purification. Then the polyA RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module NEB cat.e6150 USA under 94\u2103 5 7min. Then the cleaved RNA fragments were reverse transcribed to create the cDNA by SuperScript\u2122 II Reverse Transcriptase Invitrogen cat. 1896649 USA which were next used to synthesise U labeled second stranded DNAs with E. coli DNA polymerase I NEB cat.m0209 USA RNase H NEB cat.m0297 USA and dUTP Solution Thermo Fisher cat.R0133 USA\uff09. An A base is then added to the blunt ends of each strand preparing them for ligation to the indexed adapters. Each adapter contains a T base overhang for ligating the adapter to the A tailed fragmented DNA. Single or dual index adapters are ligated to the fragments and size selection was performed with AMPureXP beads. post the heat labile UDG enzyme NEB cat.m0280 USA treatment of the U labeled second stranded DNAs the ligated products are amplified with PCR by the following conditions: initial denaturation at 95\u2103 for 3 min; 8 cycles of denaturation at 98\u2103 for 15 sec annealing at 60\u2103 for 15 sec and extension at 72\u2103 for 30 sec; and then final extension at 72\u2103 for 5 min. The average insert size for the final cDNA library was 300\u00b150 bp. At last we performed the 2\u00d7150bp paired end sequencing PE150 on an illumina Novaseq\u2122 6000 LC Bio Technology CO. Ltd. Hangzhou China following the vendor's recommended protocol.", "Embryos were collected and cultured in egg water 0.06 mg/mL sea salt 0.5 mg/L methylene blue and incubated before 24 hpf at 28\u00b0C. To inhibit pigmentation embryos were treated with 0.003% 1 phenyl 2 thiourea PTU Aladdin starting at 24 hpf.", "tissue:Brain|treatment:DMSO", "GSM8582549", "GSM8582549: Con 2; Danio rerio; RNA Seq", "GSM8582549 r1", "GSM8582549", "1", "Total RNA was isolated and purified using TRIzol reagent Invitrogen Carlsbad CA USA following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND 1000 NanoDrop Wilmington DE USA. The RNA integrity was assessed by Bioanalyzer 2100 Agilent CA USA with RIN number >7.0 and confirmed by electrophoresis with denaturing agarose gel. Poly A RNA is purified from 1\u03bcg total RNA using Dynabeads Oligo dT25 61005 Thermo Fisher CA USA using two rounds of purification. Then the polyA RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module NEB cat.e6150 USA under 94\u2103 5 7min. Then the cleaved RNA fragments were reverse transcribed to create the cDNA by SuperScript\u2122 II Reverse Transcriptase Invitrogen cat. 1896649 USA which were next used to synthesise U labeled second stranded DNAs with E. coli DNA polymerase I NEB cat.m0209 USA RNase H NEB cat.m0297 USA and dUTP Solution Thermo Fisher cat.R0133 USA\uff09. An A base is then added to the blunt ends of each strand preparing them for ligation to the indexed adapters. Each adapter contains a T base overhang for ligating the adapter to the A tailed fragmented DNA. Single or dual index adapters are ligated to the fragments and size selection was performed with AMPureXP beads. post the heat labile UDG enzyme NEB cat.m0280 USA treatment of the U labeled second stranded DNAs the ligated products are amplified with PCR by the following conditions: initial denaturation at 95\u2103 for 3 min; 8 cycles of denaturation at 98\u2103 for 15 sec annealing at 60\u2103 for 15 sec and extension at 72\u2103 for 30 sec; and then final extension at 72\u2103 for 5 min. The average insert size for the final cDNA library was 300\u00b150 bp. At last we performed the 2\u00d7150bp paired end sequencing PE150 on an illumina Novaseq\u2122 6000 LC Bio Technology CO. Ltd. Hangzhou China following the vendor's recommended protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539617", null, null, "Con2head_Clean_Data1.fq.gz Con2head_Clean_Data2.fq.gz", "fastq fastq", 5778620515.0, 19519984.0, "GSM8582549 r1", null, null, null, null, null, null, null, null, null, null, null, "SRX26432302", "SRS22949542", "SRA1994053", "Guizhou Medical University", "Guizhou Medical University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-10-19", "Multi-stage", "Embryo", "Brain", "Nervous System"], [34093, "SRR31047788", "SRX26432301", "SRS22949541", "SRP539617", "PRJNA1175041", "6PPD induces cerebrovascular defects by triggering oxidative stress and ferroptosis in zebrafish", "GSE279887", "Transcriptome Analysis", "N 1 3 dimethylbutyl N' phenyl p phenylenediamine 6PPD which is widely used as an antiozonant in rubber tires has recently got much attention for its acute aquatic toxicity. However the developmental toxicity of 6PPD in cerebrovascular network remains unknown. Here we investigated the effects of 6PPD exposure in cerebral vascular using the larvae of zebrafish. 6PPD would not affect the body length and shape of zebrafish larvae at the concentrations ranging from 20 \u00b5g/L to 1000 \u00b5g/L. 6PPD induced developmental defects in the brain in a concentration dependent manner. The trunk vascular development would not be affected while the cerebrovascular network was disrupted upon 6PPD exposure. 6PPD would trigger excessive Reactive Oxygen Species ROS in the brain indicating abnormal oxidative stress. Mechanistically brain specific transcriptome analysis showed that 6PPD could potentially cause the blockage of arachidonic acid AA metabolism related genes and the upregulation of ferroptosis related genes. Besides treatment with ferroptosis inhibitor N Acetyl L cysteine NAC attenuated oxidative damage and improved the construction of cerebrovascular network upon 6PPD exposure. Moreover using a human vascular endothelial cell line we further confirmed that 6PPD could trigger abnormal oxidative stress and defective expansion capacity implying the conserved toxicity cross species. These findings are useful for the elucidation of toxicity underlying 6PPD in cerebrovascular systems of both zebrafish and humans. Overall design: To investigate the effects of 6PPD on zebrafish development embryos were treated with 500 \u00b5g/L 6PPD from 10 hpf until 2 dpf dpf. For transcriptomic analysis three biological replicates were prepared for both the 6PPD treatment group and the DMSO control group. For each replicate the heads of 150 embryos at 2 dpf were dissected flash frozen in liquid nitrogen and sent for transcriptomic sequencing. The raw data analysis was performed to identify differentially expressed genes between the 6PPD treated and control groups.", null, null, null, "Con 1", "GSM8582548", null, "source name:Brain|tissue:Brain|treatment:DMSO|geo loc name:missing|collection date:missing", "Con 1", "Self house pipeline Sequence reads were trimmed for adaptor sequence/low quality seguence using fastp parameter Quality limit: 20 Trimmed sequence reads were mapped to GRCz11.109 use HISAT2 Read count extraction and normalization were performed using featureCounts and StringTie Assembly: GRCz11.109 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: tab delimited text files include FPKM values for each Sample", "Brain", "For transcriptomic analysis three biological replicates were prepared for both the 500 \u03bcg/L 6PPD treatment group and the DMSO control group. The embryos were treated from 10 hpf to 2dpf.For each replicate the heads of 150 embryos at 2 dpf were dissected flash frozen in liquid nitrogen.", "Total RNA was isolated and purified using TRIzol reagent Invitrogen Carlsbad CA USA following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND 1000 NanoDrop Wilmington DE USA. The RNA integrity was assessed by Bioanalyzer 2100 Agilent CA USA with RIN number >7.0 and confirmed by electrophoresis with denaturing agarose gel. Poly A RNA is purified from 1\u03bcg total RNA using Dynabeads Oligo dT25 61005 Thermo Fisher CA USA using two rounds of purification. Then the polyA RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module NEB cat.e6150 USA under 94\u2103 5 7min. Then the cleaved RNA fragments were reverse transcribed to create the cDNA by SuperScript\u2122 II Reverse Transcriptase Invitrogen cat. 1896649 USA which were next used to synthesise U labeled second stranded DNAs with E. coli DNA polymerase I NEB cat.m0209 USA RNase H NEB cat.m0297 USA and dUTP Solution Thermo Fisher cat.R0133 USA\uff09. An A base is then added to the blunt ends of each strand preparing them for ligation to the indexed adapters. Each adapter contains a T base overhang for ligating the adapter to the A tailed fragmented DNA. Single or dual index adapters are ligated to the fragments and size selection was performed with AMPureXP beads. post the heat labile UDG enzyme NEB cat.m0280 USA treatment of the U labeled second stranded DNAs the ligated products are amplified with PCR by the following conditions: initial denaturation at 95\u2103 for 3 min; 8 cycles of denaturation at 98\u2103 for 15 sec annealing at 60\u2103 for 15 sec and extension at 72\u2103 for 30 sec; and then final extension at 72\u2103 for 5 min. The average insert size for the final cDNA library was 300\u00b150 bp. At last we performed the 2\u00d7150bp paired end sequencing PE150 on an illumina Novaseq\u2122 6000 LC Bio Technology CO. Ltd. Hangzhou China following the vendor's recommended protocol.", "Embryos were collected and cultured in egg water 0.06 mg/mL sea salt 0.5 mg/L methylene blue and incubated before 24 hpf at 28\u00b0C. To inhibit pigmentation embryos were treated with 0.003% 1 phenyl 2 thiourea PTU Aladdin starting at 24 hpf.", "tissue:Brain|treatment:DMSO", "GSM8582548", "GSM8582548: Con 1; Danio rerio; RNA Seq", "GSM8582548 r1", "GSM8582548", "1", "Total RNA was isolated and purified using TRIzol reagent Invitrogen Carlsbad CA USA following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND 1000 NanoDrop Wilmington DE USA. The RNA integrity was assessed by Bioanalyzer 2100 Agilent CA USA with RIN number >7.0 and confirmed by electrophoresis with denaturing agarose gel. Poly A RNA is purified from 1\u03bcg total RNA using Dynabeads Oligo dT25 61005 Thermo Fisher CA USA using two rounds of purification. Then the polyA RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module NEB cat.e6150 USA under 94\u2103 5 7min. Then the cleaved RNA fragments were reverse transcribed to create the cDNA by SuperScript\u2122 II Reverse Transcriptase Invitrogen cat. 1896649 USA which were next used to synthesise U labeled second stranded DNAs with E. coli DNA polymerase I NEB cat.m0209 USA RNase H NEB cat.m0297 USA and dUTP Solution Thermo Fisher cat.R0133 USA\uff09. An A base is then added to the blunt ends of each strand preparing them for ligation to the indexed adapters. Each adapter contains a T base overhang for ligating the adapter to the A tailed fragmented DNA. Single or dual index adapters are ligated to the fragments and size selection was performed with AMPureXP beads. post the heat labile UDG enzyme NEB cat.m0280 USA treatment of the U labeled second stranded DNAs the ligated products are amplified with PCR by the following conditions: initial denaturation at 95\u2103 for 3 min; 8 cycles of denaturation at 98\u2103 for 15 sec annealing at 60\u2103 for 15 sec and extension at 72\u2103 for 30 sec; and then final extension at 72\u2103 for 5 min. The average insert size for the final cDNA library was 300\u00b150 bp. At last we performed the 2\u00d7150bp paired end sequencing PE150 on an illumina Novaseq\u2122 6000 LC Bio Technology CO. Ltd. Hangzhou China following the vendor's recommended protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539617", null, null, "Con1head_Clean_Data1.fq.gz Con1head_Clean_Data2.fq.gz", "fastq fastq", 5538973366.0, 18707123.0, "GSM8582548 r1", null, null, null, null, null, null, null, null, null, null, null, "SRX26432301", "SRS22949541", "SRA1994053", "Guizhou Medical University", "Guizhou Medical University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-10-19", "Multi-stage", "Embryo", "Brain", "Nervous System"], [34547, "SRR32092978", "SRX27440700", "SRS23867512", "SRP559408", "PRJNA1214750", "Reactivation of an Embryonic Cardiac Neural Crest Transcriptional Subcircuit During Zebrafish Heart Regeneration [scRNA seq]", "GSE287811", "Other", "During vertebrate development the heart primarily arises from mesoderm with crucial contributions from cardiac neural crest cells that migrate to the heart and form a variety of cardiovascular derivatives. Here by integrating bulk and single cell RNAseq with ATAC seq we identify a gene regulatory subcircuit specific to migratory cardiac crest cells composed of key transcription factors egr1 sox9a tfap2a and ets1. Notably we show that cells expressing the canonical neural crest gene sox10 are essential for proper cardiac regeneration in adult zebrafish. Furthermore expression of all transcription factors from the migratory cardiac crest gene subcircuit are xxx post injury at the wound edge. Together our results uncover a developmental gene regulatory network that is important for cardiac neural crest fate determination with key factors re activated during regeneration. Overall design: mcherry+ cells from 16 somite stage zebrafish embryos migratory cardiac neural crest stage were FAC sorted from Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP and analyzed using 10X Chromium Single Cell three prime v3.1 sequencing.", null, null, null, "mch+ CdNC cells from 16ss zebrafish embryos", "GSM8751763", null, "source name:midbrain hindbrain boundary to somite 6|tissue:midbrain hindbrain boundary to somite 6|transgenic line:Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP|cell type:Cardiac Neural Crest|age:16 somite stage|geo loc name:missing|collection date:missing", "mch+ CdNC cells from 16ss zebrafish embryos", "Reads were mapped to GRCz11 and initial quality control was performed using Cell Ranger v7.20. Scanpy was used for further quality control filtering clustering and downstream analysis. Assembly: GRCz11 Supplementary files format and content: tab separated barcodes and features files as well as matrix file.", "midbrain hindbrain boundary to somite 6", null, "mch+ CdNC cells from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos were dissected dissociated and FAC sorted. Single cell libraries were prepared using the Chromium Single Cell 3\u2019 v3.1 reagent kit 10X Genomics PN 1000075 according to manufacturer's protocol.", null, "tissue:midbrain hindbrain boundary to somite 6|transgenic line:Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP|cell type:Cardiac Neural Crest|age:16 somite stage", "GSM8751763", "GSM8751763: mch+ CdNC cells from 16ss zebrafish embryos; Danio rerio; RNA Seq", "GSM8751763 r1", "GSM8751763", "1", "mch+ CdNC cells from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos were dissected dissociated and FAC sorted. Single cell libraries were prepared using the Chromium Single Cell three prime v3.1 reagent kit 10X Genomics PN 1000075 according to manufacturer's protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP559408", null, null, "SE6898_SA80357_S1_L001_R1_001.fastq.gz SE6898_SA80357_S1_L001_R2_001.fastq.gz", "fastq fastq", 71160584348.0, 235631074.0, "GSM8751763 r1", "0:151 1:151", "A:17520054424;C:13126677931;G:14006245844;T:26493745251;N:13860898", 151, 151, null, null, 17520054424, 13126677931, 14006245844, 26493745251, 13860898, "SRX27440700", "SRS23867512", "SRA2058075", "Martik Lab, Molecular and Cell Biology, University of California Berkeley", "Martik Lab, Molecular and Cell Biology, University of California Berkeley", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2025-01-23", "Segmentation", "Embryo", "Brain", "Nervous System"], [34554, "SRR32104359", "SRX27449951", "SRS23876473", "SRP559533", "PRJNA1214751", "Reactivation of an Embryonic Cardiac Neural Crest Transcriptional Subcircuit During Zebrafish Heart Regeneration [bulk RNA seq]", "GSE287815", "Transcriptome Analysis", "During vertebrate development the heart primarily arises from mesoderm with crucial contributions from cardiac neural crest cells that migrate to the heart and form a variety of cardiovascular derivatives. Here by integrating bulk and single cell RNAseq with ATAC seq we identify a gene regulatory subcircuit specific to migratory cardiac crest cells composed of key transcription factors egr1 sox9a tfap2a and ets1. Notably we show that cells expressing the canonical neural crest gene sox10 are essential for proper cardiac regeneration in adult zebrafish. Furthermore expression of all transcription factors from the migratory cardiac crest gene subcircuit are xxx post injury at the wound edge. Together our results uncover a developmental gene regulatory network that is important for cardiac neural crest fate determination with key factors re activated during regeneration. Overall design: Migratory cardiac neural crest cells mcherry + and non neural crest cells from the same tissue mcherry were FAC sorted from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos. Migratory trunk neural crest cells GFP + were FAC sorted from 24hpf Tg 4.9sox10:eGFP embryos.", null, null, null, "17hpf Negative CNC 3", "GSM8751784", null, "source name:non neural crest from midbrain hindbrain boundary to somite 6|tissue:non neural crest from midbrain hindbrain boundary to somite 6|cell type:non neural crest|transgenic line:Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP|age:16 somite stage 17hpf|fluorophore:mcherry |geo loc name:missing|collection date:missing", "17hpf Negative CNC 3", "Reads were mapped zebrafish genome GRCz10 using Bowtie 2. Transcript counts were determined using featureCounts Subread. Differential gene expression was performed using DEseq. Assembly: GRCz10 Supplementary files format and content: tab delimited text file included for cardiac neural crest and non neural crest samples", "non neural crest from midbrain hindbrain boundary to somite 6", null, "mch+ CdNC cells and mch non neural crest cells from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos were dissected dissociated and FAC sorted. GFP+ cells were sorted from 24hpf Tg 4.9sox10:eGFP embryos were dissected dissociated and FAC sorted. Tissues were dissociated in Accumax and then sorted BD FACSAria\u2122 Fusion Flow Cytometer. cDNA was prepared from each sample using the SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit. Standard Illumina protocols were used to construct each sequencing library and an Illumina HiSeq2500 sequencer at the Millard and Muriel Jacobs Genetics and Genomics Laboratory California Institute of Technology Pasadena CA for 50 million single ended reads.", null, "tissue:non neural crest from midbrain hindbrain boundary to somite 6|cell type:non neural crest|transgenic line:Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP|age:16 somite stage 17hpf|fluorophore:mcherry ", "GSM8751784", "GSM8751784: 17hpf Negative CNC 3; Danio rerio; RNA Seq", "GSM8751784 r1", "GSM8751784", "1", "mch+ CdNC cells and mch non neural crest cells from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos were dissected dissociated and FAC sorted. GFP+ cells were sorted from 24hpf Tg 4.9sox10:eGFP embryos were dissected dissociated and FAC sorted. Tissues were dissociated in Accumax and then sorted BD FACSAria\u2122 Fusion Flow Cytometer. cDNA was prepared from each sample using the SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit. Standard Illumina protocols were used to construct each sequencing library and an Illumina HiSeq2500 sequencer at the Millard and Muriel Jacobs Genetics and Genomics Laboratory California Institute of Technology Pasadena CA for 50 million single ended reads.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP559533", null, null, "Sox10_neg_17hpf_CNC_3_22029_combined_filtered.fastq.gz", "fastq", 6549316700.0, 65493167.0, "GSM8751784 r1", "0:100", "A:1904137226;C:1372226751;G:1395882591;T:1876995541;N:74591", 100, null, null, null, 1904137226, 1372226751, 1395882591, 1876995541, 74591, "SRX27449951", "SRS23876473", "SRA2058978", "Martik Lab, Molecular and Cell Biology, University of California Berkeley", "Martik Lab, Molecular and Cell Biology, University of California Berkeley", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2025-01-23", "Segmentation", "Embryo", "Brain", "Nervous System"], [34555, "SRR32104360", "SRX27449950", "SRS23876471", "SRP559533", "PRJNA1214751", "Reactivation of an Embryonic Cardiac Neural Crest Transcriptional Subcircuit During Zebrafish Heart Regeneration [bulk RNA seq]", "GSE287815", "Transcriptome Analysis", "During vertebrate development the heart primarily arises from mesoderm with crucial contributions from cardiac neural crest cells that migrate to the heart and form a variety of cardiovascular derivatives. Here by integrating bulk and single cell RNAseq with ATAC seq we identify a gene regulatory subcircuit specific to migratory cardiac crest cells composed of key transcription factors egr1 sox9a tfap2a and ets1. Notably we show that cells expressing the canonical neural crest gene sox10 are essential for proper cardiac regeneration in adult zebrafish. Furthermore expression of all transcription factors from the migratory cardiac crest gene subcircuit are xxx post injury at the wound edge. Together our results uncover a developmental gene regulatory network that is important for cardiac neural crest fate determination with key factors re activated during regeneration. Overall design: Migratory cardiac neural crest cells mcherry + and non neural crest cells from the same tissue mcherry were FAC sorted from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos. Migratory trunk neural crest cells GFP + were FAC sorted from 24hpf Tg 4.9sox10:eGFP embryos.", null, null, null, "17hpf Negative CNC 2", "GSM8751783", null, "source name:non neural crest from midbrain hindbrain boundary to somite 6|tissue:non neural crest from midbrain hindbrain boundary to somite 6|cell type:non neural crest|transgenic line:Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP|age:16 somite stage 17hpf|fluorophore:mcherry |geo loc name:missing|collection date:missing", "17hpf Negative CNC 2", "Reads were mapped zebrafish genome GRCz10 using Bowtie 2. Transcript counts were determined using featureCounts Subread. Differential gene expression was performed using DEseq. Assembly: GRCz10 Supplementary files format and content: tab delimited text file included for cardiac neural crest and non neural crest samples", "non neural crest from midbrain hindbrain boundary to somite 6", null, "mch+ CdNC cells and mch non neural crest cells from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos were dissected dissociated and FAC sorted. GFP+ cells were sorted from 24hpf Tg 4.9sox10:eGFP embryos were dissected dissociated and FAC sorted. Tissues were dissociated in Accumax and then sorted BD FACSAria\u2122 Fusion Flow Cytometer. cDNA was prepared from each sample using the SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit. Standard Illumina protocols were used to construct each sequencing library and an Illumina HiSeq2500 sequencer at the Millard and Muriel Jacobs Genetics and Genomics Laboratory California Institute of Technology Pasadena CA for 50 million single ended reads.", null, "tissue:non neural crest from midbrain hindbrain boundary to somite 6|cell type:non neural crest|transgenic line:Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP|age:16 somite stage 17hpf|fluorophore:mcherry ", "GSM8751783", "GSM8751783: 17hpf Negative CNC 2; Danio rerio; RNA Seq", "GSM8751783 r1", "GSM8751783", "1", "mch+ CdNC cells and mch non neural crest cells from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos were dissected dissociated and FAC sorted. GFP+ cells were sorted from 24hpf Tg 4.9sox10:eGFP embryos were dissected dissociated and FAC sorted. Tissues were dissociated in Accumax and then sorted BD FACSAria\u2122 Fusion Flow Cytometer. cDNA was prepared from each sample using the SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit. Standard Illumina protocols were used to construct each sequencing library and an Illumina HiSeq2500 sequencer at the Millard and Muriel Jacobs Genetics and Genomics Laboratory California Institute of Technology Pasadena CA for 50 million single ended reads.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP559533", null, null, "Sox10_neg_17hpf_CNC_2_21339_combined_filtered.fastq.gz", "fastq", 2595442300.0, 51908846.0, "GSM8751783 r1", "0:50", "A:735396784;C:561568693;G:572114011;T:726356371;N:6441", 50, null, null, null, 735396784, 561568693, 572114011, 726356371, 6441, "SRX27449950", "SRS23876471", "SRA2058978", "Martik Lab, Molecular and Cell Biology, University of California Berkeley", "Martik Lab, Molecular and Cell Biology, University of California Berkeley", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2025-01-23", "Segmentation", "Embryo", "Brain", "Nervous System"], [34556, "SRR32104361", "SRX27449949", "SRS23876470", "SRP559533", "PRJNA1214751", "Reactivation of an Embryonic Cardiac Neural Crest Transcriptional Subcircuit During Zebrafish Heart Regeneration [bulk RNA seq]", "GSE287815", "Transcriptome Analysis", "During vertebrate development the heart primarily arises from mesoderm with crucial contributions from cardiac neural crest cells that migrate to the heart and form a variety of cardiovascular derivatives. Here by integrating bulk and single cell RNAseq with ATAC seq we identify a gene regulatory subcircuit specific to migratory cardiac crest cells composed of key transcription factors egr1 sox9a tfap2a and ets1. Notably we show that cells expressing the canonical neural crest gene sox10 are essential for proper cardiac regeneration in adult zebrafish. Furthermore expression of all transcription factors from the migratory cardiac crest gene subcircuit are xxx post injury at the wound edge. Together our results uncover a developmental gene regulatory network that is important for cardiac neural crest fate determination with key factors re activated during regeneration. Overall design: Migratory cardiac neural crest cells mcherry + and non neural crest cells from the same tissue mcherry were FAC sorted from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos. Migratory trunk neural crest cells GFP + were FAC sorted from 24hpf Tg 4.9sox10:eGFP embryos.", null, null, null, "17hpf Negative CNC 1", "GSM8751782", null, "source name:non neural crest from midbrain hindbrain boundary to somite 6|tissue:non neural crest from midbrain hindbrain boundary to somite 6|cell type:non neural crest|transgenic line:Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP|age:16 somite stage 17hpf|fluorophore:mcherry |geo loc name:missing|collection date:missing", "17hpf Negative CNC 1", "Reads were mapped zebrafish genome GRCz10 using Bowtie 2. Transcript counts were determined using featureCounts Subread. Differential gene expression was performed using DEseq. Assembly: GRCz10 Supplementary files format and content: tab delimited text file included for cardiac neural crest and non neural crest samples", "non neural crest from midbrain hindbrain boundary to somite 6", null, "mch+ CdNC cells and mch non neural crest cells from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos were dissected dissociated and FAC sorted. GFP+ cells were sorted from 24hpf Tg 4.9sox10:eGFP embryos were dissected dissociated and FAC sorted. Tissues were dissociated in Accumax and then sorted BD FACSAria\u2122 Fusion Flow Cytometer. cDNA was prepared from each sample using the SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit. Standard Illumina protocols were used to construct each sequencing library and an Illumina HiSeq2500 sequencer at the Millard and Muriel Jacobs Genetics and Genomics Laboratory California Institute of Technology Pasadena CA for 50 million single ended reads.", null, "tissue:non neural crest from midbrain hindbrain boundary to somite 6|cell type:non neural crest|transgenic line:Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP|age:16 somite stage 17hpf|fluorophore:mcherry ", "GSM8751782", "GSM8751782: 17hpf Negative CNC 1; Danio rerio; RNA Seq", "GSM8751782 r1", "GSM8751782", "1", "mch+ CdNC cells and mch non neural crest cells from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos were dissected dissociated and FAC sorted. GFP+ cells were sorted from 24hpf Tg 4.9sox10:eGFP embryos were dissected dissociated and FAC sorted. Tissues were dissociated in Accumax and then sorted BD FACSAria\u2122 Fusion Flow Cytometer. cDNA was prepared from each sample using the SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit. Standard Illumina protocols were used to construct each sequencing library and an Illumina HiSeq2500 sequencer at the Millard and Muriel Jacobs Genetics and Genomics Laboratory California Institute of Technology Pasadena CA for 50 million single ended reads.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP559533", null, null, "Sox10_neg_17hpf_CNC_1_21310_combined_filtered.fastq.gz", "fastq", 2554400850.0, 51088017.0, "GSM8751782 r1", "0:50", "A:739730182;C:537827580;G:551508245;T:725296198;N:38645", 50, null, null, null, 739730182, 537827580, 551508245, 725296198, 38645, "SRX27449949", "SRS23876470", "SRA2058978", "Martik Lab, Molecular and Cell Biology, University of California Berkeley", "Martik Lab, Molecular and Cell Biology, University of California Berkeley", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2025-01-23", "Segmentation", "Embryo", "Brain", "Nervous System"], [35385, "SRR32649448", "SRX27953870", "SRS24319775", "SRP569567", "PRJNA1234533", "Delta family protocadhins contribute to protoglomerular targeting of olfactory sensory neuron axons in the olfactory bulb", "GSE291626", "Transcriptome Analysis", "To understand how neural circuits are assembled it is essential to identify and characterize the axonal guidance cues and receptors that determine the axonal trajectories and connections between neurons. We performed single cell RNA sequencing of olfactory sensory neurons from zebrafish to identify candidate axonal guidance related genes that are differentially expressed according to sensory axon target location in the olfactory bulb. Among the candidates we identified were several members of the non clustered delta protocadherin family of adhesion molecules. We found that two members of the delta1 protocadherin family pcdh7b and pcdh11 are most highly expressed in sensory neurons that project to the DZ protoglomerulus. Knocking down either one impairs the ability of sensory axons to terminate within the DZ protoglomerulus but does not affect the ability of other sensory axons from terminating normally in the CZ protoglomerulus. In contrast two members of the delta2 protocadherin family pcdh10b and pcdh17 are most highly expressed in sensory neurons that project to the CZ protoglomerulus. Knocking down pcdh10b induces ectopic terminations of CZ projecting sensory axons. Knocking down pcdh17 induces substantial ectopic axonal trajectories and impairs CZ projecting sensory axons from finding and terminating in the CZ protoglomerulus. Knockdowns of either pcdh10b or pcdh17 do not affect DZ projecting sensory axons. These findings suggest that delta1 protocadherins help DZ projecting sensory axons enter and remain within the DZ protoglomerulus while delta2 protocadherins help CZ projecting sensory axons navigate to the CZ protoglomerulus. Overall design: Roughly 2000 zebrafish embryos we sacraficed at 36 48 hpf and 72 hpf. Olfactory tissue was dissociated in FACSmax dissosciation medium and then FACsorted to isolate OMP:RFP positive neurons.", null, null, null, "OMP positive Olfactory Sensory Neurons from 48pf Zebrafish", "GSM8838717", null, "source name:Olfactory Sensory Tissue|tissue:Olfactory Sensory Tissue|cell line:Olactory Sensory Neurons|cell type:Neurons|sample age:48 hpf|genotype:Tgomp:lyn RFP|geo loc name:missing|collection date:missing", "OMP positive Olfactory Sensory Neurons from 48pf Zebrafish", "Cell Ranger V3.0.1 Assembly: GRCz11 Supplementary files format and content: Demultiplexed 10x Genomics Files.", "Olfactory Sensory Tissue", null, "10X Genomics V3.3", null, "tissue:Olfactory Sensory Tissue|cell line:Olactory Sensory Neurons|cell type:Neurons|sample age:48 hpf|genotype:Tgomp:lyn RFP", "GSM8838717", "GSM8838717: OMP positive Olfactory Sensory Neurons from 48pf Zebrafish; Danio rerio; RNA Seq", "GSM8838717 r1", "GSM8838717", "1", "10X Genomics V3.3", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP569567", null, "loader:fastq load.py", "97364_S5_L001_I1_001.fastq.gz 97364_S5_L001_R1_001.fastq.gz 97364_S5_L001_R2_001.fastq.gz", "fastq fastq fastq", 7455743360.0, 57351872.0, "GSM8838717 r1", "0:8 1:28 2:94", "A:1588619193;C:1118423731;G:1232237797;T:1451670240;N:125007", 8, 28, 94, null, 1588619193, 1118423731, 1232237797, 1451670240, 125007, "SRX27953870", "SRS24319775", "SRA2091725", "Department of Neuroscience, University of Pennsylvania", "Department of Neuroscience, University of Pennsylvania", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2025-03-11", "Hatching", "Embryo", "Brain", "Nervous System"], [35386, "SRR32649449", "SRX27953870", "SRS24319775", "SRP569567", "PRJNA1234533", "Delta family protocadhins contribute to protoglomerular targeting of olfactory sensory neuron axons in the olfactory bulb", "GSE291626", "Transcriptome Analysis", "To understand how neural circuits are assembled it is essential to identify and characterize the axonal guidance cues and receptors that determine the axonal trajectories and connections between neurons. We performed single cell RNA sequencing of olfactory sensory neurons from zebrafish to identify candidate axonal guidance related genes that are differentially expressed according to sensory axon target location in the olfactory bulb. Among the candidates we identified were several members of the non clustered delta protocadherin family of adhesion molecules. We found that two members of the delta1 protocadherin family pcdh7b and pcdh11 are most highly expressed in sensory neurons that project to the DZ protoglomerulus. Knocking down either one impairs the ability of sensory axons to terminate within the DZ protoglomerulus but does not affect the ability of other sensory axons from terminating normally in the CZ protoglomerulus. In contrast two members of the delta2 protocadherin family pcdh10b and pcdh17 are most highly expressed in sensory neurons that project to the CZ protoglomerulus. Knocking down pcdh10b induces ectopic terminations of CZ projecting sensory axons. Knocking down pcdh17 induces substantial ectopic axonal trajectories and impairs CZ projecting sensory axons from finding and terminating in the CZ protoglomerulus. Knockdowns of either pcdh10b or pcdh17 do not affect DZ projecting sensory axons. These findings suggest that delta1 protocadherins help DZ projecting sensory axons enter and remain within the DZ protoglomerulus while delta2 protocadherins help CZ projecting sensory axons navigate to the CZ protoglomerulus. Overall design: Roughly 2000 zebrafish embryos we sacraficed at 36 48 hpf and 72 hpf. Olfactory tissue was dissociated in FACSmax dissosciation medium and then FACsorted to isolate OMP:RFP positive neurons.", null, null, null, "OMP positive Olfactory Sensory Neurons from 48pf Zebrafish", "GSM8838717", null, "source name:Olfactory Sensory Tissue|tissue:Olfactory Sensory Tissue|cell line:Olactory Sensory Neurons|cell type:Neurons|sample age:48 hpf|genotype:Tgomp:lyn RFP|geo loc name:missing|collection date:missing", "OMP positive Olfactory Sensory Neurons from 48pf Zebrafish", "Cell Ranger V3.0.1 Assembly: GRCz11 Supplementary files format and content: Demultiplexed 10x Genomics Files.", "Olfactory Sensory Tissue", null, "10X Genomics V3.3", null, "tissue:Olfactory Sensory Tissue|cell line:Olactory Sensory Neurons|cell type:Neurons|sample age:48 hpf|genotype:Tgomp:lyn RFP", "GSM8838717", "GSM8838717: OMP positive Olfactory Sensory Neurons from 48pf Zebrafish; Danio rerio; RNA Seq", "GSM8838717 r1", "GSM8838717", "1", "10X Genomics V3.3", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP569567", null, "loader:fastq load.py", "97364_S5_L002_I1_001.fastq.gz 97364_S5_L002_R1_001.fastq.gz 97364_S5_L002_R2_001.fastq.gz", "fastq fastq fastq", 7445521460.0, 57273242.0, "GSM8838717 r2", "0:8 1:28 2:94", "A:1586585615;C:1115323543;G:1231863598;T:1449738354;N:173638", 8, 28, 94, null, 1586585615, 1115323543, 1231863598, 1449738354, 173638, "SRX27953870", "SRS24319775", "SRA2091725", "Department of Neuroscience, University of Pennsylvania", "Department of Neuroscience, University of Pennsylvania", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2025-03-11", "Hatching", "Embryo", "Brain", "Nervous System"], [35387, "SRR32649450", "SRX27953869", "SRS24319773", "SRP569567", "PRJNA1234533", "Delta family protocadhins contribute to protoglomerular targeting of olfactory sensory neuron axons in the olfactory bulb", "GSE291626", "Transcriptome Analysis", "To understand how neural circuits are assembled it is essential to identify and characterize the axonal guidance cues and receptors that determine the axonal trajectories and connections between neurons. We performed single cell RNA sequencing of olfactory sensory neurons from zebrafish to identify candidate axonal guidance related genes that are differentially expressed according to sensory axon target location in the olfactory bulb. Among the candidates we identified were several members of the non clustered delta protocadherin family of adhesion molecules. We found that two members of the delta1 protocadherin family pcdh7b and pcdh11 are most highly expressed in sensory neurons that project to the DZ protoglomerulus. Knocking down either one impairs the ability of sensory axons to terminate within the DZ protoglomerulus but does not affect the ability of other sensory axons from terminating normally in the CZ protoglomerulus. In contrast two members of the delta2 protocadherin family pcdh10b and pcdh17 are most highly expressed in sensory neurons that project to the CZ protoglomerulus. Knocking down pcdh10b induces ectopic terminations of CZ projecting sensory axons. Knocking down pcdh17 induces substantial ectopic axonal trajectories and impairs CZ projecting sensory axons from finding and terminating in the CZ protoglomerulus. Knockdowns of either pcdh10b or pcdh17 do not affect DZ projecting sensory axons. These findings suggest that delta1 protocadherins help DZ projecting sensory axons enter and remain within the DZ protoglomerulus while delta2 protocadherins help CZ projecting sensory axons navigate to the CZ protoglomerulus. Overall design: Roughly 2000 zebrafish embryos we sacraficed at 36 48 hpf and 72 hpf. Olfactory tissue was dissociated in FACSmax dissosciation medium and then FACsorted to isolate OMP:RFP positive neurons.", null, null, null, "OMP positive Olfactory Sensory Neurons from 36hpf Zebrafish", "GSM8838716", null, "source name:Olfactory Sensory Tissue|tissue:Olfactory Sensory Tissue|cell line:Olactory Sensory Neurons|cell type:Neurons|sample age:36 hpf|genotype:Tgomp:lyn RFP|geo loc name:missing|collection date:missing", "OMP positive Olfactory Sensory Neurons from 36hpf Zebrafish", "Cell Ranger V3.0.1 Assembly: GRCz11 Supplementary files format and content: Demultiplexed 10x Genomics Files.", "Olfactory Sensory Tissue", null, "10X Genomics V3.3", null, "tissue:Olfactory Sensory Tissue|cell line:Olactory Sensory Neurons|cell type:Neurons|sample age:36 hpf|genotype:Tgomp:lyn RFP", "GSM8838716", "GSM8838716: OMP positive Olfactory Sensory Neurons from 36hpf Zebrafish; Danio rerio; RNA Seq", "GSM8838716 r1", "GSM8838716", "1", "10X Genomics V3.3", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP569567", null, "loader:fastq load.py", "97366_S7_L001_I1_001.fastq.gz 97366_S7_L001_R1_001.fastq.gz 97366_S7_L001_R2_001.fastq.gz", "fastq fastq fastq", 5962313630.0, 45863951.0, "GSM8838716 r1", "0:8 1:28 2:94", "A:1285269727;C:856096209;G:931439088;T:1238303640;N:102730", 8, 28, 94, null, 1285269727, 856096209, 931439088, 1238303640, 102730, "SRX27953869", "SRS24319773", "SRA2091725", "Department of Neuroscience, University of Pennsylvania", "Department of Neuroscience, University of Pennsylvania", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2025-03-11", "Pharyngula", "Embryo", "Brain", "Nervous System"], [35388, "SRR32649451", "SRX27953869", "SRS24319773", "SRP569567", "PRJNA1234533", "Delta family protocadhins contribute to protoglomerular targeting of olfactory sensory neuron axons in the olfactory bulb", "GSE291626", "Transcriptome Analysis", "To understand how neural circuits are assembled it is essential to identify and characterize the axonal guidance cues and receptors that determine the axonal trajectories and connections between neurons. We performed single cell RNA sequencing of olfactory sensory neurons from zebrafish to identify candidate axonal guidance related genes that are differentially expressed according to sensory axon target location in the olfactory bulb. Among the candidates we identified were several members of the non clustered delta protocadherin family of adhesion molecules. We found that two members of the delta1 protocadherin family pcdh7b and pcdh11 are most highly expressed in sensory neurons that project to the DZ protoglomerulus. Knocking down either one impairs the ability of sensory axons to terminate within the DZ protoglomerulus but does not affect the ability of other sensory axons from terminating normally in the CZ protoglomerulus. In contrast two members of the delta2 protocadherin family pcdh10b and pcdh17 are most highly expressed in sensory neurons that project to the CZ protoglomerulus. Knocking down pcdh10b induces ectopic terminations of CZ projecting sensory axons. Knocking down pcdh17 induces substantial ectopic axonal trajectories and impairs CZ projecting sensory axons from finding and terminating in the CZ protoglomerulus. Knockdowns of either pcdh10b or pcdh17 do not affect DZ projecting sensory axons. These findings suggest that delta1 protocadherins help DZ projecting sensory axons enter and remain within the DZ protoglomerulus while delta2 protocadherins help CZ projecting sensory axons navigate to the CZ protoglomerulus. Overall design: Roughly 2000 zebrafish embryos we sacraficed at 36 48 hpf and 72 hpf. Olfactory tissue was dissociated in FACSmax dissosciation medium and then FACsorted to isolate OMP:RFP positive neurons.", null, null, null, "OMP positive Olfactory Sensory Neurons from 36hpf Zebrafish", "GSM8838716", null, "source name:Olfactory Sensory Tissue|tissue:Olfactory Sensory Tissue|cell line:Olactory Sensory Neurons|cell type:Neurons|sample age:36 hpf|genotype:Tgomp:lyn RFP|geo loc name:missing|collection date:missing", "OMP positive Olfactory Sensory Neurons from 36hpf Zebrafish", "Cell Ranger V3.0.1 Assembly: GRCz11 Supplementary files format and content: Demultiplexed 10x Genomics Files.", "Olfactory Sensory Tissue", null, "10X Genomics V3.3", null, "tissue:Olfactory Sensory Tissue|cell line:Olactory Sensory Neurons|cell type:Neurons|sample age:36 hpf|genotype:Tgomp:lyn RFP", "GSM8838716", "GSM8838716: OMP positive Olfactory Sensory Neurons from 36hpf Zebrafish; Danio rerio; RNA Seq", "GSM8838716 r1", "GSM8838716", "1", "10X Genomics V3.3", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP569567", null, "loader:fastq load.py", "97366_S7_L002_I1_001.fastq.gz 97366_S7_L002_R1_001.fastq.gz 97366_S7_L002_R2_001.fastq.gz", "fastq fastq fastq", 5980615420.0, 46004734.0, "GSM8838716 r2", "0:8 1:28 2:94", "A:1289600464;C:857667521;G:934976316;T:1242064603;N:136092", 8, 28, 94, null, 1289600464, 857667521, 934976316, 1242064603, 136092, "SRX27953869", "SRS24319773", "SRA2091725", "Department of Neuroscience, University of Pennsylvania", "Department of Neuroscience, University of Pennsylvania", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2025-03-11", "Pharyngula", "Embryo", "Brain", "Nervous System"], [38014, "SRR1265742", "SRX529137", "SRS598834", "SRP041544", "PRJNA245824", "Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish", "GSE57169", "Transcriptome Analysis", "The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain gut liver ovary testis eye heart and embryo of zebrafish. In brain gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2 we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0% with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.", null, "pubmed:26574018", null, "Female Brain Replicate 3 sRNAseq", "GSM1376625", null, "source name:Female Brain|gender:female|tissue:Brain|genetic background:Wild type Singapore strain", "Female Brain Replicate 3 sRNAseq", "Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedl\u00e4nder et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl p m r t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis.", "Female Brain", "N/A", "Total RNA were extracted using mirVana\u2122 miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana\u2122 miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1\u00b5g of good quality Total RNA per sample was used as starting material. 5\u2019 and 3\u2019 RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.", "Fishes were purchased from a local supplier and acclimatized before tissue extraction.", "gender:Female|tissue:Brain|genetic background:Wild type Singapore strain", "GSM1376625", "GSM1376625: Female Brain Replicate 3 sRNAseq; Danio rerio; miRNA Seq", "GSM1376625", null, "1", "Total RNA were extracted using mirVana\u2122 miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana\u2122 miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1\u00b5g of good quality Total RNA per sample was used as starting material. 5\u2019 and 3\u2019 RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.", "GEO Accession:GSM1376625", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP041544", null, null, "MZB012_CTTGTA_L007_R1.fastq.gz", "fastq", 657620928.0, 12894528.0, "GSM1376625 r1", "0:51", "A:127428594;C:157315630;G:203096060;T:169719399;N:61245", 51, null, null, null, 127428594, 157315630, 203096060, 169719399, 61245, "SRX529137", "SRS598834", "SRA160430", "GEO", "Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore", 1, 0.01165, null, 0.00109, null, 0.99622, null, 0.72322, null, 51, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Singapore", "2014-04-29", "Undetermined", "Embryo", "Brain", "Nervous System"], [38015, "SRR1265741", "SRX529136", "SRS598833", "SRP041544", "PRJNA245824", "Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish", "GSE57169", "Transcriptome Analysis", "The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain gut liver ovary testis eye heart and embryo of zebrafish. In brain gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2 we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0% with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.", null, "pubmed:26574018", null, "Female Brain Replicate 2 sRNAseq", "GSM1376624", null, "source name:Female Brain|gender:female|tissue:Brain|genetic background:Wild type Singapore strain", "Female Brain Replicate 2 sRNAseq", "Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedl\u00e4nder et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl p m r t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis.", "Female Brain", "N/A", "Total RNA were extracted using mirVana\u2122 miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana\u2122 miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1\u00b5g of good quality Total RNA per sample was used as starting material. 5\u2019 and 3\u2019 RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.", "Fishes were purchased from a local supplier and acclimatized before tissue extraction.", "gender:Female|tissue:Brain|genetic background:Wild type Singapore strain", "GSM1376624", "GSM1376624: Female Brain Replicate 2 sRNAseq; Danio rerio; miRNA Seq", "GSM1376624", null, "1", "Total RNA were extracted using mirVana\u2122 miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana\u2122 miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1\u00b5g of good quality Total RNA per sample was used as starting material. 5\u2019 and 3\u2019 RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.", "GEO Accession:GSM1376624", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP041544", null, null, "MZB011_GGCTAC_L007_R1.fastq.gz", "fastq", 197790903.0, 3878253.0, "GSM1376624 r1", "0:51", "A:39219508;C:48781853;G:60339090;T:49430999;N:19453", 51, null, null, null, 39219508, 48781853, 60339090, 49430999, 19453, "SRX529136", "SRS598833", "SRA160430", "GEO", "Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore", 1, 0.00227, null, 0.00019, null, 0.99835, null, 0.67164, null, 51, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Singapore", "2014-04-29", "Undetermined", "Embryo", "Brain", "Nervous System"], [38016, "SRR1265740", "SRX529135", "SRS598832", "SRP041544", "PRJNA245824", "Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish", "GSE57169", "Transcriptome Analysis", "The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain gut liver ovary testis eye heart and embryo of zebrafish. In brain gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2 we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0% with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.", null, "pubmed:26574018", null, "Female Brain Replicate 1 sRNAseq", "GSM1376623", null, "source name:Female Brain|gender:female|tissue:Brain|genetic background:Wild type Singapore strain", "Female Brain Replicate 1 sRNAseq", "Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedl\u00e4nder et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl p m r t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis.", "Female Brain", "N/A", "Total RNA were extracted using mirVana\u2122 miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana\u2122 miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1\u00b5g of good quality Total RNA per sample was used as starting material. 5\u2019 and 3\u2019 RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.", "Fishes were purchased from a local supplier and acclimatized before tissue extraction.", "gender:Female|tissue:Brain|genetic background:Wild type Singapore strain", "GSM1376623", "GSM1376623: Female Brain Replicate 1 sRNAseq; Danio rerio; miRNA Seq", "GSM1376623", null, "1", "Total RNA were extracted using mirVana\u2122 miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana\u2122 miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1\u00b5g of good quality Total RNA per sample was used as starting material. 5\u2019 and 3\u2019 RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.", "GEO Accession:GSM1376623", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP041544", null, null, "MZB010_TAGCTT_L007_R1.fastq.gz", "fastq", 127765710.0, 2505210.0, "GSM1376623 r1", "0:51", "A:24845648;C:31103830;G:38874684;T:32929436;N:12112", 51, null, null, null, 24845648, 31103830, 38874684, 32929436, 12112, "SRX529135", "SRS598832", "SRA160430", "GEO", "Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore", 1, 0.02647, null, 0.00307, null, 0.99368, null, 0.59472, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Singapore", "2014-04-29", "Undetermined", "Embryo", "Brain", "Nervous System"], [38017, "SRR1265739", "SRX529134", "SRS598831", "SRP041544", "PRJNA245824", "Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish", "GSE57169", "Transcriptome Analysis", "The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain gut liver ovary testis eye heart and embryo of zebrafish. In brain gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2 we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0% with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.", null, "pubmed:26574018", null, "Male Brain Replicate 3 sRNAseq", "GSM1376622", null, "source name:Male Brain|gender:male|tissue:Brain|genetic background:Wild type Singapore strain", "Male Brain Replicate 3 sRNAseq", "Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedl\u00e4nder et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl p m r t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis.", "Male Brain", "N/A", "Total RNA were extracted using mirVana\u2122 miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana\u2122 miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1\u00b5g of good quality Total RNA per sample was used as starting material. 5\u2019 and 3\u2019 RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.", "Fishes were purchased from a local supplier and acclimatized before tissue extraction.", "gender:Male|tissue:Brain|genetic background:Wild type Singapore strain", "GSM1376622", "GSM1376622: Male Brain Replicate 3 sRNAseq; Danio rerio; miRNA Seq", "GSM1376622", null, "1", "Total RNA were extracted using mirVana\u2122 miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana\u2122 miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1\u00b5g of good quality Total RNA per sample was used as starting material. 5\u2019 and 3\u2019 RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.", "GEO Accession:GSM1376622", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP041544", null, null, "MZB009_TTAGGC_L007_R1.fastq.gz", "fastq", 749856876.0, 14703076.0, "GSM1376622 r1", "0:51", "A:142133111;C:197021938;G:231006890;T:179625504;N:69433", 51, null, null, null, 142133111, 197021938, 231006890, 179625504, 69433, "SRX529134", "SRS598831", "SRA160430", "GEO", "Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore", 1, 0.00196, null, 0.00026, null, 0.99843, null, 0.64615, null, 51, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Singapore", "2014-04-29", "Undetermined", "Embryo", "Brain", "Nervous System"], [38018, "SRR1265738", "SRX529133", "SRS598830", "SRP041544", "PRJNA245824", "Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish", "GSE57169", "Transcriptome Analysis", "The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain gut liver ovary testis eye heart and embryo of zebrafish. In brain gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2 we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0% with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.", null, "pubmed:26574018", null, "Male Brain Replicate 2 sRNAseq", "GSM1376621", null, "source name:Male Brain|gender:male|tissue:Brain|genetic background:Wild type Singapore strain", "Male Brain Replicate 2 sRNAseq", "Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedl\u00e4nder et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl p m r t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis.", "Male Brain", "N/A", "Total RNA were extracted using mirVana\u2122 miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana\u2122 miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1\u00b5g of good quality Total RNA per sample was used as starting material. 5\u2019 and 3\u2019 RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.", "Fishes were purchased from a local supplier and acclimatized before tissue extraction.", "gender:Male|tissue:Brain|genetic background:Wild type Singapore strain", "GSM1376621", "GSM1376621: Male Brain Replicate 2 sRNAseq; Danio rerio; miRNA Seq", "GSM1376621", null, "1", "Total RNA were extracted using mirVana\u2122 miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana\u2122 miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1\u00b5g of good quality Total RNA per sample was used as starting material. 5\u2019 and 3\u2019 RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.", "GEO Accession:GSM1376621", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP041544", null, null, "MZB008_CGATGT_L007_R1.fastq.gz", "fastq", 394620558.0, 7737658.0, "GSM1376621 r1", "0:51", "A:68213140;C:110690478;G:127130285;T:88550429;N:36226", 51, null, null, null, 68213140, 110690478, 127130285, 88550429, 36226, "SRX529133", "SRS598830", "SRA160430", "GEO", "Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore", 1, 0.06427, null, 0.00768, null, 0.98859, null, 0.77971, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Singapore", "2014-04-29", "Undetermined", "Embryo", "Brain", "Nervous System"], [38019, "SRR1265737", "SRX529132", "SRS598829", "SRP041544", "PRJNA245824", "Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish", "GSE57169", "Transcriptome Analysis", "The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain gut liver ovary testis eye heart and embryo of zebrafish. In brain gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2 we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0% with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.", null, "pubmed:26574018", null, "Male Brain Replicate 1 sRNAseq", "GSM1376620", null, "source name:Male Brain|gender:male|tissue:Brain|genetic background:Wild type Singapore strain", "Male Brain Replicate 1 sRNAseq", "Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedl\u00e4nder et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl p m r t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis.", "Male Brain", "N/A", "Total RNA were extracted using mirVana\u2122 miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana\u2122 miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1\u00b5g of good quality Total RNA per sample was used as starting material. 5\u2019 and 3\u2019 RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.", "Fishes were purchased from a local supplier and acclimatized before tissue extraction.", "gender:Male|tissue:Brain|genetic background:Wild type Singapore strain", "GSM1376620", "GSM1376620: Male Brain Replicate 1 sRNAseq; Danio rerio; miRNA Seq", "GSM1376620", null, "1", "Total RNA were extracted using mirVana\u2122 miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana\u2122 miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1\u00b5g of good quality Total RNA per sample was used as starting material. 5\u2019 and 3\u2019 RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.", "GEO Accession:GSM1376620", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP041544", null, null, "MZB007_ATCACG_L007_R1.fastq.gz", "fastq", 329742489.0, 6465539.0, "GSM1376620 r1", "0:51", "A:60032454;C:91021987;G:104188224;T:74471433;N:28391", 51, null, null, null, 60032454, 91021987, 104188224, 74471433, 28391, "SRX529132", "SRS598829", "SRA160430", "GEO", "Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore", 1, 0.00994, null, 0.00098, null, 0.99738, null, 0.77713, null, 51, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Singapore", "2014-04-29", "Undetermined", "Embryo", "Brain", "Nervous System"], [38287, "SRR1616929", "SRX736533", "SRS724633", "SRP049069", "PRJNA264333", "A spinal opsin controls early neural activity and drives a behavioral light response", "GSE62527", "Transcriptome Analysis", "Purpose: using RNA seq as a screening tool to determine candidate genes of interest within a genetically defined neural subpopulation in the zebrafish embryonic spinal cord. Results: The early embryonic spinal cord displays patterns of spontaneous activity that generate the earliest motor behavior in the zebrafish. We show the behavior and the neural activity to be inhibited by environmental levels of light. Since at these young ages the fish is blind and since restricted illumination patterns on the trunk of the fish can elicit a photo response we hypothesized that the photo inhibition is an intrinsic property of the active central pattern generator network within the spinal cord. We FACS isolated cells from this network as well as those from a panneuronal population and sequenced mRNAs. Through differential expression analysis we identified vertebrate ancient long opsin a as a candidate and then further validated its function in the circuit through knockdown and rescue experiments. Overall design: RNA sequencing of 2 FACS purified neural populations from zebrafish spinal cord.", null, "pubmed:25484291", null, "HuC FP+", "GSM1528408", null, "tissue:spinal neurons|gal4 driver:HuC|population:panneuronal", "HuC FP+", "Illumina Casava1.8 software used for basecalling. Sequenced reads were mapped to Zv9 using Tophat v1.4.0 FPKMs were generated using Cufflinks v2.1.1 and compared using Cuffdiff Genome build: Zv9 Supplementary files format and content: tab delimited text file with FPKM for each sample", "spinal neurons", "Tails dissected free at the level of the 3rd somite and dissociated with trypsin/collagenase before FACS", "Fluorescent neural cell bodies were FACS sorted into Trizol and flash frozen before total RNA extraction and polyA selection. RNA libraries were prepared for sequencing using standard Illumina protocols", "20 hpf embryos were used", "gal4 driver:HuC|population:panneuronal", "GSM1528408", "GSM1528408: HuC FP+; Danio rerio; RNA Seq", "GSM1528408", null, "1", "Fluorescent neural cell bodies were FACS sorted into Trizol and flash frozen before total RNA extraction and polyA selection. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM1528408", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP049069", null, null, "HuCFP_R2.fastq HuCFP_R1.fastq", "fastq fastq", 5590606800.0, 27953034.0, "GSM1528408 r1", "0:100 1:100", "A:1550775239;C:1214652319;G:1269909429;T:1544634947;N:10634866", 100, 100, null, null, 1550775239, 1214652319, 1269909429, 1544634947, 10634866, "SRX736533", "SRS724633", "SRA192701", "GEO", "Isacoff, MCB, UC Berkeley", 2, 0.90003, 0.87337, 0.19389, 0.18827, 0.74594, 0.75041, 0.50589, 0.50314, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2014-10-20", "Segmentation", "Embryo", "Brain", "Nervous System"], [38288, "SRR1616928", "SRX736532", "SRS724632", "SRP049069", "PRJNA264333", "A spinal opsin controls early neural activity and drives a behavioral light response", "GSE62527", "Transcriptome Analysis", "Purpose: using RNA seq as a screening tool to determine candidate genes of interest within a genetically defined neural subpopulation in the zebrafish embryonic spinal cord. Results: The early embryonic spinal cord displays patterns of spontaneous activity that generate the earliest motor behavior in the zebrafish. We show the behavior and the neural activity to be inhibited by environmental levels of light. Since at these young ages the fish is blind and since restricted illumination patterns on the trunk of the fish can elicit a photo response we hypothesized that the photo inhibition is an intrinsic property of the active central pattern generator network within the spinal cord. We FACS isolated cells from this network as well as those from a panneuronal population and sequenced mRNAs. Through differential expression analysis we identified vertebrate ancient long opsin a as a candidate and then further validated its function in the circuit through knockdown and rescue experiments. Overall design: RNA sequencing of 2 FACS purified neural populations from zebrafish spinal cord.", null, "pubmed:25484291", null, "1020 FP+", "GSM1528407", null, "tissue:spinal neurons|gal4 driver:1020st|population:olig2+ subpopulation", "1020 FP+", "Illumina Casava1.8 software used for basecalling. Sequenced reads were mapped to Zv9 using Tophat v1.4.0 FPKMs were generated using Cufflinks v2.1.1 and compared using Cuffdiff Genome build: Zv9 Supplementary files format and content: tab delimited text file with FPKM for each sample", "spinal neurons", "Tails dissected free at the level of the 3rd somite and dissociated with trypsin/collagenase before FACS", "Fluorescent neural cell bodies were FACS sorted into Trizol and flash frozen before total RNA extraction and polyA selection. RNA libraries were prepared for sequencing using standard Illumina protocols", "20 hpf embryos were used", "gal4 driver:1020st|population:olig2+ subpopulation", "GSM1528407", "GSM1528407: 1020 FP+; Danio rerio; RNA Seq", "GSM1528407", null, "1", "Fluorescent neural cell bodies were FACS sorted into Trizol and flash frozen before total RNA extraction and polyA selection. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM1528407", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP049069", null, null, "1020FP_R2.fastq 1020FP_R1.fastq", "fastq fastq", 9750838400.0, 48754192.0, "GSM1528407 r1", "0:100 1:100", "A:2741372249;C:2106643378;G:2204482450;T:2679721349;N:18618974", 100, 100, null, null, 2741372249, 2106643378, 2204482450, 2679721349, 18618974, "SRX736532", "SRS724632", "SRA192701", "GEO", "Isacoff, MCB, UC Berkeley", 2, 0.9073, 0.88227, 0.16046, 0.15465, 0.74385, 0.7469, 0.50468, 0.50034, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2014-10-20", "Segmentation", "Embryo", "Brain", "Nervous System"], [39827, "SRR2441454", "SRX1321833", "SRS1109642", "SRP062493", "PRJNA293106", "Danio rerio Raw sequence reads", "PRJNA293106", "Metagenomics", "Zebrafish Hypoxia RNAseq", null, null, "RNAseq at 24hpf following hypoxia", null, "24hpf hypoxia", null, "strain:TU|age:24hpf|sex:not determined|tissue:brain|treatment:hypoxia|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "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\u2019s 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\u2019s CASAVA version 1.8.2 software.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", "500Application ReadForward1", "SRP062493", null, null, "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, null, null, null, 299680333, 267717935, 264833481, 357936794, 15279407, "SRX1321833", "SRS1109642", "SRA289450", "University of Utah|Bonkowsky", "University of Utah", 1, 0.87455, null, 0.24266, null, 0.74121, null, 0.57777, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2015-10-10", "Pharyngula", "Embryo", "Brain", "Nervous System"], [39828, "SRR2437828", "SRX1321832", "SRS1109643", "SRP062493", "PRJNA293106", "Danio rerio Raw sequence reads", "PRJNA293106", "Metagenomics", "Zebrafish Hypoxia RNAseq", null, null, "RNAseq at 48hpf following normoxia", null, "48hpf normoxia", null, "strain:TU|age:48hpf|sex:not determined|tissue:brain|treatment:normoxia|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "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\u2019s 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\u2019s CASAVA version 1.8.2 software.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", "500Application ReadForward1", "SRP062493", null, null, "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, null, null, null, 251856100, 223081125, 216430606, 294554748, 19921, "SRX1321832", "SRS1109643", "SRA289450", "University of Utah|Bonkowsky", "University of Utah", 1, 0.94791, null, 0.26704, null, 0.68708, null, 0.54445, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2015-10-10", "Hatching", "Embryo", "Brain", "Nervous System"], [39829, "SRR2434699", "SRX1321831", "SRS1109642", "SRP062493", "PRJNA293106", "Danio rerio Raw sequence reads", "PRJNA293106", "Metagenomics", "Zebrafish Hypoxia RNAseq", null, null, "RNAseq at 24hpf following hypoxia", null, "24hpf hypoxia", null, "strain:TU|age:24hpf|sex:not determined|tissue:brain|treatment:hypoxia|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "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\u2019s 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\u2019s CASAVA version 1.8.2 software.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", "500Application ReadForward1", "SRP062493", null, null, "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, null, null, null, 299759613, 292757497, 281904026, 353193075, 68539, "SRX1321831", "SRS1109642", "SRA289450", "University of Utah|Bonkowsky", "University of Utah", 1, 0.94855, null, 0.27579, null, 0.73298, null, 0.58307, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2015-10-07", "Pharyngula", "Embryo", "Brain", "Nervous System"], [39830, "SRR2433795", "SRX1321830", "SRS1109644", "SRP062493", "PRJNA293106", "Danio rerio Raw sequence reads", "PRJNA293106", "Metagenomics", "Zebrafish Hypoxia RNAseq", null, null, "RNAseq at 60hpf following normoxia", null, "60hpf Normoxia", null, "strain:TU|age:60hpf|sex:not determined|tissue:brain|treatment:normoxia|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "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\u2019s 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\u2019s CASAVA version 1.8.2 software.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", "500Application ReadForward1", "SRP062493", null, null, "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, null, null, null, 294304558, 248234752, 238088577, 332109252, 62811, "SRX1321830", "SRS1109644", "SRA289450", "University of Utah|Bonkowsky", "University of Utah", 1, 0.94922, null, 0.34314, null, 0.67838, null, 0.51455, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2015-10-10", "Hatching", "Embryo", "Brain", "Nervous System"], [39831, "SRR2426760", "SRX1321829", "SRS1109645", "SRP062493", "PRJNA293106", "Danio rerio Raw sequence reads", "PRJNA293106", "Metagenomics", "Zebrafish Hypoxia RNAseq", null, null, "RNAseq at 36hpf following hypoxia", null, "36hpf hypoxia", null, "strain:TU|age:36hpf|sex:not determined|tissue:brain|treatment:hypoxia|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "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\u2019s 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\u2019s CASAVA version 1.8.2 software.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", "500Application ReadForward1", "SRP062493", null, null, "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, null, null, null, 395786409, 358263833, 358391489, 491601452, 64267, "SRX1321829", "SRS1109645", "SRA289450", "University of Utah|Bonkowsky", "University of Utah", 1, 0.95408, null, 0.28965, null, 0.69593, null, 0.54826, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2015-10-10", "Pharyngula", "Embryo", "Brain", "Nervous System"], [39832, "SRR2417497", "SRX1321828", "SRS1109646", "SRP062493", "PRJNA293106", "Danio rerio Raw sequence reads", "PRJNA293106", "Metagenomics", "Zebrafish Hypoxia RNAseq", null, null, "RNAseq at 48hpf following hypoxia", null, "48hpf hypoxia", null, "strain:TU|age:48hpf|sex:not determined|tissue:brain|treatment:hypoxia|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "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\u2019s 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\u2019s CASAVA version 1.8.2 software.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", "500Application ReadForward1", "SRP062493", null, null, "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, null, null, null, 309392529, 284311489, 275471070, 365515358, 20054, "SRX1321828", "SRS1109646", "SRA289450", "University of Utah|Bonkowsky", "University of Utah", 1, 0.94675, null, 0.25877, null, 0.71453, null, 0.5239, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2015-09-16", "Hatching", "Embryo", "Brain", "Nervous System"], [39833, "SRR2417496", "SRX1321827", "SRS1109644", "SRP062493", "PRJNA293106", "Danio rerio Raw sequence reads", "PRJNA293106", "Metagenomics", "Zebrafish Hypoxia RNAseq", null, null, "RNAseq at 60hpf following normoxia", null, "60hpf Normoxia", null, "strain:TU|age:60hpf|sex:not determined|tissue:brain|treatment:normoxia|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "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\u2019s 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\u2019s CASAVA version 1.8.2 software.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", "500Application ReadForward1", "SRP062493", null, null, "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, null, null, null, 259102784, 230364456, 226008843, 300294199, 16468, "SRX1321827", "SRS1109644", "SRA289450", "University of Utah|Bonkowsky", "University of Utah", 1, 0.95197, null, 0.30503, null, 0.68333, null, 0.52243, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2015-09-16", "Hatching", "Embryo", "Brain", "Nervous System"], [39834, "SRR2400601", "SRX1321826", "SRS1109642", "SRP062493", "PRJNA293106", "Danio rerio Raw sequence reads", "PRJNA293106", "Metagenomics", "Zebrafish Hypoxia RNAseq", null, null, "RNAseq at 24hpf following hypoxia", null, "24hpf hypoxia", null, "strain:TU|age:24hpf|sex:not determined|tissue:brain|treatment:hypoxia|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "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\u2019s 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\u2019s CASAVA version 1.8.2 software.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", "500Application ReadForward1", "SRP062493", null, null, "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, null, null, null, 309098695, 281875016, 278706888, 379315616, 50135, "SRX1321826", "SRS1109642", "SRA289450", "University of Utah|Bonkowsky", "University of Utah", 1, 0.95443, null, 0.27405, null, 0.69747, null, 0.40987, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2015-10-10", "Pharyngula", "Embryo", "Brain", "Nervous System"], [39837, "SRR2342161", "SRX1321823", "SRS1109648", "SRP062493", "PRJNA293106", "Danio rerio Raw sequence reads", "PRJNA293106", "Metagenomics", "Zebrafish Hypoxia RNAseq", null, null, "RNAseq at 60hpf following hypoxia", null, "60hpf hypoxia", null, "strain:TU|age:60hpf|sex:not determined|tissue:brain|treatment:hypoxia|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "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\u2019s 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\u2019s CASAVA version 1.8.2 software.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", "500Application ReadForward1", "SRP062493", null, null, "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, null, null, null, 280500644, 237758835, 234061287, 320931292, 17442, "SRX1321823", "SRS1109648", "SRA289450", "University of Utah|Bonkowsky", "University of Utah", 1, 0.94774, null, 0.36354, null, 0.70065, null, 0.51075, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2015-10-10", "Hatching", "Embryo", "Brain", "Nervous System"], [39838, "SRR2341509", "SRX1321822", "SRS1109643", "SRP062493", "PRJNA293106", "Danio rerio Raw sequence reads", "PRJNA293106", "Metagenomics", "Zebrafish Hypoxia RNAseq", null, null, "RNAseq at 48hpf following normoxia", null, "48hpf normoxia", null, "strain:TU|age:48hpf|sex:not determined|tissue:brain|treatment:normoxia|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "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\u2019s 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\u2019s CASAVA version 1.8.2 software.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", "500Application ReadForward1", "SRP062493", null, null, "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, null, null, null, 271795722, 246789566, 240496674, 316769688, 17200, "SRX1321822", "SRS1109643", "SRA289450", "University of Utah|Bonkowsky", "University of Utah", 1, 0.94644, null, 0.26805, null, 0.68745, null, 0.53833, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2015-10-10", "Hatching", "Embryo", "Brain", "Nervous System"], [39839, "SRR2340149", "SRX1321821", "SRS1109650", "SRP062493", "PRJNA293106", "Danio rerio Raw sequence reads", "PRJNA293106", "Metagenomics", "Zebrafish Hypoxia RNAseq", null, null, "RNAseq at 36hpf following normoxia", null, "36hpf normoxia", null, "strain:TU|age:36hpf|sex:not determined|tissue:brain|treatment:normoxia|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "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\u2019s 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\u2019s CASAVA version 1.8.2 software.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", "500Application ReadForward1", "SRP062493", null, null, "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, null, null, null, 404319446, 349459823, 346545846, 468209953, 20095682, "SRX1321821", "SRS1109650", "SRA289450", "University of Utah|Bonkowsky", "University of Utah", 1, 0.8739, null, 0.32489, null, 0.71701, null, 0.51646, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2015-10-10", "Pharyngula", "Embryo", "Brain", "Nervous System"], [39840, "SRR2245887", "SRX1321820", "SRS1109645", "SRP062493", "PRJNA293106", "Danio rerio Raw sequence reads", "PRJNA293106", "Metagenomics", "Zebrafish Hypoxia RNAseq", null, null, "RNAseq at 36hpf following hypoxia", null, "36hpf hypoxia", null, "strain:TU|age:36hpf|sex:not determined|tissue:brain|treatment:hypoxia|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "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\u2019s 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\u2019s CASAVA version 1.8.2 software.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", "500Application ReadForward1", "SRP062493", null, null, "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, null, null, null, 305628501, 266059461, 259888045, 360487730, 15267613, "SRX1321820", "SRS1109645", "SRA289450", "University of Utah|Bonkowsky", "University of Utah", 1, 0.87814, null, 0.27249, null, 0.72853, null, 0.53527, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2015-10-10", "Pharyngula", "Embryo", "Brain", "Nervous System"], [39841, "SRR2245257", "SRX1321819", "SRS1109651", "SRP062493", "PRJNA293106", "Danio rerio Raw sequence reads", "PRJNA293106", "Metagenomics", "Zebrafish Hypoxia RNAseq", null, null, "RNAseq at 24hpf following normoxia", null, "24hpf normoxia", null, "strain:TU|age:24hpf|sex:not determined|tissue:brain|treatment:normoxia|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "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\u2019s 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\u2019s CASAVA version 1.8.2 software.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", "500Application ReadForward1", "SRP062493", null, null, "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, null, null, null, 320558638, 275312235, 271710647, 373637690, 15939840, "SRX1321819", "SRS1109651", "SRA289450", "University of Utah|Bonkowsky", "University of Utah", 1, 0.87634, null, 0.30298, null, 0.71356, null, 0.54673, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2015-10-10", "Pharyngula", "Embryo", "Brain", "Nervous System"], [39844, "SRR2241311", "SRX1321816", "SRS1109644", "SRP062493", "PRJNA293106", "Danio rerio Raw sequence reads", "PRJNA293106", "Metagenomics", "Zebrafish Hypoxia RNAseq", null, null, "RNAseq at 60hpf following normoxia", null, "60hpf Normoxia", null, "strain:TU|age:60hpf|sex:not determined|tissue:brain|treatment:normoxia|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "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\u2019s 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\u2019s CASAVA version 1.8.2 software.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", "500Application ReadForward1", "SRP062493", null, null, "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, null, null, null, 287072563, 255244675, 248573701, 327203388, 20723, "SRX1321816", "SRS1109644", "SRA289450", "University of Utah|Bonkowsky", "University of Utah", 1, 0.93238, null, 0.30064, null, 0.68574, null, 0.51934, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2015-10-10", "Hatching", "Embryo", "Brain", "Nervous System"], [39845, "SRR2240748", "SRX1321815", "SRS1109648", "SRP062493", "PRJNA293106", "Danio rerio Raw sequence reads", "PRJNA293106", "Metagenomics", "Zebrafish Hypoxia RNAseq", null, null, "RNAseq at 60hpf following hypoxia", null, "60hpf hypoxia", null, "strain:TU|age:60hpf|sex:not determined|tissue:brain|treatment:hypoxia|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "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\u2019s 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\u2019s CASAVA version 1.8.2 software.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", "500Application ReadForward1", "SRP062493", null, null, "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, null, null, null, 276432361, 244039609, 234638386, 319556004, 20540, "SRX1321815", "SRS1109648", "SRA289450", "University of Utah|Bonkowsky", "University of Utah", 1, 0.9502, null, 0.3077, null, 0.6899, null, 0.50645, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2015-09-03", "Hatching", "Embryo", "Brain", "Nervous System"], [39846, "SRR2239869", "SRX1321814", "SRS1109646", "SRP062493", "PRJNA293106", "Danio rerio Raw sequence reads", "PRJNA293106", "Metagenomics", "Zebrafish Hypoxia RNAseq", null, null, "RNAseq at 48hpf following hypoxia", null, "48hpf hypoxia", null, "strain:TU|age:48hpf|sex:not determined|tissue:brain|treatment:hypoxia|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "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\u2019s 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\u2019s CASAVA version 1.8.2 software.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", "500Application ReadForward1", "SRP062493", null, null, "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, null, null, null, 288023952, 248947169, 243195362, 331723738, 23329, "SRX1321814", "SRS1109646", "SRA289450", "University of Utah|Bonkowsky", "University of Utah", 1, 0.93753, null, 0.34521, null, 0.70246, null, 0.51535, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2015-10-10", "Hatching", "Embryo", "Brain", "Nervous System"], [39847, "SRR2239772", "SRX1321813", "SRS1109650", "SRP062493", "PRJNA293106", "Danio rerio Raw sequence reads", "PRJNA293106", "Metagenomics", "Zebrafish Hypoxia RNAseq", null, null, "RNAseq at 36hpf following normoxia", null, "36hpf normoxia", null, "strain:TU|age:36hpf|sex:not determined|tissue:brain|treatment:normoxia|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "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\u2019s 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\u2019s CASAVA version 1.8.2 software.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", "500Application ReadForward1", "SRP062493", null, null, "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, null, null, null, 392813056, 354469675, 348871622, 437692730, 38117, "SRX1321813", "SRS1109650", "SRA289450", "University of Utah|Bonkowsky", "University of Utah", 1, 0.91439, null, 0.31812, null, 0.70863, null, 0.51667, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2015-10-10", "Pharyngula", "Embryo", "Brain", "Nervous System"], [39848, "SRR2232685", "SRX1321812", "SRS1109645", "SRP062493", "PRJNA293106", "Danio rerio Raw sequence reads", "PRJNA293106", "Metagenomics", "Zebrafish Hypoxia RNAseq", null, null, "RNAseq at 36hpf following hypoxia", null, "36hpf hypoxia", null, "strain:TU|age:36hpf|sex:not determined|tissue:brain|treatment:hypoxia|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "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\u2019s 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\u2019s CASAVA version 1.8.2 software.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", "500Application ReadForward1", "SRP062493", null, null, "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, null, null, null, 279147206, 259582122, 249642505, 324452965, 21402, "SRX1321812", "SRS1109645", "SRA289450", "University of Utah|Bonkowsky", "University of Utah", 1, 0.94469, null, 0.25952, null, 0.72243, null, 0.52701, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2015-10-10", "Pharyngula", "Embryo", "Brain", "Nervous System"], [39849, "SRR2227658", "SRX1321811", "SRS1109651", "SRP062493", "PRJNA293106", "Danio rerio Raw sequence reads", "PRJNA293106", "Metagenomics", "Zebrafish Hypoxia RNAseq", null, null, "RNAseq at 24hpf following normoxia", null, "24hpf normoxia", null, "strain:TU|age:24hpf|sex:not determined|tissue:brain|treatment:normoxia|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "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\u2019s 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\u2019s CASAVA version 1.8.2 software.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", "500Application ReadForward1", "SRP062493", null, null, "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, null, null, null, 317179221, 285081899, 274648790, 366643275, 70565, "SRX1321811", "SRS1109651", "SRA289450", "University of Utah|Bonkowsky", "University of Utah", 1, 0.95045, null, 0.27525, null, 0.69688, null, 0.53555, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2015-09-01", "Pharyngula", "Embryo", "Brain", "Nervous System"], [39852, "SRR2225888", "SRX1321808", "SRS1109648", "SRP062493", "PRJNA293106", "Danio rerio Raw sequence reads", "PRJNA293106", "Metagenomics", "Zebrafish Hypoxia RNAseq", null, null, "RNAseq at 60hpf following hypoxia", null, "60hpf hypoxia", null, "strain:TU|age:60hpf|sex:not determined|tissue:brain|treatment:hypoxia|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "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\u2019s 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\u2019s CASAVA version 1.8.2 software.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", "500Application ReadForward1", "SRP062493", null, null, "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, null, null, null, 288570352, 247978180, 238128703, 327492563, 62552, "SRX1321808", "SRS1109648", "SRA289450", "University of Utah|Bonkowsky", "University of Utah", 1, 0.94824, null, 0.31808, null, 0.69244, null, 0.51505, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2015-10-10", "Hatching", "Embryo", "Brain", "Nervous System"], [39853, "SRR2225789", "SRX1321807", "SRS1109646", "SRP062493", "PRJNA293106", "Danio rerio Raw sequence reads", "PRJNA293106", "Metagenomics", "Zebrafish Hypoxia RNAseq", null, null, "RNAseq at 48hpf following hypoxia", null, "48hpf hypoxia", null, "strain:TU|age:48hpf|sex:not determined|tissue:brain|treatment:hypoxia|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "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\u2019s 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\u2019s CASAVA version 1.8.2 software.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", "500Application ReadForward1", "SRP062493", null, null, "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, null, null, null, 312511165, 283310381, 277279378, 376891744, 50282, "SRX1321807", "SRS1109646", "SRA289450", "University of Utah|Bonkowsky", "University of Utah", 1, 0.94959, null, 0.28331, null, 0.68757, null, 0.53976, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2015-09-01", "Hatching", "Embryo", "Brain", "Nervous System"], [39854, "SRR2225675", "SRX1321806", "SRS1109650", "SRP062493", "PRJNA293106", "Danio rerio Raw sequence reads", "PRJNA293106", "Metagenomics", "Zebrafish Hypoxia RNAseq", null, null, "RNAseq at 36hpf following normoxia", null, "36hpf normoxia", null, "strain:TU|age:36hpf|sex:not determined|tissue:brain|treatment:normoxia|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "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\u2019s 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\u2019s CASAVA version 1.8.2 software.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", "500Application ReadForward1", "SRP062493", null, null, "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, null, null, null, 301597123, 287750990, 281194881, 374152417, 49289, "SRX1321806", "SRS1109650", "SRA289450", "University of Utah|Bonkowsky", "University of Utah", 1, 0.95571, null, 0.22791, null, 0.71177, null, 0.53801, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2015-10-10", "Pharyngula", "Embryo", "Brain", "Nervous System"], [39855, "SRR2225572", "SRX1321805", "SRS1109651", "SRP062493", "PRJNA293106", "Danio rerio Raw sequence reads", "PRJNA293106", "Metagenomics", "Zebrafish Hypoxia RNAseq", null, null, "RNAseq at 24hpf following normoxia", null, "24hpf normoxia", null, "strain:TU|age:24hpf|sex:not determined|tissue:brain|treatment:normoxia|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "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\u2019s 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\u2019s CASAVA version 1.8.2 software.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", "500Application ReadForward1", "SRP062493", null, null, "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, null, null, null, 310265067, 296406990, 295054246, 391826687, 52510, "SRX1321805", "SRS1109651", "SRA289450", "University of Utah|Bonkowsky", "University of Utah", 1, 0.95596, null, 0.21907, null, 0.71512, null, 0.39029, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2015-09-01", "Pharyngula", "Embryo", "Brain", "Nervous System"], [39856, "SRR2222835", "SRX1321804", "SRS1109643", "SRP062493", "PRJNA293106", "Danio rerio Raw sequence reads", "PRJNA293106", "Metagenomics", "Zebrafish Hypoxia RNAseq", null, null, "RNAseq at 48hpf following normoxia", null, "48hpf normoxia", null, "strain:TU|age:48hpf|sex:not determined|tissue:brain|treatment:normoxia|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "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\u2019s 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\u2019s CASAVA version 1.8.2 software.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", "500Application ReadForward1", "SRP062493", null, null, "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, null, null, null, 291802893, 276442849, 277217342, 369624915, 48451, "SRX1321804", "SRS1109643", "SRA289450", "University of Utah|Bonkowsky", "University of Utah", 1, 0.95575, null, 0.23021, null, 0.72679, null, 0.60296, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2015-09-01", "Hatching", "Embryo", "Brain", "Nervous System"], [39962, "SRR2567886", "SRX1309247", "SRS1102442", "SRP064535", "PRJNA297905", "Methylmercury MeHg induced Transgenerational Inheritance of Brain Transcriptome in Zebrafish Danio rerio [brain]", "GSE73794", "Transcriptome Analysis", "Methylmercury MeHg is a ubiquitous environmental toxicant that is often detected in the tissues of fish eating species. It has been well established that prenatal exposure to MeHg can lead to widespread brain damage and impaired neurological development resulting in defects ranging from severe cerebral palsy and cognitive deficits to impaired motor and sensory function. A wide range of environmental toxicants have been shown to induce transgenerational inheritance of diseases via changes in DNA methylation\u2014a well known epigenetic modification. Our previous research has demonstrated that developmental MeHg exposure may yield transgenerational inheritance of neurological dysfunction in adult F3 lineage zebrafish via quantitative neurobehavioral assays that evaluated the visual startle response retinal electrophysiology and locomotor function. The objective of the current study was to examine the correlation between neurobehavioral phenotypes and the transcriptome activity in the brain and retina of F3 zebrafish by RNA sequencing RNAseq. Transcriptomic analyses of F3 generation MeHg treated zebrafish compared to control revealed significant gene dysregulation in both the brain and retina. There were 1648 and 138 differentially expressed genes in the retina and brain respectively FDR <0.05. Thirty five genes were commonly dysregulated in both organs. Gene set enrichment analysis revealed significantly enriched pathways including: neurodevelopment visual functions phototransduction and motor movement. Moreover commonly dysregulated genes were associated with circadian rhythm and metabolic pathways as well as arginine and proline metabolism. To our knowledge this is the first evidence of a transgenerational transcriptome induced by ancestral developmental exposure to MeHg in any species. If the transgenerational phenotypes transcriptome homologous biomarkers or similar molecular pathways hold true for human populations our findings have significant impact on global public health in terms of identifying the susceptible populations using biomarkers and preventing transgenerational inheritance of MeHg induced neurobehavioral deficits. Overall design: Eggs of EK strain zebrafish were exposed to methylmercury 0.0 and 0.03\u00b5M with ethanol as the vehicle for 24 hours then raised normally. This represents the F1 generation of each respective lineage. F2 and F3 generations were created for each lineage. The F2 and F3 generations were never exposed to exogenous MeHg. The brain were collected from F3 generation fish of each lineage. 12 samples of total RNA isolated from adult zebrafish brain were analyzed. There were 6 biological replicates for vehicle control 0 \u00b5M MeHg and exposure 0.03 \u00b5M MeHg groups.", "parent bioproject:PRJNA297897", null, null, "T8B", "GSM1902837", null, "source name:Brain|tissue:Brain|generation:F3|strain:EK|mehg conc:0.03\u00b5M MeHg", "T8B", "Basecalling was performed using CASAVA 1.8.2. Adapters and low quality bases were removed from the initial 2x101bp Illumina TruSeq reads and trimmed using Cutadapt FastQC was used to ensure that cleaned reads were of higher quality than initial raw reads supplied by the sequencer The cleaned reads for each sample were independently aligned to the reference zebrafish genome Zv9 UCSC using TopHat Aligned reads were used to generate count and fpkm data using Cuffnorm against Zv9 trainscriptome Genome build: UCSC Zv9 Supplementary files format and content: Tab delimited matrix of gene counts and FPKM normalized counts", "Brain", "The F1 generation embryos were exposed to MeHg. Brain of F3 generation was used for isolating RNA.", "High quality total RNA was extracted from the brain using RNeasy Micro Kit QIAGEN Valencia CA USA. Illumina TruSeq RNA Library Preparation and Sequencing was performed at the Biotechnology Center at the University of Wisconsin Madison. Each library was generated using a paired end approach following the Illumina \u201cTruSeq RNA Sample Preparation Guide\u201d and the Illumina TruSeq RNA Sample Preparation Kit Illumina Inc. San Diego CA USA. Samples were run with 12 samples per lane with 100 base pair paired end reads. Sequencing depth was 14 32 million reads per sample.", "Eggs of EK strain zebrafish were exposed to methylmercury\u00a00.0 and 0.03\u03bcM with ethanol as the vehicle for 24 hours then raised normally.\u00a0This represents the F1 generation of each respective lineage. F2 and F3 generations were created for each lineage.\u00a0The F2 and F3 generations were never exposed to exogenous MeHg.\u00a0", "tissue:Brain|generation:F3|strain:EK|mehg conc:0.03\u00b5M MeHg", "GSM1902837", "GSM1902837: T8B; Danio rerio; RNA Seq", "GSM1902837", null, "1", "High quality total RNA was extracted from the brain using RNeasy Micro Kit QIAGEN Valencia CA USA. Illumina TruSeq RNA Library Preparation and Sequencing was performed at the Biotechnology Center at the University of Wisconsin Madison. Each library was generated using a paired end approach following the Illumina \u201cTruSeq RNA Sample Preparation Guide\u201d and the Illumina TruSeq RNA Sample Preparation Kit Illumina Inc. San Diego CA USA. Samples were run with 12 samples per lane with 100 base pair paired end reads. Sequencing depth was 14 32 million reads per sample.", "GEO Accession:GSM1902837", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP064535", null, null, "run483.T8B_ATGTCA_L001_R1.fastq.gz run483.T8B_ATGTCA_L001_R2.fastq.gz", "fastq fastq", 1215203114.0, 6015857.0, "GSM1902837 r1", "0:101 1:101", "A:336424390;C:273606117;G:269346180;T:334985251;N:841176", 101, 101, null, null, 336424390, 273606117, 269346180, 334985251, 841176, "SRX1309247", "SRS1102442", "SRA303285", "GEO", "Carvan Lab, School of Freshwater Sciences, University of Wisconsin-Milwaukee", 2, 0.92535, 0.92517, 0.11781, 0.11929, 0.68578, 0.69142, 0.50751, 0.50704, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2015-10-06", "Undetermined", "Embryo", "Brain", "Nervous System"], [39963, "SRR2567885", "SRX1309246", "SRS1102444", "SRP064535", "PRJNA297905", "Methylmercury MeHg induced Transgenerational Inheritance of Brain Transcriptome in Zebrafish Danio rerio [brain]", "GSE73794", "Transcriptome Analysis", "Methylmercury MeHg is a ubiquitous environmental toxicant that is often detected in the tissues of fish eating species. It has been well established that prenatal exposure to MeHg can lead to widespread brain damage and impaired neurological development resulting in defects ranging from severe cerebral palsy and cognitive deficits to impaired motor and sensory function. A wide range of environmental toxicants have been shown to induce transgenerational inheritance of diseases via changes in DNA methylation\u2014a well known epigenetic modification. Our previous research has demonstrated that developmental MeHg exposure may yield transgenerational inheritance of neurological dysfunction in adult F3 lineage zebrafish via quantitative neurobehavioral assays that evaluated the visual startle response retinal electrophysiology and locomotor function. The objective of the current study was to examine the correlation between neurobehavioral phenotypes and the transcriptome activity in the brain and retina of F3 zebrafish by RNA sequencing RNAseq. Transcriptomic analyses of F3 generation MeHg treated zebrafish compared to control revealed significant gene dysregulation in both the brain and retina. There were 1648 and 138 differentially expressed genes in the retina and brain respectively FDR <0.05. Thirty five genes were commonly dysregulated in both organs. Gene set enrichment analysis revealed significantly enriched pathways including: neurodevelopment visual functions phototransduction and motor movement. Moreover commonly dysregulated genes were associated with circadian rhythm and metabolic pathways as well as arginine and proline metabolism. To our knowledge this is the first evidence of a transgenerational transcriptome induced by ancestral developmental exposure to MeHg in any species. If the transgenerational phenotypes transcriptome homologous biomarkers or similar molecular pathways hold true for human populations our findings have significant impact on global public health in terms of identifying the susceptible populations using biomarkers and preventing transgenerational inheritance of MeHg induced neurobehavioral deficits. Overall design: Eggs of EK strain zebrafish were exposed to methylmercury 0.0 and 0.03\u00b5M with ethanol as the vehicle for 24 hours then raised normally. This represents the F1 generation of each respective lineage. F2 and F3 generations were created for each lineage. The F2 and F3 generations were never exposed to exogenous MeHg. The brain were collected from F3 generation fish of each lineage. 12 samples of total RNA isolated from adult zebrafish brain were analyzed. There were 6 biological replicates for vehicle control 0 \u00b5M MeHg and exposure 0.03 \u00b5M MeHg groups.", "parent bioproject:PRJNA297897", null, null, "T7B", "GSM1902836", null, "source name:Brain|tissue:Brain|generation:F3|strain:EK|mehg conc:0.03\u00b5M MeHg", "T7B", "Basecalling was performed using CASAVA 1.8.2. Adapters and low quality bases were removed from the initial 2x101bp Illumina TruSeq reads and trimmed using Cutadapt FastQC was used to ensure that cleaned reads were of higher quality than initial raw reads supplied by the sequencer The cleaned reads for each sample were independently aligned to the reference zebrafish genome Zv9 UCSC using TopHat Aligned reads were used to generate count and fpkm data using Cuffnorm against Zv9 trainscriptome Genome build: UCSC Zv9 Supplementary files format and content: Tab delimited matrix of gene counts and FPKM normalized counts", "Brain", "The F1 generation embryos were exposed to MeHg. Brain of F3 generation was used for isolating RNA.", "High quality total RNA was extracted from the brain using RNeasy Micro Kit QIAGEN Valencia CA USA. Illumina TruSeq RNA Library Preparation and Sequencing was performed at the Biotechnology Center at the University of Wisconsin Madison. Each library was generated using a paired end approach following the Illumina \u201cTruSeq RNA Sample Preparation Guide\u201d and the Illumina TruSeq RNA Sample Preparation Kit Illumina Inc. San Diego CA USA. Samples were run with 12 samples per lane with 100 base pair paired end reads. Sequencing depth was 14 32 million reads per sample.", "Eggs of EK strain zebrafish were exposed to methylmercury\u00a00.0 and 0.03\u03bcM with ethanol as the vehicle for 24 hours then raised normally.\u00a0This represents the F1 generation of each respective lineage. F2 and F3 generations were created for each lineage.\u00a0The F2 and F3 generations were never exposed to exogenous MeHg.\u00a0", "tissue:Brain|generation:F3|strain:EK|mehg conc:0.03\u00b5M MeHg", "GSM1902836", "GSM1902836: T7B; Danio rerio; RNA Seq", "GSM1902836", null, "1", "High quality total RNA was extracted from the brain using RNeasy Micro Kit QIAGEN Valencia CA USA. Illumina TruSeq RNA Library Preparation and Sequencing was performed at the Biotechnology Center at the University of Wisconsin Madison. Each library was generated using a paired end approach following the Illumina \u201cTruSeq RNA Sample Preparation Guide\u201d and the Illumina TruSeq RNA Sample Preparation Kit Illumina Inc. San Diego CA USA. Samples were run with 12 samples per lane with 100 base pair paired end reads. Sequencing depth was 14 32 million reads per sample.", "GEO Accession:GSM1902836", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP064535", null, null, "run483.T7B_CCGTCC_L001_R1.fastq.gz run483.T7B_CCGTCC_L001_R2.fastq.gz", "fastq fastq", 1068777354.0, 5290977.0, "GSM1902836 r1", "0:101 1:101", "A:276820316;C:258980317;G:256182197;T:276058514;N:736010", 101, 101, null, null, 276820316, 258980317, 256182197, 276058514, 736010, "SRX1309246", "SRS1102444", "SRA303285", "GEO", "Carvan Lab, School of Freshwater Sciences, University of Wisconsin-Milwaukee", 2, 0.94967, 0.94754, 0.08415, 0.08514, 0.68288, 0.68909, 0.5163, 0.51635, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2015-10-06", "Undetermined", "Embryo", "Brain", "Nervous System"], [39964, "SRR2567884", "SRX1309245", "SRS1102445", "SRP064535", "PRJNA297905", "Methylmercury MeHg induced Transgenerational Inheritance of Brain Transcriptome in Zebrafish Danio rerio [brain]", "GSE73794", "Transcriptome Analysis", "Methylmercury MeHg is a ubiquitous environmental toxicant that is often detected in the tissues of fish eating species. It has been well established that prenatal exposure to MeHg can lead to widespread brain damage and impaired neurological development resulting in defects ranging from severe cerebral palsy and cognitive deficits to impaired motor and sensory function. A wide range of environmental toxicants have been shown to induce transgenerational inheritance of diseases via changes in DNA methylation\u2014a well known epigenetic modification. Our previous research has demonstrated that developmental MeHg exposure may yield transgenerational inheritance of neurological dysfunction in adult F3 lineage zebrafish via quantitative neurobehavioral assays that evaluated the visual startle response retinal electrophysiology and locomotor function. The objective of the current study was to examine the correlation between neurobehavioral phenotypes and the transcriptome activity in the brain and retina of F3 zebrafish by RNA sequencing RNAseq. Transcriptomic analyses of F3 generation MeHg treated zebrafish compared to control revealed significant gene dysregulation in both the brain and retina. There were 1648 and 138 differentially expressed genes in the retina and brain respectively FDR <0.05. Thirty five genes were commonly dysregulated in both organs. Gene set enrichment analysis revealed significantly enriched pathways including: neurodevelopment visual functions phototransduction and motor movement. Moreover commonly dysregulated genes were associated with circadian rhythm and metabolic pathways as well as arginine and proline metabolism. To our knowledge this is the first evidence of a transgenerational transcriptome induced by ancestral developmental exposure to MeHg in any species. If the transgenerational phenotypes transcriptome homologous biomarkers or similar molecular pathways hold true for human populations our findings have significant impact on global public health in terms of identifying the susceptible populations using biomarkers and preventing transgenerational inheritance of MeHg induced neurobehavioral deficits. Overall design: Eggs of EK strain zebrafish were exposed to methylmercury 0.0 and 0.03\u00b5M with ethanol as the vehicle for 24 hours then raised normally. This represents the F1 generation of each respective lineage. F2 and F3 generations were created for each lineage. The F2 and F3 generations were never exposed to exogenous MeHg. The brain were collected from F3 generation fish of each lineage. 12 samples of total RNA isolated from adult zebrafish brain were analyzed. There were 6 biological replicates for vehicle control 0 \u00b5M MeHg and exposure 0.03 \u00b5M MeHg groups.", "parent bioproject:PRJNA297897", null, null, "T5B", "GSM1902835", null, "source name:Brain|tissue:Brain|generation:F3|strain:EK|mehg conc:0.03\u00b5M MeHg", "T5B", "Basecalling was performed using CASAVA 1.8.2. Adapters and low quality bases were removed from the initial 2x101bp Illumina TruSeq reads and trimmed using Cutadapt FastQC was used to ensure that cleaned reads were of higher quality than initial raw reads supplied by the sequencer The cleaned reads for each sample were independently aligned to the reference zebrafish genome Zv9 UCSC using TopHat Aligned reads were used to generate count and fpkm data using Cuffnorm against Zv9 trainscriptome Genome build: UCSC Zv9 Supplementary files format and content: Tab delimited matrix of gene counts and FPKM normalized counts", "Brain", "The F1 generation embryos were exposed to MeHg. Brain of F3 generation was used for isolating RNA.", "High quality total RNA was extracted from the brain using RNeasy Micro Kit QIAGEN Valencia CA USA. Illumina TruSeq RNA Library Preparation and Sequencing was performed at the Biotechnology Center at the University of Wisconsin Madison. Each library was generated using a paired end approach following the Illumina \u201cTruSeq RNA Sample Preparation Guide\u201d and the Illumina TruSeq RNA Sample Preparation Kit Illumina Inc. San Diego CA USA. Samples were run with 12 samples per lane with 100 base pair paired end reads. Sequencing depth was 14 32 million reads per sample.", "Eggs of EK strain zebrafish were exposed to methylmercury\u00a00.0 and 0.03\u03bcM with ethanol as the vehicle for 24 hours then raised normally.\u00a0This represents the F1 generation of each respective lineage. F2 and F3 generations were created for each lineage.\u00a0The F2 and F3 generations were never exposed to exogenous MeHg.\u00a0", "tissue:Brain|generation:F3|strain:EK|mehg conc:0.03\u00b5M MeHg", "GSM1902835", "GSM1902835: T5B; Danio rerio; RNA Seq", "GSM1902835", null, "1", "High quality total RNA was extracted from the brain using RNeasy Micro Kit QIAGEN Valencia CA USA. Illumina TruSeq RNA Library Preparation and Sequencing was performed at the Biotechnology Center at the University of Wisconsin Madison. Each library was generated using a paired end approach following the Illumina \u201cTruSeq RNA Sample Preparation Guide\u201d and the Illumina TruSeq RNA Sample Preparation Kit Illumina Inc. San Diego CA USA. Samples were run with 12 samples per lane with 100 base pair paired end reads. Sequencing depth was 14 32 million reads per sample.", "GEO Accession:GSM1902835", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP064535", null, null, "run483.T5B_GTCCGC_L001_R1.fastq.gz run483.T5B_GTCCGC_L001_R2.fastq.gz", "fastq fastq", 2187826852.0, 10830826.0, "GSM1902835 r1", "0:101 1:101", "A:605541583;C:491166655;G:484174584;T:605442496;N:1501534", 101, 101, null, null, 605541583, 491166655, 484174584, 605442496, 1501534, "SRX1309245", "SRS1102445", "SRA303285", "GEO", "Carvan Lab, School of Freshwater Sciences, University of Wisconsin-Milwaukee", 2, 0.93199, 0.93113, 0.10539, 0.1068, 0.67998, 0.68373, 0.50227, 0.50521, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2015-10-06", "Undetermined", "Embryo", "Brain", "Nervous System"], [39965, "SRR2567883", "SRX1309244", "SRS1102443", "SRP064535", "PRJNA297905", "Methylmercury MeHg induced Transgenerational Inheritance of Brain Transcriptome in Zebrafish Danio rerio [brain]", "GSE73794", "Transcriptome Analysis", "Methylmercury MeHg is a ubiquitous environmental toxicant that is often detected in the tissues of fish eating species. It has been well established that prenatal exposure to MeHg can lead to widespread brain damage and impaired neurological development resulting in defects ranging from severe cerebral palsy and cognitive deficits to impaired motor and sensory function. A wide range of environmental toxicants have been shown to induce transgenerational inheritance of diseases via changes in DNA methylation\u2014a well known epigenetic modification. Our previous research has demonstrated that developmental MeHg exposure may yield transgenerational inheritance of neurological dysfunction in adult F3 lineage zebrafish via quantitative neurobehavioral assays that evaluated the visual startle response retinal electrophysiology and locomotor function. The objective of the current study was to examine the correlation between neurobehavioral phenotypes and the transcriptome activity in the brain and retina of F3 zebrafish by RNA sequencing RNAseq. Transcriptomic analyses of F3 generation MeHg treated zebrafish compared to control revealed significant gene dysregulation in both the brain and retina. There were 1648 and 138 differentially expressed genes in the retina and brain respectively FDR <0.05. Thirty five genes were commonly dysregulated in both organs. Gene set enrichment analysis revealed significantly enriched pathways including: neurodevelopment visual functions phototransduction and motor movement. Moreover commonly dysregulated genes were associated with circadian rhythm and metabolic pathways as well as arginine and proline metabolism. To our knowledge this is the first evidence of a transgenerational transcriptome induced by ancestral developmental exposure to MeHg in any species. If the transgenerational phenotypes transcriptome homologous biomarkers or similar molecular pathways hold true for human populations our findings have significant impact on global public health in terms of identifying the susceptible populations using biomarkers and preventing transgenerational inheritance of MeHg induced neurobehavioral deficits. Overall design: Eggs of EK strain zebrafish were exposed to methylmercury 0.0 and 0.03\u00b5M with ethanol as the vehicle for 24 hours then raised normally. This represents the F1 generation of each respective lineage. F2 and F3 generations were created for each lineage. The F2 and F3 generations were never exposed to exogenous MeHg. The brain were collected from F3 generation fish of each lineage. 12 samples of total RNA isolated from adult zebrafish brain were analyzed. There were 6 biological replicates for vehicle control 0 \u00b5M MeHg and exposure 0.03 \u00b5M MeHg groups.", "parent bioproject:PRJNA297897", null, null, "T4B", "GSM1902834", null, "source name:Brain|tissue:Brain|generation:F3|strain:EK|mehg conc:0.03\u00b5M MeHg", "T4B", "Basecalling was performed using CASAVA 1.8.2. Adapters and low quality bases were removed from the initial 2x101bp Illumina TruSeq reads and trimmed using Cutadapt FastQC was used to ensure that cleaned reads were of higher quality than initial raw reads supplied by the sequencer The cleaned reads for each sample were independently aligned to the reference zebrafish genome Zv9 UCSC using TopHat Aligned reads were used to generate count and fpkm data using Cuffnorm against Zv9 trainscriptome Genome build: UCSC Zv9 Supplementary files format and content: Tab delimited matrix of gene counts and FPKM normalized counts", "Brain", "The F1 generation embryos were exposed to MeHg. Brain of F3 generation was used for isolating RNA.", "High quality total RNA was extracted from the brain using RNeasy Micro Kit QIAGEN Valencia CA USA. Illumina TruSeq RNA Library Preparation and Sequencing was performed at the Biotechnology Center at the University of Wisconsin Madison. Each library was generated using a paired end approach following the Illumina \u201cTruSeq RNA Sample Preparation Guide\u201d and the Illumina TruSeq RNA Sample Preparation Kit Illumina Inc. San Diego CA USA. Samples were run with 12 samples per lane with 100 base pair paired end reads. Sequencing depth was 14 32 million reads per sample.", "Eggs of EK strain zebrafish were exposed to methylmercury\u00a00.0 and 0.03\u03bcM with ethanol as the vehicle for 24 hours then raised normally.\u00a0This represents the F1 generation of each respective lineage. F2 and F3 generations were created for each lineage.\u00a0The F2 and F3 generations were never exposed to exogenous MeHg.\u00a0", "tissue:Brain|generation:F3|strain:EK|mehg conc:0.03\u00b5M MeHg", "GSM1902834", "GSM1902834: T4B; Danio rerio; RNA Seq", "GSM1902834", null, "1", "High quality total RNA was extracted from the brain using RNeasy Micro Kit QIAGEN Valencia CA USA. Illumina TruSeq RNA Library Preparation and Sequencing was performed at the Biotechnology Center at the University of Wisconsin Madison. Each library was generated using a paired end approach following the Illumina \u201cTruSeq RNA Sample Preparation Guide\u201d and the Illumina TruSeq RNA Sample Preparation Kit Illumina Inc. San Diego CA USA. Samples were run with 12 samples per lane with 100 base pair paired end reads. Sequencing depth was 14 32 million reads per sample.", "GEO Accession:GSM1902834", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP064535", null, null, "run483.T4B_GTGAAA_L001_R1.fastq.gz run483.T4B_GTGAAA_L001_R2.fastq.gz", "fastq fastq", 1236398570.0, 6120785.0, "GSM1902834 r1", "0:101 1:101", "A:339837695;C:280036230;G:277105567;T:338557657;N:861421", 101, 101, null, null, 339837695, 280036230, 277105567, 338557657, 861421, "SRX1309244", "SRS1102443", "SRA303285", "GEO", "Carvan Lab, School of Freshwater Sciences, University of Wisconsin-Milwaukee", 2, 0.92827, 0.92699, 0.11555, 0.11706, 0.66281, 0.66854, 0.51102, 0.5084, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2015-10-06", "Undetermined", "Embryo", "Brain", "Nervous System"], [39966, "SRR2567882", "SRX1309243", "SRS1102446", "SRP064535", "PRJNA297905", "Methylmercury MeHg induced Transgenerational Inheritance of Brain Transcriptome in Zebrafish Danio rerio [brain]", "GSE73794", "Transcriptome Analysis", "Methylmercury MeHg is a ubiquitous environmental toxicant that is often detected in the tissues of fish eating species. It has been well established that prenatal exposure to MeHg can lead to widespread brain damage and impaired neurological development resulting in defects ranging from severe cerebral palsy and cognitive deficits to impaired motor and sensory function. A wide range of environmental toxicants have been shown to induce transgenerational inheritance of diseases via changes in DNA methylation\u2014a well known epigenetic modification. Our previous research has demonstrated that developmental MeHg exposure may yield transgenerational inheritance of neurological dysfunction in adult F3 lineage zebrafish via quantitative neurobehavioral assays that evaluated the visual startle response retinal electrophysiology and locomotor function. The objective of the current study was to examine the correlation between neurobehavioral phenotypes and the transcriptome activity in the brain and retina of F3 zebrafish by RNA sequencing RNAseq. Transcriptomic analyses of F3 generation MeHg treated zebrafish compared to control revealed significant gene dysregulation in both the brain and retina. There were 1648 and 138 differentially expressed genes in the retina and brain respectively FDR <0.05. Thirty five genes were commonly dysregulated in both organs. Gene set enrichment analysis revealed significantly enriched pathways including: neurodevelopment visual functions phototransduction and motor movement. Moreover commonly dysregulated genes were associated with circadian rhythm and metabolic pathways as well as arginine and proline metabolism. To our knowledge this is the first evidence of a transgenerational transcriptome induced by ancestral developmental exposure to MeHg in any species. If the transgenerational phenotypes transcriptome homologous biomarkers or similar molecular pathways hold true for human populations our findings have significant impact on global public health in terms of identifying the susceptible populations using biomarkers and preventing transgenerational inheritance of MeHg induced neurobehavioral deficits. Overall design: Eggs of EK strain zebrafish were exposed to methylmercury 0.0 and 0.03\u00b5M with ethanol as the vehicle for 24 hours then raised normally. This represents the F1 generation of each respective lineage. F2 and F3 generations were created for each lineage. The F2 and F3 generations were never exposed to exogenous MeHg. The brain were collected from F3 generation fish of each lineage. 12 samples of total RNA isolated from adult zebrafish brain were analyzed. There were 6 biological replicates for vehicle control 0 \u00b5M MeHg and exposure 0.03 \u00b5M MeHg groups.", "parent bioproject:PRJNA297897", null, null, "T2B", "GSM1902833", null, "source name:Brain|tissue:Brain|generation:F3|strain:EK|mehg conc:0.03\u00b5M MeHg", "T2B", "Basecalling was performed using CASAVA 1.8.2. Adapters and low quality bases were removed from the initial 2x101bp Illumina TruSeq reads and trimmed using Cutadapt FastQC was used to ensure that cleaned reads were of higher quality than initial raw reads supplied by the sequencer The cleaned reads for each sample were independently aligned to the reference zebrafish genome Zv9 UCSC using TopHat Aligned reads were used to generate count and fpkm data using Cuffnorm against Zv9 trainscriptome Genome build: UCSC Zv9 Supplementary files format and content: Tab delimited matrix of gene counts and FPKM normalized counts", "Brain", "The F1 generation embryos were exposed to MeHg. Brain of F3 generation was used for isolating RNA.", "High quality total RNA was extracted from the brain using RNeasy Micro Kit QIAGEN Valencia CA USA. Illumina TruSeq RNA Library Preparation and Sequencing was performed at the Biotechnology Center at the University of Wisconsin Madison. Each library was generated using a paired end approach following the Illumina \u201cTruSeq RNA Sample Preparation Guide\u201d and the Illumina TruSeq RNA Sample Preparation Kit Illumina Inc. San Diego CA USA. Samples were run with 12 samples per lane with 100 base pair paired end reads. Sequencing depth was 14 32 million reads per sample.", "Eggs of EK strain zebrafish were exposed to methylmercury\u00a00.0 and 0.03\u03bcM with ethanol as the vehicle for 24 hours then raised normally.\u00a0This represents the F1 generation of each respective lineage. F2 and F3 generations were created for each lineage.\u00a0The F2 and F3 generations were never exposed to exogenous MeHg.\u00a0", "tissue:Brain|generation:F3|strain:EK|mehg conc:0.03\u00b5M MeHg", "GSM1902833", "GSM1902833: T2B; Danio rerio; RNA Seq", "GSM1902833", null, "1", "High quality total RNA was extracted from the brain using RNeasy Micro Kit QIAGEN Valencia CA USA. Illumina TruSeq RNA Library Preparation and Sequencing was performed at the Biotechnology Center at the University of Wisconsin Madison. Each library was generated using a paired end approach following the Illumina \u201cTruSeq RNA Sample Preparation Guide\u201d and the Illumina TruSeq RNA Sample Preparation Kit Illumina Inc. San Diego CA USA. Samples were run with 12 samples per lane with 100 base pair paired end reads. Sequencing depth was 14 32 million reads per sample.", "GEO Accession:GSM1902833", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP064535", null, null, "run483.T2B_GTGGCC_L001_R1.fastq.gz run483.T2B_GTGGCC_L001_R2.fastq.gz", "fastq fastq", 968024198.0, 4792199.0, "GSM1902833 r1", "0:101 1:101", "A:267829480;C:217619913;G:214446470;T:267459510;N:668825", 101, 101, null, null, 267829480, 217619913, 214446470, 267459510, 668825, "SRX1309243", "SRS1102446", "SRA303285", "GEO", "Carvan Lab, School of Freshwater Sciences, University of Wisconsin-Milwaukee", 2, 0.92689, 0.92638, 0.11349, 0.11441, 0.68767, 0.69256, 0.49742, 0.51565, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2015-10-06", "Undetermined", "Embryo", "Brain", "Nervous System"], [39967, "SRR2567881", "SRX1309242", "SRS1102447", "SRP064535", "PRJNA297905", "Methylmercury MeHg induced Transgenerational Inheritance of Brain Transcriptome in Zebrafish Danio rerio [brain]", "GSE73794", "Transcriptome Analysis", "Methylmercury MeHg is a ubiquitous environmental toxicant that is often detected in the tissues of fish eating species. It has been well established that prenatal exposure to MeHg can lead to widespread brain damage and impaired neurological development resulting in defects ranging from severe cerebral palsy and cognitive deficits to impaired motor and sensory function. A wide range of environmental toxicants have been shown to induce transgenerational inheritance of diseases via changes in DNA methylation\u2014a well known epigenetic modification. Our previous research has demonstrated that developmental MeHg exposure may yield transgenerational inheritance of neurological dysfunction in adult F3 lineage zebrafish via quantitative neurobehavioral assays that evaluated the visual startle response retinal electrophysiology and locomotor function. The objective of the current study was to examine the correlation between neurobehavioral phenotypes and the transcriptome activity in the brain and retina of F3 zebrafish by RNA sequencing RNAseq. Transcriptomic analyses of F3 generation MeHg treated zebrafish compared to control revealed significant gene dysregulation in both the brain and retina. There were 1648 and 138 differentially expressed genes in the retina and brain respectively FDR <0.05. Thirty five genes were commonly dysregulated in both organs. Gene set enrichment analysis revealed significantly enriched pathways including: neurodevelopment visual functions phototransduction and motor movement. Moreover commonly dysregulated genes were associated with circadian rhythm and metabolic pathways as well as arginine and proline metabolism. To our knowledge this is the first evidence of a transgenerational transcriptome induced by ancestral developmental exposure to MeHg in any species. If the transgenerational phenotypes transcriptome homologous biomarkers or similar molecular pathways hold true for human populations our findings have significant impact on global public health in terms of identifying the susceptible populations using biomarkers and preventing transgenerational inheritance of MeHg induced neurobehavioral deficits. Overall design: Eggs of EK strain zebrafish were exposed to methylmercury 0.0 and 0.03\u00b5M with ethanol as the vehicle for 24 hours then raised normally. This represents the F1 generation of each respective lineage. F2 and F3 generations were created for each lineage. The F2 and F3 generations were never exposed to exogenous MeHg. The brain were collected from F3 generation fish of each lineage. 12 samples of total RNA isolated from adult zebrafish brain were analyzed. There were 6 biological replicates for vehicle control 0 \u00b5M MeHg and exposure 0.03 \u00b5M MeHg groups.", "parent bioproject:PRJNA297897", null, null, "T1B", "GSM1902832", null, "source name:Brain|tissue:Brain|generation:F3|strain:EK|mehg conc:0.03\u00b5M MeHg", "T1B", "Basecalling was performed using CASAVA 1.8.2. Adapters and low quality bases were removed from the initial 2x101bp Illumina TruSeq reads and trimmed using Cutadapt FastQC was used to ensure that cleaned reads were of higher quality than initial raw reads supplied by the sequencer The cleaned reads for each sample were independently aligned to the reference zebrafish genome Zv9 UCSC using TopHat Aligned reads were used to generate count and fpkm data using Cuffnorm against Zv9 trainscriptome Genome build: UCSC Zv9 Supplementary files format and content: Tab delimited matrix of gene counts and FPKM normalized counts", "Brain", "The F1 generation embryos were exposed to MeHg. Brain of F3 generation was used for isolating RNA.", "High quality total RNA was extracted from the brain using RNeasy Micro Kit QIAGEN Valencia CA USA. Illumina TruSeq RNA Library Preparation and Sequencing was performed at the Biotechnology Center at the University of Wisconsin Madison. Each library was generated using a paired end approach following the Illumina \u201cTruSeq RNA Sample Preparation Guide\u201d and the Illumina TruSeq RNA Sample Preparation Kit Illumina Inc. San Diego CA USA. Samples were run with 12 samples per lane with 100 base pair paired end reads. Sequencing depth was 14 32 million reads per sample.", "Eggs of EK strain zebrafish were exposed to methylmercury\u00a00.0 and 0.03\u03bcM with ethanol as the vehicle for 24 hours then raised normally.\u00a0This represents the F1 generation of each respective lineage. F2 and F3 generations were created for each lineage.\u00a0The F2 and F3 generations were never exposed to exogenous MeHg.\u00a0", "tissue:Brain|generation:F3|strain:EK|mehg conc:0.03\u00b5M MeHg", "GSM1902832", "GSM1902832: T1B; Danio rerio; RNA Seq", "GSM1902832", null, "1", "High quality total RNA was extracted from the brain using RNeasy Micro Kit QIAGEN Valencia CA USA. Illumina TruSeq RNA Library Preparation and Sequencing was performed at the Biotechnology Center at the University of Wisconsin Madison. Each library was generated using a paired end approach following the Illumina \u201cTruSeq RNA Sample Preparation Guide\u201d and the Illumina TruSeq RNA Sample Preparation Kit Illumina Inc. San Diego CA USA. Samples were run with 12 samples per lane with 100 base pair paired end reads. Sequencing depth was 14 32 million reads per sample.", "GEO Accession:GSM1902832", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP064535", null, null, "run483.T1B_GTTTCG_L001_R1.fastq.gz run483.T1B_GTTTCG_L001_R2.fastq.gz", "fastq fastq", 1051995598.0, 5207899.0, "GSM1902832 r1", "0:101 1:101", "A:289897650;C:238229837;G:234365589;T:288770640;N:731882", 101, 101, null, null, 289897650, 238229837, 234365589, 288770640, 731882, "SRX1309242", "SRS1102447", "SRA303285", "GEO", "Carvan Lab, School of Freshwater Sciences, University of Wisconsin-Milwaukee", 2, 0.9281, 0.92817, 0.11314, 0.11542, 0.68479, 0.6896, 0.51374, 0.51693, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2015-10-06", "Undetermined", "Embryo", "Brain", "Nervous System"], [39968, "SRR2567880", "SRX1309241", "SRS1102448", "SRP064535", "PRJNA297905", "Methylmercury MeHg induced Transgenerational Inheritance of Brain Transcriptome in Zebrafish Danio rerio [brain]", "GSE73794", "Transcriptome Analysis", "Methylmercury MeHg is a ubiquitous environmental toxicant that is often detected in the tissues of fish eating species. It has been well established that prenatal exposure to MeHg can lead to widespread brain damage and impaired neurological development resulting in defects ranging from severe cerebral palsy and cognitive deficits to impaired motor and sensory function. A wide range of environmental toxicants have been shown to induce transgenerational inheritance of diseases via changes in DNA methylation\u2014a well known epigenetic modification. Our previous research has demonstrated that developmental MeHg exposure may yield transgenerational inheritance of neurological dysfunction in adult F3 lineage zebrafish via quantitative neurobehavioral assays that evaluated the visual startle response retinal electrophysiology and locomotor function. The objective of the current study was to examine the correlation between neurobehavioral phenotypes and the transcriptome activity in the brain and retina of F3 zebrafish by RNA sequencing RNAseq. Transcriptomic analyses of F3 generation MeHg treated zebrafish compared to control revealed significant gene dysregulation in both the brain and retina. There were 1648 and 138 differentially expressed genes in the retina and brain respectively FDR <0.05. Thirty five genes were commonly dysregulated in both organs. Gene set enrichment analysis revealed significantly enriched pathways including: neurodevelopment visual functions phototransduction and motor movement. Moreover commonly dysregulated genes were associated with circadian rhythm and metabolic pathways as well as arginine and proline metabolism. To our knowledge this is the first evidence of a transgenerational transcriptome induced by ancestral developmental exposure to MeHg in any species. If the transgenerational phenotypes transcriptome homologous biomarkers or similar molecular pathways hold true for human populations our findings have significant impact on global public health in terms of identifying the susceptible populations using biomarkers and preventing transgenerational inheritance of MeHg induced neurobehavioral deficits. Overall design: Eggs of EK strain zebrafish were exposed to methylmercury 0.0 and 0.03\u00b5M with ethanol as the vehicle for 24 hours then raised normally. This represents the F1 generation of each respective lineage. F2 and F3 generations were created for each lineage. The F2 and F3 generations were never exposed to exogenous MeHg. The brain were collected from F3 generation fish of each lineage. 12 samples of total RNA isolated from adult zebrafish brain were analyzed. There were 6 biological replicates for vehicle control 0 \u00b5M MeHg and exposure 0.03 \u00b5M MeHg groups.", "parent bioproject:PRJNA297897", null, null, "C8B", "GSM1902831", null, "source name:Brain|tissue:Brain|generation:F3|strain:EK|mehg conc:0\u00b5M MeHg", "C8B", "Basecalling was performed using CASAVA 1.8.2. Adapters and low quality bases were removed from the initial 2x101bp Illumina TruSeq reads and trimmed using Cutadapt FastQC was used to ensure that cleaned reads were of higher quality than initial raw reads supplied by the sequencer The cleaned reads for each sample were independently aligned to the reference zebrafish genome Zv9 UCSC using TopHat Aligned reads were used to generate count and fpkm data using Cuffnorm against Zv9 trainscriptome Genome build: UCSC Zv9 Supplementary files format and content: Tab delimited matrix of gene counts and FPKM normalized counts", "Brain", "The F1 generation embryos were exposed to MeHg. Brain of F3 generation was used for isolating RNA.", "High quality total RNA was extracted from the brain using RNeasy Micro Kit QIAGEN Valencia CA USA. Illumina TruSeq RNA Library Preparation and Sequencing was performed at the Biotechnology Center at the University of Wisconsin Madison. Each library was generated using a paired end approach following the Illumina \u201cTruSeq RNA Sample Preparation Guide\u201d and the Illumina TruSeq RNA Sample Preparation Kit Illumina Inc. San Diego CA USA. Samples were run with 12 samples per lane with 100 base pair paired end reads. Sequencing depth was 14 32 million reads per sample.", "Eggs of EK strain zebrafish were exposed to methylmercury\u00a00.0 and 0.03\u03bcM with ethanol as the vehicle for 24 hours then raised normally.\u00a0This represents the F1 generation of each respective lineage. F2 and F3 generations were created for each lineage.\u00a0The F2 and F3 generations were never exposed to exogenous MeHg.\u00a0", "tissue:Brain|generation:F3|strain:EK|mehg conc:0\u00b5M MeHg", "GSM1902831", "GSM1902831: C8B; Danio rerio; RNA Seq", "GSM1902831", null, "1", "High quality total RNA was extracted from the brain using RNeasy Micro Kit QIAGEN Valencia CA USA. Illumina TruSeq RNA Library Preparation and Sequencing was performed at the Biotechnology Center at the University of Wisconsin Madison. Each library was generated using a paired end approach following the Illumina \u201cTruSeq RNA Sample Preparation Guide\u201d and the Illumina TruSeq RNA Sample Preparation Kit Illumina Inc. San Diego CA USA. Samples were run with 12 samples per lane with 100 base pair paired end reads. Sequencing depth was 14 32 million reads per sample.", "GEO Accession:GSM1902831", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP064535", null, null, "run483.C8B_AGTTCC_L001_R1.fastq.gz run483.C8B_AGTTCC_L001_R2.fastq.gz", "fastq fastq", 1877693828.0, 9295514.0, "GSM1902831 r1", "0:101 1:101", "A:522927396;C:418793561;G:412874043;T:521793163;N:1305665", 101, 101, null, null, 522927396, 418793561, 412874043, 521793163, 1305665, "SRX1309241", "SRS1102448", "SRA303285", "GEO", "Carvan Lab, School of Freshwater Sciences, University of Wisconsin-Milwaukee", 2, 0.92751, 0.9266, 0.12001, 0.12105, 0.69714, 0.70236, 0.50871, 0.49883, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2015-10-06", "Undetermined", "Embryo", "Brain", "Nervous System"], [39969, "SRR2567879", "SRX1309240", "SRS1102449", "SRP064535", "PRJNA297905", "Methylmercury MeHg induced Transgenerational Inheritance of Brain Transcriptome in Zebrafish Danio rerio [brain]", "GSE73794", "Transcriptome Analysis", "Methylmercury MeHg is a ubiquitous environmental toxicant that is often detected in the tissues of fish eating species. It has been well established that prenatal exposure to MeHg can lead to widespread brain damage and impaired neurological development resulting in defects ranging from severe cerebral palsy and cognitive deficits to impaired motor and sensory function. A wide range of environmental toxicants have been shown to induce transgenerational inheritance of diseases via changes in DNA methylation\u2014a well known epigenetic modification. Our previous research has demonstrated that developmental MeHg exposure may yield transgenerational inheritance of neurological dysfunction in adult F3 lineage zebrafish via quantitative neurobehavioral assays that evaluated the visual startle response retinal electrophysiology and locomotor function. The objective of the current study was to examine the correlation between neurobehavioral phenotypes and the transcriptome activity in the brain and retina of F3 zebrafish by RNA sequencing RNAseq. Transcriptomic analyses of F3 generation MeHg treated zebrafish compared to control revealed significant gene dysregulation in both the brain and retina. There were 1648 and 138 differentially expressed genes in the retina and brain respectively FDR <0.05. Thirty five genes were commonly dysregulated in both organs. Gene set enrichment analysis revealed significantly enriched pathways including: neurodevelopment visual functions phototransduction and motor movement. Moreover commonly dysregulated genes were associated with circadian rhythm and metabolic pathways as well as arginine and proline metabolism. To our knowledge this is the first evidence of a transgenerational transcriptome induced by ancestral developmental exposure to MeHg in any species. If the transgenerational phenotypes transcriptome homologous biomarkers or similar molecular pathways hold true for human populations our findings have significant impact on global public health in terms of identifying the susceptible populations using biomarkers and preventing transgenerational inheritance of MeHg induced neurobehavioral deficits. Overall design: Eggs of EK strain zebrafish were exposed to methylmercury 0.0 and 0.03\u00b5M with ethanol as the vehicle for 24 hours then raised normally. This represents the F1 generation of each respective lineage. F2 and F3 generations were created for each lineage. The F2 and F3 generations were never exposed to exogenous MeHg. The brain were collected from F3 generation fish of each lineage. 12 samples of total RNA isolated from adult zebrafish brain were analyzed. There were 6 biological replicates for vehicle control 0 \u00b5M MeHg and exposure 0.03 \u00b5M MeHg groups.", "parent bioproject:PRJNA297897", null, null, "C6B", "GSM1902830", null, "source name:Brain|tissue:Brain|generation:F3|strain:EK|mehg conc:0\u00b5M MeHg", "C6B", "Basecalling was performed using CASAVA 1.8.2. Adapters and low quality bases were removed from the initial 2x101bp Illumina TruSeq reads and trimmed using Cutadapt FastQC was used to ensure that cleaned reads were of higher quality than initial raw reads supplied by the sequencer The cleaned reads for each sample were independently aligned to the reference zebrafish genome Zv9 UCSC using TopHat Aligned reads were used to generate count and fpkm data using Cuffnorm against Zv9 trainscriptome Genome build: UCSC Zv9 Supplementary files format and content: Tab delimited matrix of gene counts and FPKM normalized counts", "Brain", "The F1 generation embryos were exposed to MeHg. Brain of F3 generation was used for isolating RNA.", "High quality total RNA was extracted from the brain using RNeasy Micro Kit QIAGEN Valencia CA USA. Illumina TruSeq RNA Library Preparation and Sequencing was performed at the Biotechnology Center at the University of Wisconsin Madison. Each library was generated using a paired end approach following the Illumina \u201cTruSeq RNA Sample Preparation Guide\u201d and the Illumina TruSeq RNA Sample Preparation Kit Illumina Inc. San Diego CA USA. Samples were run with 12 samples per lane with 100 base pair paired end reads. Sequencing depth was 14 32 million reads per sample.", "Eggs of EK strain zebrafish were exposed to methylmercury\u00a00.0 and 0.03\u03bcM with ethanol as the vehicle for 24 hours then raised normally.\u00a0This represents the F1 generation of each respective lineage. F2 and F3 generations were created for each lineage.\u00a0The F2 and F3 generations were never exposed to exogenous MeHg.\u00a0", "tissue:Brain|generation:F3|strain:EK|mehg conc:0\u00b5M MeHg", "GSM1902830", "GSM1902830: C6B; Danio rerio; RNA Seq", "GSM1902830", null, "1", "High quality total RNA was extracted from the brain using RNeasy Micro Kit QIAGEN Valencia CA USA. Illumina TruSeq RNA Library Preparation and Sequencing was performed at the Biotechnology Center at the University of Wisconsin Madison. Each library was generated using a paired end approach following the Illumina \u201cTruSeq RNA Sample Preparation Guide\u201d and the Illumina TruSeq RNA Sample Preparation Kit Illumina Inc. San Diego CA USA. Samples were run with 12 samples per lane with 100 base pair paired end reads. Sequencing depth was 14 32 million reads per sample.", "GEO Accession:GSM1902830", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP064535", null, null, "run483.C6B_AGTCAA_L001_R1.fastq.gz run483.C6B_AGTCAA_L001_R2.fastq.gz", "fastq fastq", 1621396228.0, 8026714.0, "GSM1902830 r1", "0:101 1:101", "A:445607490;C:367908457;G:364215334;T:442547659;N:1117288", 101, 101, null, null, 445607490, 367908457, 364215334, 442547659, 1117288, "SRX1309240", "SRS1102449", "SRA303285", "GEO", "Carvan Lab, School of Freshwater Sciences, University of Wisconsin-Milwaukee", 2, 0.93412, 0.93278, 0.10925, 0.10996, 0.69069, 0.69581, 0.52912, 0.5284, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2015-10-06", "Undetermined", "Embryo", "Brain", "Nervous System"], [39970, "SRR2567878", "SRX1309239", "SRS1102450", "SRP064535", "PRJNA297905", "Methylmercury MeHg induced Transgenerational Inheritance of Brain Transcriptome in Zebrafish Danio rerio [brain]", "GSE73794", "Transcriptome Analysis", "Methylmercury MeHg is a ubiquitous environmental toxicant that is often detected in the tissues of fish eating species. It has been well established that prenatal exposure to MeHg can lead to widespread brain damage and impaired neurological development resulting in defects ranging from severe cerebral palsy and cognitive deficits to impaired motor and sensory function. A wide range of environmental toxicants have been shown to induce transgenerational inheritance of diseases via changes in DNA methylation\u2014a well known epigenetic modification. Our previous research has demonstrated that developmental MeHg exposure may yield transgenerational inheritance of neurological dysfunction in adult F3 lineage zebrafish via quantitative neurobehavioral assays that evaluated the visual startle response retinal electrophysiology and locomotor function. The objective of the current study was to examine the correlation between neurobehavioral phenotypes and the transcriptome activity in the brain and retina of F3 zebrafish by RNA sequencing RNAseq. Transcriptomic analyses of F3 generation MeHg treated zebrafish compared to control revealed significant gene dysregulation in both the brain and retina. There were 1648 and 138 differentially expressed genes in the retina and brain respectively FDR <0.05. Thirty five genes were commonly dysregulated in both organs. Gene set enrichment analysis revealed significantly enriched pathways including: neurodevelopment visual functions phototransduction and motor movement. Moreover commonly dysregulated genes were associated with circadian rhythm and metabolic pathways as well as arginine and proline metabolism. To our knowledge this is the first evidence of a transgenerational transcriptome induced by ancestral developmental exposure to MeHg in any species. If the transgenerational phenotypes transcriptome homologous biomarkers or similar molecular pathways hold true for human populations our findings have significant impact on global public health in terms of identifying the susceptible populations using biomarkers and preventing transgenerational inheritance of MeHg induced neurobehavioral deficits. Overall design: Eggs of EK strain zebrafish were exposed to methylmercury 0.0 and 0.03\u00b5M with ethanol as the vehicle for 24 hours then raised normally. This represents the F1 generation of each respective lineage. F2 and F3 generations were created for each lineage. The F2 and F3 generations were never exposed to exogenous MeHg. The brain were collected from F3 generation fish of each lineage. 12 samples of total RNA isolated from adult zebrafish brain were analyzed. There were 6 biological replicates for vehicle control 0 \u00b5M MeHg and exposure 0.03 \u00b5M MeHg groups.", "parent bioproject:PRJNA297897", null, null, "C5B", "GSM1902829", null, "source name:Brain|tissue:Brain|generation:F3|strain:EK|mehg conc:0\u00b5M MeHg", "C5B", "Basecalling was performed using CASAVA 1.8.2. Adapters and low quality bases were removed from the initial 2x101bp Illumina TruSeq reads and trimmed using Cutadapt FastQC was used to ensure that cleaned reads were of higher quality than initial raw reads supplied by the sequencer The cleaned reads for each sample were independently aligned to the reference zebrafish genome Zv9 UCSC using TopHat Aligned reads were used to generate count and fpkm data using Cuffnorm against Zv9 trainscriptome Genome build: UCSC Zv9 Supplementary files format and content: Tab delimited matrix of gene counts and FPKM normalized counts", "Brain", "The F1 generation embryos were exposed to MeHg. Brain of F3 generation was used for isolating RNA.", "High quality total RNA was extracted from the brain using RNeasy Micro Kit QIAGEN Valencia CA USA. Illumina TruSeq RNA Library Preparation and Sequencing was performed at the Biotechnology Center at the University of Wisconsin Madison. Each library was generated using a paired end approach following the Illumina \u201cTruSeq RNA Sample Preparation Guide\u201d and the Illumina TruSeq RNA Sample Preparation Kit Illumina Inc. San Diego CA USA. Samples were run with 12 samples per lane with 100 base pair paired end reads. Sequencing depth was 14 32 million reads per sample.", "Eggs of EK strain zebrafish were exposed to methylmercury\u00a00.0 and 0.03\u03bcM with ethanol as the vehicle for 24 hours then raised normally.\u00a0This represents the F1 generation of each respective lineage. F2 and F3 generations were created for each lineage.\u00a0The F2 and F3 generations were never exposed to exogenous MeHg.\u00a0", "tissue:Brain|generation:F3|strain:EK|mehg conc:0\u00b5M MeHg", "GSM1902829", "GSM1902829: C5B; Danio rerio; RNA Seq", "GSM1902829", null, "1", "High quality total RNA was extracted from the brain using RNeasy Micro Kit QIAGEN Valencia CA USA. Illumina TruSeq RNA Library Preparation and Sequencing was performed at the Biotechnology Center at the University of Wisconsin Madison. Each library was generated using a paired end approach following the Illumina \u201cTruSeq RNA Sample Preparation Guide\u201d and the Illumina TruSeq RNA Sample Preparation Kit Illumina Inc. San Diego CA USA. Samples were run with 12 samples per lane with 100 base pair paired end reads. Sequencing depth was 14 32 million reads per sample.", "GEO Accession:GSM1902829", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP064535", null, null, "run483.C5B_CTTGTA_L001_R1.fastq.gz run483.C5B_CTTGTA_L001_R2.fastq.gz", "fastq fastq", 1673526166.0, 8284783.0, "GSM1902829 r1", "0:101 1:101", "A:427947977;C:411201544;G:407473106;T:425744400;N:1159139", 101, 101, null, null, 427947977, 411201544, 407473106, 425744400, 1159139, "SRX1309239", "SRS1102450", "SRA303285", "GEO", "Carvan Lab, School of Freshwater Sciences, University of Wisconsin-Milwaukee", 2, 0.94838, 0.94675, 0.07444, 0.07533, 0.68661, 0.68998, 0.49768, 0.5058, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2015-10-06", "Undetermined", "Embryo", "Brain", "Nervous System"], [39971, "SRR2567877", "SRX1309238", "SRS1102451", "SRP064535", "PRJNA297905", "Methylmercury MeHg induced Transgenerational Inheritance of Brain Transcriptome in Zebrafish Danio rerio [brain]", "GSE73794", "Transcriptome Analysis", "Methylmercury MeHg is a ubiquitous environmental toxicant that is often detected in the tissues of fish eating species. It has been well established that prenatal exposure to MeHg can lead to widespread brain damage and impaired neurological development resulting in defects ranging from severe cerebral palsy and cognitive deficits to impaired motor and sensory function. A wide range of environmental toxicants have been shown to induce transgenerational inheritance of diseases via changes in DNA methylation\u2014a well known epigenetic modification. Our previous research has demonstrated that developmental MeHg exposure may yield transgenerational inheritance of neurological dysfunction in adult F3 lineage zebrafish via quantitative neurobehavioral assays that evaluated the visual startle response retinal electrophysiology and locomotor function. The objective of the current study was to examine the correlation between neurobehavioral phenotypes and the transcriptome activity in the brain and retina of F3 zebrafish by RNA sequencing RNAseq. Transcriptomic analyses of F3 generation MeHg treated zebrafish compared to control revealed significant gene dysregulation in both the brain and retina. There were 1648 and 138 differentially expressed genes in the retina and brain respectively FDR <0.05. Thirty five genes were commonly dysregulated in both organs. Gene set enrichment analysis revealed significantly enriched pathways including: neurodevelopment visual functions phototransduction and motor movement. Moreover commonly dysregulated genes were associated with circadian rhythm and metabolic pathways as well as arginine and proline metabolism. To our knowledge this is the first evidence of a transgenerational transcriptome induced by ancestral developmental exposure to MeHg in any species. If the transgenerational phenotypes transcriptome homologous biomarkers or similar molecular pathways hold true for human populations our findings have significant impact on global public health in terms of identifying the susceptible populations using biomarkers and preventing transgenerational inheritance of MeHg induced neurobehavioral deficits. Overall design: Eggs of EK strain zebrafish were exposed to methylmercury 0.0 and 0.03\u00b5M with ethanol as the vehicle for 24 hours then raised normally. This represents the F1 generation of each respective lineage. F2 and F3 generations were created for each lineage. The F2 and F3 generations were never exposed to exogenous MeHg. The brain were collected from F3 generation fish of each lineage. 12 samples of total RNA isolated from adult zebrafish brain were analyzed. There were 6 biological replicates for vehicle control 0 \u00b5M MeHg and exposure 0.03 \u00b5M MeHg groups.", "parent bioproject:PRJNA297897", null, null, "C4B", "GSM1902828", null, "source name:Brain|tissue:Brain|generation:F3|strain:EK|mehg conc:0\u00b5M MeHg", "C4B", "Basecalling was performed using CASAVA 1.8.2. Adapters and low quality bases were removed from the initial 2x101bp Illumina TruSeq reads and trimmed using Cutadapt FastQC was used to ensure that cleaned reads were of higher quality than initial raw reads supplied by the sequencer The cleaned reads for each sample were independently aligned to the reference zebrafish genome Zv9 UCSC using TopHat Aligned reads were used to generate count and fpkm data using Cuffnorm against Zv9 trainscriptome Genome build: UCSC Zv9 Supplementary files format and content: Tab delimited matrix of gene counts and FPKM normalized counts", "Brain", "The F1 generation embryos were exposed to MeHg. Brain of F3 generation was used for isolating RNA.", "High quality total RNA was extracted from the brain using RNeasy Micro Kit QIAGEN Valencia CA USA. Illumina TruSeq RNA Library Preparation and Sequencing was performed at the Biotechnology Center at the University of Wisconsin Madison. Each library was generated using a paired end approach following the Illumina \u201cTruSeq RNA Sample Preparation Guide\u201d and the Illumina TruSeq RNA Sample Preparation Kit Illumina Inc. San Diego CA USA. Samples were run with 12 samples per lane with 100 base pair paired end reads. Sequencing depth was 14 32 million reads per sample.", "Eggs of EK strain zebrafish were exposed to methylmercury\u00a00.0 and 0.03\u03bcM with ethanol as the vehicle for 24 hours then raised normally.\u00a0This represents the F1 generation of each respective lineage. F2 and F3 generations were created for each lineage.\u00a0The F2 and F3 generations were never exposed to exogenous MeHg.\u00a0", "tissue:Brain|generation:F3|strain:EK|mehg conc:0\u00b5M MeHg", "GSM1902828", "GSM1902828: C4B; Danio rerio; RNA Seq", "GSM1902828", null, "1", "High quality total RNA was extracted from the brain using RNeasy Micro Kit QIAGEN Valencia CA USA. Illumina TruSeq RNA Library Preparation and Sequencing was performed at the Biotechnology Center at the University of Wisconsin Madison. Each library was generated using a paired end approach following the Illumina \u201cTruSeq RNA Sample Preparation Guide\u201d and the Illumina TruSeq RNA Sample Preparation Kit Illumina Inc. San Diego CA USA. Samples were run with 12 samples per lane with 100 base pair paired end reads. Sequencing depth was 14 32 million reads per sample.", "GEO Accession:GSM1902828", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP064535", null, null, "run483.C4B_GGCTAC_L001_R2.fastq.gz run483.C4B_GGCTAC_L001_R1.fastq.gz", "fastq fastq", 787342874.0, 3897737.0, "GSM1902828 r1", "0:101 1:101", "A:221071638;C:173927956;G:172321230;T:219487360;N:534690", 101, 101, null, null, 221071638, 173927956, 172321230, 219487360, 534690, "SRX1309238", "SRS1102451", "SRA303285", "GEO", "Carvan Lab, School of Freshwater Sciences, University of Wisconsin-Milwaukee", 2, 0.93526, 0.93535, 0.10425, 0.10623, 0.69867, 0.70307, 0.53432, 0.5404, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2015-10-06", "Undetermined", "Embryo", "Brain", "Nervous System"], [39972, "SRR2567876", "SRX1309237", "SRS1102453", "SRP064535", "PRJNA297905", "Methylmercury MeHg induced Transgenerational Inheritance of Brain Transcriptome in Zebrafish Danio rerio [brain]", "GSE73794", "Transcriptome Analysis", "Methylmercury MeHg is a ubiquitous environmental toxicant that is often detected in the tissues of fish eating species. It has been well established that prenatal exposure to MeHg can lead to widespread brain damage and impaired neurological development resulting in defects ranging from severe cerebral palsy and cognitive deficits to impaired motor and sensory function. A wide range of environmental toxicants have been shown to induce transgenerational inheritance of diseases via changes in DNA methylation\u2014a well known epigenetic modification. Our previous research has demonstrated that developmental MeHg exposure may yield transgenerational inheritance of neurological dysfunction in adult F3 lineage zebrafish via quantitative neurobehavioral assays that evaluated the visual startle response retinal electrophysiology and locomotor function. The objective of the current study was to examine the correlation between neurobehavioral phenotypes and the transcriptome activity in the brain and retina of F3 zebrafish by RNA sequencing RNAseq. Transcriptomic analyses of F3 generation MeHg treated zebrafish compared to control revealed significant gene dysregulation in both the brain and retina. There were 1648 and 138 differentially expressed genes in the retina and brain respectively FDR <0.05. Thirty five genes were commonly dysregulated in both organs. Gene set enrichment analysis revealed significantly enriched pathways including: neurodevelopment visual functions phototransduction and motor movement. Moreover commonly dysregulated genes were associated with circadian rhythm and metabolic pathways as well as arginine and proline metabolism. To our knowledge this is the first evidence of a transgenerational transcriptome induced by ancestral developmental exposure to MeHg in any species. If the transgenerational phenotypes transcriptome homologous biomarkers or similar molecular pathways hold true for human populations our findings have significant impact on global public health in terms of identifying the susceptible populations using biomarkers and preventing transgenerational inheritance of MeHg induced neurobehavioral deficits. Overall design: Eggs of EK strain zebrafish were exposed to methylmercury 0.0 and 0.03\u00b5M with ethanol as the vehicle for 24 hours then raised normally. This represents the F1 generation of each respective lineage. F2 and F3 generations were created for each lineage. The F2 and F3 generations were never exposed to exogenous MeHg. The brain were collected from F3 generation fish of each lineage. 12 samples of total RNA isolated from adult zebrafish brain were analyzed. There were 6 biological replicates for vehicle control 0 \u00b5M MeHg and exposure 0.03 \u00b5M MeHg groups.", "parent bioproject:PRJNA297897", null, null, "C2B", "GSM1902827", null, "source name:Brain|tissue:Brain|generation:F3|strain:EK|mehg conc:0\u00b5M MeHg", "C2B", "Basecalling was performed using CASAVA 1.8.2. Adapters and low quality bases were removed from the initial 2x101bp Illumina TruSeq reads and trimmed using Cutadapt FastQC was used to ensure that cleaned reads were of higher quality than initial raw reads supplied by the sequencer The cleaned reads for each sample were independently aligned to the reference zebrafish genome Zv9 UCSC using TopHat Aligned reads were used to generate count and fpkm data using Cuffnorm against Zv9 trainscriptome Genome build: UCSC Zv9 Supplementary files format and content: Tab delimited matrix of gene counts and FPKM normalized counts", "Brain", "The F1 generation embryos were exposed to MeHg. Brain of F3 generation was used for isolating RNA.", "High quality total RNA was extracted from the brain using RNeasy Micro Kit QIAGEN Valencia CA USA. Illumina TruSeq RNA Library Preparation and Sequencing was performed at the Biotechnology Center at the University of Wisconsin Madison. Each library was generated using a paired end approach following the Illumina \u201cTruSeq RNA Sample Preparation Guide\u201d and the Illumina TruSeq RNA Sample Preparation Kit Illumina Inc. San Diego CA USA. Samples were run with 12 samples per lane with 100 base pair paired end reads. Sequencing depth was 14 32 million reads per sample.", "Eggs of EK strain zebrafish were exposed to methylmercury\u00a00.0 and 0.03\u03bcM with ethanol as the vehicle for 24 hours then raised normally.\u00a0This represents the F1 generation of each respective lineage. F2 and F3 generations were created for each lineage.\u00a0The F2 and F3 generations were never exposed to exogenous MeHg.\u00a0", "tissue:Brain|generation:F3|strain:EK|mehg conc:0\u00b5M MeHg", "GSM1902827", "GSM1902827: C2B; Danio rerio; RNA Seq", "GSM1902827", null, "1", "High quality total RNA was extracted from the brain using RNeasy Micro Kit QIAGEN Valencia CA USA. Illumina TruSeq RNA Library Preparation and Sequencing was performed at the Biotechnology Center at the University of Wisconsin Madison. Each library was generated using a paired end approach following the Illumina \u201cTruSeq RNA Sample Preparation Guide\u201d and the Illumina TruSeq RNA Sample Preparation Kit Illumina Inc. San Diego CA USA. Samples were run with 12 samples per lane with 100 base pair paired end reads. Sequencing depth was 14 32 million reads per sample.", "GEO Accession:GSM1902827", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP064535", null, null, "run483.C2B_TAGCTT_L001_R1.fastq.gz run483.C2B_TAGCTT_L001_R2.fastq.gz", "fastq fastq", 878460428.0, 4348814.0, "GSM1902827 r1", "0:101 1:101", "A:242678583;C:198371572;G:197648225;T:239155749;N:606299", 101, 101, null, null, 242678583, 198371572, 197648225, 239155749, 606299, "SRX1309237", "SRS1102453", "SRA303285", "GEO", "Carvan Lab, School of Freshwater Sciences, University of Wisconsin-Milwaukee", 2, 0.92587, 0.924, 0.11454, 0.11584, 0.6636, 0.66894, 0.49249, 0.48554, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2015-10-06", "Undetermined", "Embryo", "Brain", "Nervous System"], [39973, "SRR2567875", "SRX1309236", "SRS1102454", "SRP064535", "PRJNA297905", "Methylmercury MeHg induced Transgenerational Inheritance of Brain Transcriptome in Zebrafish Danio rerio [brain]", "GSE73794", "Transcriptome Analysis", "Methylmercury MeHg is a ubiquitous environmental toxicant that is often detected in the tissues of fish eating species. It has been well established that prenatal exposure to MeHg can lead to widespread brain damage and impaired neurological development resulting in defects ranging from severe cerebral palsy and cognitive deficits to impaired motor and sensory function. A wide range of environmental toxicants have been shown to induce transgenerational inheritance of diseases via changes in DNA methylation\u2014a well known epigenetic modification. Our previous research has demonstrated that developmental MeHg exposure may yield transgenerational inheritance of neurological dysfunction in adult F3 lineage zebrafish via quantitative neurobehavioral assays that evaluated the visual startle response retinal electrophysiology and locomotor function. The objective of the current study was to examine the correlation between neurobehavioral phenotypes and the transcriptome activity in the brain and retina of F3 zebrafish by RNA sequencing RNAseq. Transcriptomic analyses of F3 generation MeHg treated zebrafish compared to control revealed significant gene dysregulation in both the brain and retina. There were 1648 and 138 differentially expressed genes in the retina and brain respectively FDR <0.05. Thirty five genes were commonly dysregulated in both organs. Gene set enrichment analysis revealed significantly enriched pathways including: neurodevelopment visual functions phototransduction and motor movement. Moreover commonly dysregulated genes were associated with circadian rhythm and metabolic pathways as well as arginine and proline metabolism. To our knowledge this is the first evidence of a transgenerational transcriptome induced by ancestral developmental exposure to MeHg in any species. If the transgenerational phenotypes transcriptome homologous biomarkers or similar molecular pathways hold true for human populations our findings have significant impact on global public health in terms of identifying the susceptible populations using biomarkers and preventing transgenerational inheritance of MeHg induced neurobehavioral deficits. Overall design: Eggs of EK strain zebrafish were exposed to methylmercury 0.0 and 0.03\u00b5M with ethanol as the vehicle for 24 hours then raised normally. This represents the F1 generation of each respective lineage. F2 and F3 generations were created for each lineage. The F2 and F3 generations were never exposed to exogenous MeHg. The brain were collected from F3 generation fish of each lineage. 12 samples of total RNA isolated from adult zebrafish brain were analyzed. There were 6 biological replicates for vehicle control 0 \u00b5M MeHg and exposure 0.03 \u00b5M MeHg groups.", "parent bioproject:PRJNA297897", null, null, "C1B", "GSM1902826", null, "source name:Brain|tissue:Brain|generation:F3|strain:EK|mehg conc:0\u00b5M MeHg", "C1B", "Basecalling was performed using CASAVA 1.8.2. Adapters and low quality bases were removed from the initial 2x101bp Illumina TruSeq reads and trimmed using Cutadapt FastQC was used to ensure that cleaned reads were of higher quality than initial raw reads supplied by the sequencer The cleaned reads for each sample were independently aligned to the reference zebrafish genome Zv9 UCSC using TopHat Aligned reads were used to generate count and fpkm data using Cuffnorm against Zv9 trainscriptome Genome build: UCSC Zv9 Supplementary files format and content: Tab delimited matrix of gene counts and FPKM normalized counts", "Brain", "The F1 generation embryos were exposed to MeHg. Brain of F3 generation was used for isolating RNA.", "High quality total RNA was extracted from the brain using RNeasy Micro Kit QIAGEN Valencia CA USA. Illumina TruSeq RNA Library Preparation and Sequencing was performed at the Biotechnology Center at the University of Wisconsin Madison. Each library was generated using a paired end approach following the Illumina \u201cTruSeq RNA Sample Preparation Guide\u201d and the Illumina TruSeq RNA Sample Preparation Kit Illumina Inc. San Diego CA USA. Samples were run with 12 samples per lane with 100 base pair paired end reads. Sequencing depth was 14 32 million reads per sample.", "Eggs of EK strain zebrafish were exposed to methylmercury\u00a00.0 and 0.03\u03bcM with ethanol as the vehicle for 24 hours then raised normally.\u00a0This represents the F1 generation of each respective lineage. F2 and F3 generations were created for each lineage.\u00a0The F2 and F3 generations were never exposed to exogenous MeHg.\u00a0", "tissue:Brain|generation:F3|strain:EK|mehg conc:0\u00b5M MeHg", "GSM1902826", "GSM1902826: C1B; Danio rerio; RNA Seq", "GSM1902826", null, "1", "High quality total RNA was extracted from the brain using RNeasy Micro Kit QIAGEN Valencia CA USA. Illumina TruSeq RNA Library Preparation and Sequencing was performed at the Biotechnology Center at the University of Wisconsin Madison. Each library was generated using a paired end approach following the Illumina \u201cTruSeq RNA Sample Preparation Guide\u201d and the Illumina TruSeq RNA Sample Preparation Kit Illumina Inc. San Diego CA USA. Samples were run with 12 samples per lane with 100 base pair paired end reads. Sequencing depth was 14 32 million reads per sample.", "GEO Accession:GSM1902826", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP064535", null, null, "run483.C1B_ACTTGA_L001_R1.fastq.gz run483.C1B_ACTTGA_L001_R2.fastq.gz", "fastq fastq", 585273184.0, 2897392.0, "GSM1902826 r1", "0:101 1:101", "A:153545646;C:140573158;G:141864081;T:148892588;N:397711", 101, 101, null, null, 153545646, 140573158, 141864081, 148892588, 397711, "SRX1309236", "SRS1102454", "SRA303285", "GEO", "Carvan Lab, School of Freshwater Sciences, University of Wisconsin-Milwaukee", 2, 0.94847, 0.94697, 0.0745, 0.07549, 0.69061, 0.69503, 0.50737, 0.50558, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2015-10-06", "Undetermined", "Embryo", "Brain", "Nervous System"], [41297, "SRR8173226", "SRX4993779", "SRS4029191", "SRP168138", "PRJNA340009", "RNASeq of OMP and TRPC2 neuronal population of zebrafish olfactory sensory neurons", "GSE86023", "Transcriptome Analysis", "RNASeq was performed on mRNA obtained from OMP expressing and TRPC2 expressing olfactory sensory neurons from 48hpf zebrafish embryos. Single cell suspensions of 48hpf olfactory epithelia were FAC sorted to obtain RFP expressing or venus expressing cells RFP sample1: 3500 cells RFP sample2: 5500 cells. Venus sample1: 676 cells venus sample2:201 cells. RNA was extracted using QIAGEN RNEasy kit and cDNA was synthesized using a custom oligo dT primer containing T7 promoter sequence courtesy of Jim Eberwine University of Pennsylvanina. In vitro RNA amplification was carried out through one round for OMP:RFP neurons and through two rounds for TRPC2:venus neurons as per the protocol in Morris et al 2011. Adapter tagged libraries were synthesized using Illumina TruSeq v2.0 and deep sequenced on HiSeq2500 to obtain 100million reads per sample. Overall design: Examination of mRNA expression profiles from 2 types of olfactory sensory neurons", null, "pubmed:29020985", null, "TRPC2 2", "GSM2290761", null, "tissue:TRPC2 expressing olfactory sensory neurons|strain:Tubingen/TLF|embryo stage:48hpf|cell type:olfactory sensory neurons|neuron subtype:TRPC2", "TRPC2 2", "Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped tozebrafish GRCz10 whole genome. Reads per millionrpm values were calculated by dividing the number of read counts for a gene by the total number of uniquely mapped reads in million for that sample. Alignment \u2013 STAR algorithm Gene counts \u2013 VERSE Genome build: Ensemble zebrafish assembly GRCz10 Supplementary files format and content: Comma separated text files include raw gene counts or gene counts in reads per million for each sample", "TRPC2 expressing olfactory sensory neurons", "Olfactory epithelia were dissected and single cell suspensions were prepared using trypsin to dissociate the cells. Fluorescence assisted cell sorting FACS was used to obtain RFP only and venus only cell populations. Cells were collected in RNA lysis buffer.", "Total cellular RNA was extracted using Qiagen Rneasy micro kit. T7 oligodT primers were used for reverse transcription of mRNA during cDNA synthesis. RNA amplification was performed using T7 Megascript kit through one for OMP neurons two rounds for TRPC2 neurons. Illumina TruSeq v2.0 kit was used as per manufacturer's protocol.", "Zebrafish embryos expressing OMP:RFP or TRPC2:venus were harvested and incubated at 28.5oC till 48hpf.", "strain:Tubingen/TLF|embryo stage:48hpf|cell type:olfactory sensory neurons|neuron subtype:TRPC2", "GSM2290761", "GSM2290761: TRPC2 2; Danio rerio; RNA Seq", "GSM2290761", null, "1", "Total cellular RNA was extracted using Qiagen Rneasy micro kit. T7 oligodT primers were used for reverse transcription of mRNA during cDNA synthesis. RNA amplification was performed using T7 Megascript kit through one for OMP neurons two rounds for TRPC2 neurons. Illumina TruSeq v2.0 kit was used as per manufacturer's protocol.", "GEO Accession:GSM2290761", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP168138", null, null, "FGC0977_s_3_1_CTTGTA.fastq.gz FGC0977_s_3_2_CTTGTA.fastq.gz", "fastq fastq", 19333122000.0, 96665610.0, "GSM2290761 r1", "0:100 1:100", "A:5708354504;C:3932203444;G:3891575387;T:5798440967;N:2547698", 100, 100, null, null, 5708354504, 3932203444, 3891575387, 5798440967, 2547698, "SRX4993779", "SRS4029191", "SRA807287", "GEO", "Jonathan Raper, Neuroscience, University of Pennsylvania", 2, 0.89122, 0.8929, 0.18042, 0.18083, 0.7903, 0.79182, 0.61137, 0.61123, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-08-24", "Hatching", "Embryo", "Brain", "Nervous System"], [41298, "SRR8173225", "SRX4993778", "SRS4029190", "SRP168138", "PRJNA340009", "RNASeq of OMP and TRPC2 neuronal population of zebrafish olfactory sensory neurons", "GSE86023", "Transcriptome Analysis", "RNASeq was performed on mRNA obtained from OMP expressing and TRPC2 expressing olfactory sensory neurons from 48hpf zebrafish embryos. Single cell suspensions of 48hpf olfactory epithelia were FAC sorted to obtain RFP expressing or venus expressing cells RFP sample1: 3500 cells RFP sample2: 5500 cells. Venus sample1: 676 cells venus sample2:201 cells. RNA was extracted using QIAGEN RNEasy kit and cDNA was synthesized using a custom oligo dT primer containing T7 promoter sequence courtesy of Jim Eberwine University of Pennsylvanina. In vitro RNA amplification was carried out through one round for OMP:RFP neurons and through two rounds for TRPC2:venus neurons as per the protocol in Morris et al 2011. Adapter tagged libraries were synthesized using Illumina TruSeq v2.0 and deep sequenced on HiSeq2500 to obtain 100million reads per sample. Overall design: Examination of mRNA expression profiles from 2 types of olfactory sensory neurons", null, "pubmed:29020985", null, "TRPC2 1", "GSM2290760", null, "tissue:TRPC2 expressing olfactory sensory neurons|strain:Tubingen/TLF|embryo stage:48hpf|cell type:olfactory sensory neurons|neuron subtype:TRPC2", "TRPC2 1", "Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped tozebrafish GRCz10 whole genome. Reads per millionrpm values were calculated by dividing the number of read counts for a gene by the total number of uniquely mapped reads in million for that sample. Alignment \u2013 STAR algorithm Gene counts \u2013 VERSE Genome build: Ensemble zebrafish assembly GRCz10 Supplementary files format and content: Comma separated text files include raw gene counts or gene counts in reads per million for each sample", "TRPC2 expressing olfactory sensory neurons", "Olfactory epithelia were dissected and single cell suspensions were prepared using trypsin to dissociate the cells. Fluorescence assisted cell sorting FACS was used to obtain RFP only and venus only cell populations. Cells were collected in RNA lysis buffer.", "Total cellular RNA was extracted using Qiagen Rneasy micro kit. T7 oligodT primers were used for reverse transcription of mRNA during cDNA synthesis. RNA amplification was performed using T7 Megascript kit through one for OMP neurons two rounds for TRPC2 neurons. Illumina TruSeq v2.0 kit was used as per manufacturer's protocol.", "Zebrafish embryos expressing OMP:RFP or TRPC2:venus were harvested and incubated at 28.5oC till 48hpf.", "strain:Tubingen/TLF|embryo stage:48hpf|cell type:olfactory sensory neurons|neuron subtype:TRPC2", "GSM2290760", "GSM2290760: TRPC2 1; Danio rerio; RNA Seq", "GSM2290760", null, "1", "Total cellular RNA was extracted using Qiagen Rneasy micro kit. T7 oligodT primers were used for reverse transcription of mRNA during cDNA synthesis. RNA amplification was performed using T7 Megascript kit through one for OMP neurons two rounds for TRPC2 neurons. Illumina TruSeq v2.0 kit was used as per manufacturer's protocol.", "GEO Accession:GSM2290760", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP168138", null, null, "FGC0977_s_3_1_GCCAAT.fastq.gz FGC0977_s_3_2_GCCAAT.fastq.gz", "fastq fastq", 19933298800.0, 99666494.0, "GSM2290760 r1", "0:100 1:100", "A:5663223656;C:4194804658;G:4197360143;T:5875323942;N:2586401", 100, 100, null, null, 5663223656, 4194804658, 4197360143, 5875323942, 2586401, "SRX4993778", "SRS4029190", "SRA807287", "GEO", "Jonathan Raper, Neuroscience, University of Pennsylvania", 2, 0.84844, 0.84265, 0.10791, 0.1071, 0.80886, 0.81026, 0.57202, 0.57988, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-08-24", "Hatching", "Embryo", "Brain", "Nervous System"], [41299, "SRR8173224", "SRX4993777", "SRS4029189", "SRP168138", "PRJNA340009", "RNASeq of OMP and TRPC2 neuronal population of zebrafish olfactory sensory neurons", "GSE86023", "Transcriptome Analysis", "RNASeq was performed on mRNA obtained from OMP expressing and TRPC2 expressing olfactory sensory neurons from 48hpf zebrafish embryos. Single cell suspensions of 48hpf olfactory epithelia were FAC sorted to obtain RFP expressing or venus expressing cells RFP sample1: 3500 cells RFP sample2: 5500 cells. Venus sample1: 676 cells venus sample2:201 cells. RNA was extracted using QIAGEN RNEasy kit and cDNA was synthesized using a custom oligo dT primer containing T7 promoter sequence courtesy of Jim Eberwine University of Pennsylvanina. In vitro RNA amplification was carried out through one round for OMP:RFP neurons and through two rounds for TRPC2:venus neurons as per the protocol in Morris et al 2011. Adapter tagged libraries were synthesized using Illumina TruSeq v2.0 and deep sequenced on HiSeq2500 to obtain 100million reads per sample. Overall design: Examination of mRNA expression profiles from 2 types of olfactory sensory neurons", null, "pubmed:29020985", null, "OMP 2", "GSM2290759", null, "tissue:OMP expressing olfactory sensory neurons|strain:Tubingen/TLF|embryo stage:48hpf|cell type:olfactory sensory neurons|neuron subtype:OMP", "OMP 2", "Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped tozebrafish GRCz10 whole genome. Reads per millionrpm values were calculated by dividing the number of read counts for a gene by the total number of uniquely mapped reads in million for that sample. Alignment \u2013 STAR algorithm Gene counts \u2013 VERSE Genome build: Ensemble zebrafish assembly GRCz10 Supplementary files format and content: Comma separated text files include raw gene counts or gene counts in reads per million for each sample", "OMP expressing olfactory sensory neurons", "Olfactory epithelia were dissected and single cell suspensions were prepared using trypsin to dissociate the cells. Fluorescence assisted cell sorting FACS was used to obtain RFP only and venus only cell populations. Cells were collected in RNA lysis buffer.", "Total cellular RNA was extracted using Qiagen Rneasy micro kit. T7 oligodT primers were used for reverse transcription of mRNA during cDNA synthesis. RNA amplification was performed using T7 Megascript kit through one for OMP neurons two rounds for TRPC2 neurons. Illumina TruSeq v2.0 kit was used as per manufacturer's protocol.", "Zebrafish embryos expressing OMP:RFP or TRPC2:venus were harvested and incubated at 28.5oC till 48hpf.", "strain:Tubingen/TLF|embryo stage:48hpf|cell type:olfactory sensory neurons|neuron subtype:OMP", "GSM2290759", "GSM2290759: OMP 2; Danio rerio; RNA Seq", "GSM2290759", null, "1", "Total cellular RNA was extracted using Qiagen Rneasy micro kit. T7 oligodT primers were used for reverse transcription of mRNA during cDNA synthesis. RNA amplification was performed using T7 Megascript kit through one for OMP neurons two rounds for TRPC2 neurons. Illumina TruSeq v2.0 kit was used as per manufacturer's protocol.", "GEO Accession:GSM2290759", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP168138", null, null, "FGC0805_s_6_1_CTTGTA.fastq.gz FGC0805_s_6_2_CTTGTA.fastq.gz", "fastq fastq", 25768751000.0, 128843755.0, "GSM2290759 r1", "0:100 1:100", "A:6815152641;C:6065596177;G:5514207833;T:7360566579;N:13227770", 100, 100, null, null, 6815152641, 6065596177, 5514207833, 7360566579, 13227770, "SRX4993777", "SRS4029189", "SRA807287", "GEO", "Jonathan Raper, Neuroscience, University of Pennsylvania", 2, 0.94122, 0.87325, 0.12592, 0.11103, 0.7235, 0.73563, 0.4808, 0.5167, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-08-24", "Hatching", "Embryo", "Brain", "Nervous System"], [41300, "SRR8173223", "SRX4993776", "SRS4029188", "SRP168138", "PRJNA340009", "RNASeq of OMP and TRPC2 neuronal population of zebrafish olfactory sensory neurons", "GSE86023", "Transcriptome Analysis", "RNASeq was performed on mRNA obtained from OMP expressing and TRPC2 expressing olfactory sensory neurons from 48hpf zebrafish embryos. Single cell suspensions of 48hpf olfactory epithelia were FAC sorted to obtain RFP expressing or venus expressing cells RFP sample1: 3500 cells RFP sample2: 5500 cells. Venus sample1: 676 cells venus sample2:201 cells. RNA was extracted using QIAGEN RNEasy kit and cDNA was synthesized using a custom oligo dT primer containing T7 promoter sequence courtesy of Jim Eberwine University of Pennsylvanina. In vitro RNA amplification was carried out through one round for OMP:RFP neurons and through two rounds for TRPC2:venus neurons as per the protocol in Morris et al 2011. Adapter tagged libraries were synthesized using Illumina TruSeq v2.0 and deep sequenced on HiSeq2500 to obtain 100million reads per sample. Overall design: Examination of mRNA expression profiles from 2 types of olfactory sensory neurons", null, "pubmed:29020985", null, "OMP 1", "GSM2290758", null, "tissue:OMP expressing olfactory sensory neurons|strain:Tubingen/TLF|embryo stage:48hpf|cell type:olfactory sensory neurons|neuron subtype:OMP", "OMP 1", "Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped tozebrafish GRCz10 whole genome. Reads per millionrpm values were calculated by dividing the number of read counts for a gene by the total number of uniquely mapped reads in million for that sample. Alignment \u2013 STAR algorithm Gene counts \u2013 VERSE Genome build: Ensemble zebrafish assembly GRCz10 Supplementary files format and content: Comma separated text files include raw gene counts or gene counts in reads per million for each sample", "OMP expressing olfactory sensory neurons", "Olfactory epithelia were dissected and single cell suspensions were prepared using trypsin to dissociate the cells. Fluorescence assisted cell sorting FACS was used to obtain RFP only and venus only cell populations. Cells were collected in RNA lysis buffer.", "Total cellular RNA was extracted using Qiagen Rneasy micro kit. T7 oligodT primers were used for reverse transcription of mRNA during cDNA synthesis. RNA amplification was performed using T7 Megascript kit through one for OMP neurons two rounds for TRPC2 neurons. Illumina TruSeq v2.0 kit was used as per manufacturer's protocol.", "Zebrafish embryos expressing OMP:RFP or TRPC2:venus were harvested and incubated at 28.5oC till 48hpf.", "strain:Tubingen/TLF|embryo stage:48hpf|cell type:olfactory sensory neurons|neuron subtype:OMP", "GSM2290758", "GSM2290758: OMP 1; Danio rerio; RNA Seq", "GSM2290758", null, "1", "Total cellular RNA was extracted using Qiagen Rneasy micro kit. T7 oligodT primers were used for reverse transcription of mRNA during cDNA synthesis. RNA amplification was performed using T7 Megascript kit through one for OMP neurons two rounds for TRPC2 neurons. Illumina TruSeq v2.0 kit was used as per manufacturer's protocol.", "GEO Accession:GSM2290758", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP168138", null, null, "FGC0805_s_6_2_GCCAAT.fastq.gz FGC0805_s_6_1_GCCAAT.fastq.gz", "fastq fastq", 24051320600.0, 120256603.0, "GSM2290758 r1", "0:100 1:100", "A:6601023193;C:5427909703;G:4902326306;T:7107644194;N:12417204", 100, 100, null, null, 6601023193, 5427909703, 4902326306, 7107644194, 12417204, "SRX4993776", "SRS4029188", "SRA807287", "GEO", "Jonathan Raper, Neuroscience, University of Pennsylvania", 2, 0.92859, 0.84572, 0.19924, 0.173, 0.71713, 0.73154, 0.54902, 0.55157, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-08-24", "Hatching", "Embryo", "Brain", "Nervous System"], [41529, "SRR5006042", "SRX2337870", "SRS1791088", "SRP092952", "PRJNA352869", "The Biotagging toolkit for analysis of specific cell populations in zebrafish reveals gene regulatory logic encoded in the nuclear transcriptome", "GSE89670", "Other", "Interrogation of gene regulatory circuits in complex organisms requires precise tools for the selection of individual cell types as well as robust methods for tissue specific labeling and biochemical profiling of target proteins. By exploiting multiple transgenesis strategies we have developed a tissue specific binary in vivo biotinylation system in zebrafish termed \"biotagging\" a versatile methodology that uses genetically encoded components to biotinylate target proteins enabling in depth genome wide analyses of their molecular interactions. Using tissue specific transgenic drivers and individual cell compartment effector lines from our \"biotagging\" toolkit we demonstrate the specificity of our approach at the biochemical cellular and transcriptional levels. By characterizing the in vivo transcriptional landscape of migratory neural crest and myocardial cells in two different cellular compartments ribosomes and nucleus we identify a comprehensive network of protein coding and non coding RNAs and uncover cis regulatory modules and regulatory logic conferring cell specific identity embedded in the complexity of the non coding nuclear transcriptomes. Our study demonstrates that \"biotagging\" eliminates background inherent to complex embryonic environments and allows analyses of molecular interactions in any cellular context at highest resolution. Overall design: Examination of RNA seq and ATAC seq using in vivo biotinylated nuclei and polysomes.", null, "pubmed:28402863", null, "Sox10 RNASeq Whole Cell 18ss", "GSM2386505", null, "source name:Sox10 RNASeq Whole Cell 18ss|strain/background:AB/TU|tissue:neural crest and otic|developmental stage:18ss|assay:RNA seq stranded|cellular comp1nt:whole cell|ribodepleted:ribodepleted|isolation method:FACS|strand:reverse", "Sox10 RNASeq Whole Cell 18ss", "ATAC seq reads were trimmed for quality using sickle v 1.33 and mapped using bowtie v.1.0.0. Smoothened bigWig files were generated using an enhanced Perl script courtesy of Jim Hughes. RNA seq reads were mapped using STAR v.2.4.2a. BAM files incorporating reads belonging to either DNA strand were generated using custom python script. Genome build: danRer7 Zv9 Supplementary files format and content: bigWig files", "Sox10 RNASeq Whole Cell 18ss", null, "Nuclei isolation using biotin tagged outer nuclear envelope adapted from INTACT procedure. Polyribosome isolation using biotin tagged Rpl10 protein adapted from TRAP procedure. FACS procedure using cell specific fluorescent marker following gentle dissociation of embryonic tissue. ATAC procedure adapted from Buenostro et al. 2013 adapted for FACS sorted embryonic cells. RNA pools extracted using RNAqueous Micro Scale Total RNA Isolation Kit. Non directional sequencing libraries post polyA selection of RNA transcripts NEBNext\u00ae PolyA mRNA Magnetic Isolation Module NEB were built using NEBnext Ultra RNA library kit for Illumina NEB. Following ribodepletion using Ribo ZeroTM Magnetic Kit Epicentre directional RNA seq libraries were constructed using Stranded RNA Seq Library Preparation Kit KAPABiosystems.", null, "strain/background:AB/TU|tissue:neural crest and otic|developmental stage:18ss|assay:RNA seq stranded|cellular comp1nt:whole cell|ribodepleted:ribodepleted|isolation method:FACS|strand:reverse", "GSM2386505", "GSM2386505: Sox10 RNASeq Whole Cell 18ss; Danio rerio; RNA Seq", "GSM2386505", null, "1", "Nuclei isolation using biotin tagged outer nuclear envelope adapted from INTACT procedure. Polyribosome isolation using biotin tagged Rpl10 protein adapted from TRAP procedure. FACS procedure using cell specific fluorescent marker following gentle dissociation of embryonic tissue. ATAC procedure adapted from Buenostro et al. 2013 adapted for FACS sorted embryonic cells. RNA pools extracted using RNAqueous Micro Scale Total RNA Isolation Kit. Non directional sequencing libraries post polyA selection of RNA transcripts NEBNext\u00ae PolyA mRNA Magnetic Isolation Module NEB were built using NEBnext Ultra RNA library kit for Illumina NEB. Following ribodepletion using Ribo ZeroTM Magnetic Kit Epicentre directional RNA seq libraries were constructed using Stranded RNA Seq Library Preparation Kit KAPABiosystems.", "GEO Accession:GSM2386505", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP092952", null, null, "Sox10_RNASeq_Whole_Cell_18ss_R1.fastq.gz Sox10_RNASeq_Whole_Cell_18ss_R2.fastq.gz", "fastq fastq", 3178698216.0, 31163708.0, "GSM2386505 r1", "0:51 1:51", "A:660891203;C:888101751;G:964664681;T:664877794;N:162787", 51, 51, null, null, 660891203, 888101751, 964664681, 664877794, 162787, "SRX2337870", "SRS1791088", "SRA491940", "GEO", "Sauka-Spengler lab, University of Oxford, MRC Weatherall Institute of Molecular Medicine", 2, 0.70589, 0.71523, 0.16345, 0.16503, 0.75747, 0.75586, 0.54687, 0.55162, 51, 51, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "United Kingdom", "2016-11-08", "Undetermined", "Embryo", "Brain", "Nervous System"], [41534, "SRR5006037", "SRX2337865", "SRS1791084", "SRP092952", "PRJNA352869", "The Biotagging toolkit for analysis of specific cell populations in zebrafish reveals gene regulatory logic encoded in the nuclear transcriptome", "GSE89670", "Other", "Interrogation of gene regulatory circuits in complex organisms requires precise tools for the selection of individual cell types as well as robust methods for tissue specific labeling and biochemical profiling of target proteins. By exploiting multiple transgenesis strategies we have developed a tissue specific binary in vivo biotinylation system in zebrafish termed \"biotagging\" a versatile methodology that uses genetically encoded components to biotinylate target proteins enabling in depth genome wide analyses of their molecular interactions. Using tissue specific transgenic drivers and individual cell compartment effector lines from our \"biotagging\" toolkit we demonstrate the specificity of our approach at the biochemical cellular and transcriptional levels. By characterizing the in vivo transcriptional landscape of migratory neural crest and myocardial cells in two different cellular compartments ribosomes and nucleus we identify a comprehensive network of protein coding and non coding RNAs and uncover cis regulatory modules and regulatory logic conferring cell specific identity embedded in the complexity of the non coding nuclear transcriptomes. Our study demonstrates that \"biotagging\" eliminates background inherent to complex embryonic environments and allows analyses of molecular interactions in any cellular context at highest resolution. Overall design: Examination of RNA seq and ATAC seq using in vivo biotinylated nuclei and polysomes.", null, "pubmed:28402863", null, "Sox10 RNASeq Nuclear PolyA 2", "GSM2386500", null, "source name:Sox10 RNASeq Nuclear PolyA|strain/background:AB/TU|tissue:neural crest and otic|developmental stage:26hpf|assay:RNA seq|cellular comp1nt:nuclear|ribodepleted:polyA|isolation method:InVivoBiotinylatedNuclei|strand:unstranded", "Sox10 RNASeq Nuclear PolyA 2", "ATAC seq reads were trimmed for quality using sickle v 1.33 and mapped using bowtie v.1.0.0. Smoothened bigWig files were generated using an enhanced Perl script courtesy of Jim Hughes. RNA seq reads were mapped using STAR v.2.4.2a. BAM files incorporating reads belonging to either DNA strand were generated using custom python script. Genome build: danRer7 Zv9 Supplementary files format and content: bigWig files", "Sox10 RNASeq Nuclear PolyA", null, "Nuclei isolation using biotin tagged outer nuclear envelope adapted from INTACT procedure. Polyribosome isolation using biotin tagged Rpl10 protein adapted from TRAP procedure. FACS procedure using cell specific fluorescent marker following gentle dissociation of embryonic tissue. ATAC procedure adapted from Buenostro et al. 2013 adapted for FACS sorted embryonic cells. RNA pools extracted using RNAqueous Micro Scale Total RNA Isolation Kit. Non directional sequencing libraries post polyA selection of RNA transcripts NEBNext\u00ae PolyA mRNA Magnetic Isolation Module NEB were built using NEBnext Ultra RNA library kit for Illumina NEB. Following ribodepletion using Ribo ZeroTM Magnetic Kit Epicentre directional RNA seq libraries were constructed using Stranded RNA Seq Library Preparation Kit KAPABiosystems.", null, "strain/background:AB/TU|tissue:neural crest and otic|developmental stage:26hpf|assay:RNA seq|cellular comp1nt:nuclear|ribodepleted:polyA|isolation method:InVivoBiotinylatedNuclei|strand:unstranded", "GSM2386500", "GSM2386500: Sox10 RNASeq Nuclear PolyA 2; Danio rerio; RNA Seq", "GSM2386500", null, "1", "Nuclei isolation using biotin tagged outer nuclear envelope adapted from INTACT procedure. Polyribosome isolation using biotin tagged Rpl10 protein adapted from TRAP procedure. FACS procedure using cell specific fluorescent marker following gentle dissociation of embryonic tissue. ATAC procedure adapted from Buenostro et al. 2013 adapted for FACS sorted embryonic cells. RNA pools extracted using RNAqueous Micro Scale Total RNA Isolation Kit. Non directional sequencing libraries post polyA selection of RNA transcripts NEBNext\u00ae PolyA mRNA Magnetic Isolation Module NEB were built using NEBnext Ultra RNA library kit for Illumina NEB. Following ribodepletion using Ribo ZeroTM Magnetic Kit Epicentre directional RNA seq libraries were constructed using Stranded RNA Seq Library Preparation Kit KAPABiosystems.", "GEO Accession:GSM2386500", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP092952", null, null, "Sox10_RNASeq_Nuclear_PolyA_2.fastq.gz", "fastq", 1790084450.0, 35801689.0, "GSM2386500 r1", "0:50", "A:459421587;C:440246036;G:440346791;T:450052845;N:17191", 50, null, null, null, 459421587, 440246036, 440346791, 450052845, 17191, "SRX2337865", "SRS1791084", "SRA491940", "GEO", "Sauka-Spengler lab, University of Oxford, MRC Weatherall Institute of Molecular Medicine", 1, 0.40624, null, 0.06355, null, 0.79859, null, 0.47871, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "United Kingdom", "2016-11-08", "Pharyngula", "Embryo", "Brain", "Nervous System"], [41535, "SRR5006036", "SRX2337864", "SRS1791082", "SRP092952", "PRJNA352869", "The Biotagging toolkit for analysis of specific cell populations in zebrafish reveals gene regulatory logic encoded in the nuclear transcriptome", "GSE89670", "Other", "Interrogation of gene regulatory circuits in complex organisms requires precise tools for the selection of individual cell types as well as robust methods for tissue specific labeling and biochemical profiling of target proteins. By exploiting multiple transgenesis strategies we have developed a tissue specific binary in vivo biotinylation system in zebrafish termed \"biotagging\" a versatile methodology that uses genetically encoded components to biotinylate target proteins enabling in depth genome wide analyses of their molecular interactions. Using tissue specific transgenic drivers and individual cell compartment effector lines from our \"biotagging\" toolkit we demonstrate the specificity of our approach at the biochemical cellular and transcriptional levels. By characterizing the in vivo transcriptional landscape of migratory neural crest and myocardial cells in two different cellular compartments ribosomes and nucleus we identify a comprehensive network of protein coding and non coding RNAs and uncover cis regulatory modules and regulatory logic conferring cell specific identity embedded in the complexity of the non coding nuclear transcriptomes. Our study demonstrates that \"biotagging\" eliminates background inherent to complex embryonic environments and allows analyses of molecular interactions in any cellular context at highest resolution. Overall design: Examination of RNA seq and ATAC seq using in vivo biotinylated nuclei and polysomes.", null, "pubmed:28402863", null, "Sox10 RNASeq Nuclear PolyA 1", "GSM2386499", null, "source name:Sox10 RNASeq Nuclear PolyA|strain/background:AB/TU|tissue:neural crest|developmental stage:24hpf|assay:RNA seq|cellular comp1nt:nuclear|ribodepleted:polyA|isolation method:InVivoBiotinylatedNuclei|strand:unstranded", "Sox10 RNASeq Nuclear PolyA 1", "ATAC seq reads were trimmed for quality using sickle v 1.33 and mapped using bowtie v.1.0.0. Smoothened bigWig files were generated using an enhanced Perl script courtesy of Jim Hughes. RNA seq reads were mapped using STAR v.2.4.2a. BAM files incorporating reads belonging to either DNA strand were generated using custom python script. Genome build: danRer7 Zv9 Supplementary files format and content: bigWig files", "Sox10 RNASeq Nuclear PolyA", null, "Nuclei isolation using biotin tagged outer nuclear envelope adapted from INTACT procedure. Polyribosome isolation using biotin tagged Rpl10 protein adapted from TRAP procedure. FACS procedure using cell specific fluorescent marker following gentle dissociation of embryonic tissue. ATAC procedure adapted from Buenostro et al. 2013 adapted for FACS sorted embryonic cells. RNA pools extracted using RNAqueous Micro Scale Total RNA Isolation Kit. Non directional sequencing libraries post polyA selection of RNA transcripts NEBNext\u00ae PolyA mRNA Magnetic Isolation Module NEB were built using NEBnext Ultra RNA library kit for Illumina NEB. Following ribodepletion using Ribo ZeroTM Magnetic Kit Epicentre directional RNA seq libraries were constructed using Stranded RNA Seq Library Preparation Kit KAPABiosystems.", null, "strain/background:AB/TU|tissue:neural crest|developmental stage:24hpf|assay:RNA seq|cellular comp1nt:nuclear|ribodepleted:polyA|isolation method:InVivoBiotinylatedNuclei|strand:unstranded", "GSM2386499", "GSM2386499: Sox10 RNASeq Nuclear PolyA 1; Danio rerio; RNA Seq", "GSM2386499", null, "1", "Nuclei isolation using biotin tagged outer nuclear envelope adapted from INTACT procedure. Polyribosome isolation using biotin tagged Rpl10 protein adapted from TRAP procedure. FACS procedure using cell specific fluorescent marker following gentle dissociation of embryonic tissue. ATAC procedure adapted from Buenostro et al. 2013 adapted for FACS sorted embryonic cells. RNA pools extracted using RNAqueous Micro Scale Total RNA Isolation Kit. Non directional sequencing libraries post polyA selection of RNA transcripts NEBNext\u00ae PolyA mRNA Magnetic Isolation Module NEB were built using NEBnext Ultra RNA library kit for Illumina NEB. Following ribodepletion using Ribo ZeroTM Magnetic Kit Epicentre directional RNA seq libraries were constructed using Stranded RNA Seq Library Preparation Kit KAPABiosystems.", "GEO Accession:GSM2386499", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP092952", null, null, "Sox10_RNASeq_Nuclear_PolyA_1.fastq.gz", "fastq", 1579629350.0, 31592587.0, "GSM2386499 r1", "0:50", "A:432689406;C:359111028;G:365435408;T:422298396;N:95112", 50, null, null, null, 432689406, 359111028, 365435408, 422298396, 95112, "SRX2337864", "SRS1791082", "SRA491940", "GEO", "Sauka-Spengler lab, University of Oxford, MRC Weatherall Institute of Molecular Medicine", 1, 0.81632, null, 0.13449, null, 0.69956, null, 0.45825, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "United Kingdom", "2016-11-08", "Pharyngula", "Embryo", "Brain", "Nervous System"], [41538, "SRR5006031", "SRX2337859", "SRS1791077", "SRP092952", "PRJNA352869", "The Biotagging toolkit for analysis of specific cell populations in zebrafish reveals gene regulatory logic encoded in the nuclear transcriptome", "GSE89670", "Other", "Interrogation of gene regulatory circuits in complex organisms requires precise tools for the selection of individual cell types as well as robust methods for tissue specific labeling and biochemical profiling of target proteins. By exploiting multiple transgenesis strategies we have developed a tissue specific binary in vivo biotinylation system in zebrafish termed \"biotagging\" a versatile methodology that uses genetically encoded components to biotinylate target proteins enabling in depth genome wide analyses of their molecular interactions. Using tissue specific transgenic drivers and individual cell compartment effector lines from our \"biotagging\" toolkit we demonstrate the specificity of our approach at the biochemical cellular and transcriptional levels. By characterizing the in vivo transcriptional landscape of migratory neural crest and myocardial cells in two different cellular compartments ribosomes and nucleus we identify a comprehensive network of protein coding and non coding RNAs and uncover cis regulatory modules and regulatory logic conferring cell specific identity embedded in the complexity of the non coding nuclear transcriptomes. Our study demonstrates that \"biotagging\" eliminates background inherent to complex embryonic environments and allows analyses of molecular interactions in any cellular context at highest resolution. Overall design: Examination of RNA seq and ATAC seq using in vivo biotinylated nuclei and polysomes.", null, "pubmed:28402863", null, "Sox10 RNASeq Ribo 16ss 2", "GSM2386494", null, "source name:Sox10 RNASeq Ribo 16ss|strain/background:AB/TU|tissue:neural crest and otic|developmental stage:16ss|assay:RNA seq stranded|cellular comp1nt:polyribosome associated|ribodepleted:ribodepleted|isolation method:InVivoBiotinylatedPolysomes|strand:reverse", "Sox10 RNASeq Ribo 16ss 2", "ATAC seq reads were trimmed for quality using sickle v 1.33 and mapped using bowtie v.1.0.0. Smoothened bigWig files were generated using an enhanced Perl script courtesy of Jim Hughes. RNA seq reads were mapped using STAR v.2.4.2a. BAM files incorporating reads belonging to either DNA strand were generated using custom python script. Genome build: danRer7 Zv9 Supplementary files format and content: bigWig files", "Sox10 RNASeq Ribo 16ss", null, "Nuclei isolation using biotin tagged outer nuclear envelope adapted from INTACT procedure. Polyribosome isolation using biotin tagged Rpl10 protein adapted from TRAP procedure. FACS procedure using cell specific fluorescent marker following gentle dissociation of embryonic tissue. ATAC procedure adapted from Buenostro et al. 2013 adapted for FACS sorted embryonic cells. RNA pools extracted using RNAqueous Micro Scale Total RNA Isolation Kit. Non directional sequencing libraries post polyA selection of RNA transcripts NEBNext\u00ae PolyA mRNA Magnetic Isolation Module NEB were built using NEBnext Ultra RNA library kit for Illumina NEB. Following ribodepletion using Ribo ZeroTM Magnetic Kit Epicentre directional RNA seq libraries were constructed using Stranded RNA Seq Library Preparation Kit KAPABiosystems.", null, "strain/background:AB/TU|tissue:neural crest and otic|developmental stage:16ss|assay:RNA seq stranded|cellular comp1nt:polyribosome associated|ribodepleted:ribodepleted|isolation method:InVivoBiotinylatedPolysomes|strand:reverse", "GSM2386494", "GSM2386494: Sox10 RNASeq Ribo 16ss 2; Danio rerio; RNA Seq", "GSM2386494", null, "1", "Nuclei isolation using biotin tagged outer nuclear envelope adapted from INTACT procedure. Polyribosome isolation using biotin tagged Rpl10 protein adapted from TRAP procedure. FACS procedure using cell specific fluorescent marker following gentle dissociation of embryonic tissue. ATAC procedure adapted from Buenostro et al. 2013 adapted for FACS sorted embryonic cells. RNA pools extracted using RNAqueous Micro Scale Total RNA Isolation Kit. Non directional sequencing libraries post polyA selection of RNA transcripts NEBNext\u00ae PolyA mRNA Magnetic Isolation Module NEB were built using NEBnext Ultra RNA library kit for Illumina NEB. Following ribodepletion using Ribo ZeroTM Magnetic Kit Epicentre directional RNA seq libraries were constructed using Stranded RNA Seq Library Preparation Kit KAPABiosystems.", "GEO Accession:GSM2386494", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP092952", null, null, "Sox10_RNASeq_Ribo_16ss_2_R1.fastq.gz Sox10_RNASeq_Ribo_16ss_2_R2.fastq.gz", "fastq fastq", 5287990896.0, 51843048.0, "GSM2386494 r1", "0:51 1:51", "A:1204370777;C:1407058076;G:1465472994;T:1210820868;N:268181", 51, 51, null, null, 1204370777, 1407058076, 1465472994, 1210820868, 268181, "SRX2337859", "SRS1791077", "SRA491940", "GEO", "Sauka-Spengler lab, University of Oxford, MRC Weatherall Institute of Molecular Medicine", 2, 0.81831, 0.83714, 0.12373, 0.12275, 0.72198, 0.72206, 0.5121, 0.53314, 51, 51, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "United Kingdom", "2016-11-08", "Undetermined", "Embryo", "Brain", "Nervous System"], [41539, "SRR5006030", "SRX2337858", "SRS1791076", "SRP092952", "PRJNA352869", "The Biotagging toolkit for analysis of specific cell populations in zebrafish reveals gene regulatory logic encoded in the nuclear transcriptome", "GSE89670", "Other", "Interrogation of gene regulatory circuits in complex organisms requires precise tools for the selection of individual cell types as well as robust methods for tissue specific labeling and biochemical profiling of target proteins. By exploiting multiple transgenesis strategies we have developed a tissue specific binary in vivo biotinylation system in zebrafish termed \"biotagging\" a versatile methodology that uses genetically encoded components to biotinylate target proteins enabling in depth genome wide analyses of their molecular interactions. Using tissue specific transgenic drivers and individual cell compartment effector lines from our \"biotagging\" toolkit we demonstrate the specificity of our approach at the biochemical cellular and transcriptional levels. By characterizing the in vivo transcriptional landscape of migratory neural crest and myocardial cells in two different cellular compartments ribosomes and nucleus we identify a comprehensive network of protein coding and non coding RNAs and uncover cis regulatory modules and regulatory logic conferring cell specific identity embedded in the complexity of the non coding nuclear transcriptomes. Our study demonstrates that \"biotagging\" eliminates background inherent to complex embryonic environments and allows analyses of molecular interactions in any cellular context at highest resolution. Overall design: Examination of RNA seq and ATAC seq using in vivo biotinylated nuclei and polysomes.", null, "pubmed:28402863", null, "Sox10 RNASeq Ribo 16ss 1", "GSM2386493", null, "source name:Sox10 RNASeq Ribo 16ss|strain/background:AB/TU|tissue:neural crest and otic|developmental stage:16ss|assay:RNA seq stranded|cellular comp1nt:polyribosome associated|ribodepleted:ribodepleted|isolation method:InVivoBiotinylatedPolysomes|strand:reverse", "Sox10 RNASeq Ribo 16ss 1", "ATAC seq reads were trimmed for quality using sickle v 1.33 and mapped using bowtie v.1.0.0. Smoothened bigWig files were generated using an enhanced Perl script courtesy of Jim Hughes. RNA seq reads were mapped using STAR v.2.4.2a. BAM files incorporating reads belonging to either DNA strand were generated using custom python script. Genome build: danRer7 Zv9 Supplementary files format and content: bigWig files", "Sox10 RNASeq Ribo 16ss", null, "Nuclei isolation using biotin tagged outer nuclear envelope adapted from INTACT procedure. Polyribosome isolation using biotin tagged Rpl10 protein adapted from TRAP procedure. FACS procedure using cell specific fluorescent marker following gentle dissociation of embryonic tissue. ATAC procedure adapted from Buenostro et al. 2013 adapted for FACS sorted embryonic cells. RNA pools extracted using RNAqueous Micro Scale Total RNA Isolation Kit. Non directional sequencing libraries post polyA selection of RNA transcripts NEBNext\u00ae PolyA mRNA Magnetic Isolation Module NEB were built using NEBnext Ultra RNA library kit for Illumina NEB. Following ribodepletion using Ribo ZeroTM Magnetic Kit Epicentre directional RNA seq libraries were constructed using Stranded RNA Seq Library Preparation Kit KAPABiosystems.", null, "strain/background:AB/TU|tissue:neural crest and otic|developmental stage:16ss|assay:RNA seq stranded|cellular comp1nt:polyribosome associated|ribodepleted:ribodepleted|isolation method:InVivoBiotinylatedPolysomes|strand:reverse", "GSM2386493", "GSM2386493: Sox10 RNASeq Ribo 16ss 1; Danio rerio; RNA Seq", "GSM2386493", null, "1", "Nuclei isolation using biotin tagged outer nuclear envelope adapted from INTACT procedure. Polyribosome isolation using biotin tagged Rpl10 protein adapted from TRAP procedure. FACS procedure using cell specific fluorescent marker following gentle dissociation of embryonic tissue. ATAC procedure adapted from Buenostro et al. 2013 adapted for FACS sorted embryonic cells. RNA pools extracted using RNAqueous Micro Scale Total RNA Isolation Kit. Non directional sequencing libraries post polyA selection of RNA transcripts NEBNext\u00ae PolyA mRNA Magnetic Isolation Module NEB were built using NEBnext Ultra RNA library kit for Illumina NEB. Following ribodepletion using Ribo ZeroTM Magnetic Kit Epicentre directional RNA seq libraries were constructed using Stranded RNA Seq Library Preparation Kit KAPABiosystems.", "GEO Accession:GSM2386493", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP092952", null, null, "Sox10_RNASeq_Ribo_16ss_1_R1.fastq.gz Sox10_RNASeq_Ribo_16ss_1_R2.fastq.gz", "fastq fastq", 4230919506.0, 41479603.0, "GSM2386493 r1", "0:51 1:51", "A:919131551;C:1164206796;G:1220728885;T:925734669;N:1117605", 51, 51, null, null, 919131551, 1164206796, 1220728885, 925734669, 1117605, "SRX2337858", "SRS1791076", "SRA491940", "GEO", "Sauka-Spengler lab, University of Oxford, MRC Weatherall Institute of Molecular Medicine", 2, 0.66796, 0.67548, 0.12592, 0.12637, 0.73316, 0.73245, 0.50194, 0.5059, 51, 51, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "United Kingdom", "2016-11-08", "Undetermined", "Embryo", "Brain", "Nervous System"], [41542, "SRR5006027", "SRX2337855", "SRS1791074", "SRP092952", "PRJNA352869", "The Biotagging toolkit for analysis of specific cell populations in zebrafish reveals gene regulatory logic encoded in the nuclear transcriptome", "GSE89670", "Other", "Interrogation of gene regulatory circuits in complex organisms requires precise tools for the selection of individual cell types as well as robust methods for tissue specific labeling and biochemical profiling of target proteins. By exploiting multiple transgenesis strategies we have developed a tissue specific binary in vivo biotinylation system in zebrafish termed \"biotagging\" a versatile methodology that uses genetically encoded components to biotinylate target proteins enabling in depth genome wide analyses of their molecular interactions. Using tissue specific transgenic drivers and individual cell compartment effector lines from our \"biotagging\" toolkit we demonstrate the specificity of our approach at the biochemical cellular and transcriptional levels. By characterizing the in vivo transcriptional landscape of migratory neural crest and myocardial cells in two different cellular compartments ribosomes and nucleus we identify a comprehensive network of protein coding and non coding RNAs and uncover cis regulatory modules and regulatory logic conferring cell specific identity embedded in the complexity of the non coding nuclear transcriptomes. Our study demonstrates that \"biotagging\" eliminates background inherent to complex embryonic environments and allows analyses of molecular interactions in any cellular context at highest resolution. Overall design: Examination of RNA seq and ATAC seq using in vivo biotinylated nuclei and polysomes.", null, "pubmed:28402863", null, "Sox10 RNASeq Nuclear 18s", "GSM2386490", null, "source name:Sox10 RNASeq Nuclear 18ss|strain/background:AB/TU|tissue:neural crest and otic|developmental stage:18ss|assay:RNA seq stranded|cellular comp1nt:nuclear|ribodepleted:ribodepleted|isolation method:InVivoBiotinylatedNuclei|strand:reverse", "Sox10 RNASeq Nuclear 18s", "ATAC seq reads were trimmed for quality using sickle v 1.33 and mapped using bowtie v.1.0.0. Smoothened bigWig files were generated using an enhanced Perl script courtesy of Jim Hughes. RNA seq reads were mapped using STAR v.2.4.2a. BAM files incorporating reads belonging to either DNA strand were generated using custom python script. Genome build: danRer7 Zv9 Supplementary files format and content: bigWig files", "Sox10 RNASeq Nuclear 18ss", null, "Nuclei isolation using biotin tagged outer nuclear envelope adapted from INTACT procedure. Polyribosome isolation using biotin tagged Rpl10 protein adapted from TRAP procedure. FACS procedure using cell specific fluorescent marker following gentle dissociation of embryonic tissue. ATAC procedure adapted from Buenostro et al. 2013 adapted for FACS sorted embryonic cells. RNA pools extracted using RNAqueous Micro Scale Total RNA Isolation Kit. Non directional sequencing libraries post polyA selection of RNA transcripts NEBNext\u00ae PolyA mRNA Magnetic Isolation Module NEB were built using NEBnext Ultra RNA library kit for Illumina NEB. Following ribodepletion using Ribo ZeroTM Magnetic Kit Epicentre directional RNA seq libraries were constructed using Stranded RNA Seq Library Preparation Kit KAPABiosystems.", null, "strain/background:AB/TU|tissue:neural crest and otic|developmental stage:18ss|assay:RNA seq stranded|cellular comp1nt:nuclear|ribodepleted:ribodepleted|isolation method:InVivoBiotinylatedNuclei|strand:reverse", "GSM2386490", "GSM2386490: Sox10 RNASeq Nuclear 18s; Danio rerio; RNA Seq", "GSM2386490", null, "1", "Nuclei isolation using biotin tagged outer nuclear envelope adapted from INTACT procedure. Polyribosome isolation using biotin tagged Rpl10 protein adapted from TRAP procedure. FACS procedure using cell specific fluorescent marker following gentle dissociation of embryonic tissue. ATAC procedure adapted from Buenostro et al. 2013 adapted for FACS sorted embryonic cells. RNA pools extracted using RNAqueous Micro Scale Total RNA Isolation Kit. Non directional sequencing libraries post polyA selection of RNA transcripts NEBNext\u00ae PolyA mRNA Magnetic Isolation Module NEB were built using NEBnext Ultra RNA library kit for Illumina NEB. Following ribodepletion using Ribo ZeroTM Magnetic Kit Epicentre directional RNA seq libraries were constructed using Stranded RNA Seq Library Preparation Kit KAPABiosystems.", "GEO Accession:GSM2386490", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP092952", null, null, "Sox10_RNASeq_Nuclear_18s_R1.fastq.gz Sox10_RNASeq_Nuclear_18s_R2.fastq.gz", "fastq fastq", 6596030124.0, 64666962.0, "GSM2386490 r1", "0:51 1:51", "A:1414741697;C:1834441752;G:1907448457;T:1439065963;N:332255", 51, 51, null, null, 1414741697, 1834441752, 1907448457, 1439065963, 332255, "SRX2337855", "SRS1791074", "SRA491940", "GEO", "Sauka-Spengler lab, University of Oxford, MRC Weatherall Institute of Molecular Medicine", 2, 0.83508, 0.84262, 0.19684, 0.19773, 0.73241, 0.73164, 0.60536, 0.61019, 51, 51, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "United Kingdom", "2016-11-08", "Undetermined", "Embryo", "Brain", "Nervous System"], [41543, "SRR5006026", "SRX2337854", "SRS1791073", "SRP092952", "PRJNA352869", "The Biotagging toolkit for analysis of specific cell populations in zebrafish reveals gene regulatory logic encoded in the nuclear transcriptome", "GSE89670", "Other", "Interrogation of gene regulatory circuits in complex organisms requires precise tools for the selection of individual cell types as well as robust methods for tissue specific labeling and biochemical profiling of target proteins. By exploiting multiple transgenesis strategies we have developed a tissue specific binary in vivo biotinylation system in zebrafish termed \"biotagging\" a versatile methodology that uses genetically encoded components to biotinylate target proteins enabling in depth genome wide analyses of their molecular interactions. Using tissue specific transgenic drivers and individual cell compartment effector lines from our \"biotagging\" toolkit we demonstrate the specificity of our approach at the biochemical cellular and transcriptional levels. By characterizing the in vivo transcriptional landscape of migratory neural crest and myocardial cells in two different cellular compartments ribosomes and nucleus we identify a comprehensive network of protein coding and non coding RNAs and uncover cis regulatory modules and regulatory logic conferring cell specific identity embedded in the complexity of the non coding nuclear transcriptomes. Our study demonstrates that \"biotagging\" eliminates background inherent to complex embryonic environments and allows analyses of molecular interactions in any cellular context at highest resolution. Overall design: Examination of RNA seq and ATAC seq using in vivo biotinylated nuclei and polysomes.", null, "pubmed:28402863", null, "Sox10 RNASeq Nuclear 16ss 2", "GSM2386489", null, "source name:Sox10 RNASeq Nuclear 16ss|strain/background:AB/TU|tissue:neural crest and otic|developmental stage:16ss|assay:RNA seq stranded|cellular comp1nt:nuclear|ribodepleted:ribodepleted|isolation method:InVivoBiotinylatedNuclei|strand:reverse", "Sox10 RNASeq Nuclear 16ss 2", "ATAC seq reads were trimmed for quality using sickle v 1.33 and mapped using bowtie v.1.0.0. Smoothened bigWig files were generated using an enhanced Perl script courtesy of Jim Hughes. RNA seq reads were mapped using STAR v.2.4.2a. BAM files incorporating reads belonging to either DNA strand were generated using custom python script. Genome build: danRer7 Zv9 Supplementary files format and content: bigWig files", "Sox10 RNASeq Nuclear 16ss", null, "Nuclei isolation using biotin tagged outer nuclear envelope adapted from INTACT procedure. Polyribosome isolation using biotin tagged Rpl10 protein adapted from TRAP procedure. FACS procedure using cell specific fluorescent marker following gentle dissociation of embryonic tissue. ATAC procedure adapted from Buenostro et al. 2013 adapted for FACS sorted embryonic cells. RNA pools extracted using RNAqueous Micro Scale Total RNA Isolation Kit. Non directional sequencing libraries post polyA selection of RNA transcripts NEBNext\u00ae PolyA mRNA Magnetic Isolation Module NEB were built using NEBnext Ultra RNA library kit for Illumina NEB. Following ribodepletion using Ribo ZeroTM Magnetic Kit Epicentre directional RNA seq libraries were constructed using Stranded RNA Seq Library Preparation Kit KAPABiosystems.", null, "strain/background:AB/TU|tissue:neural crest and otic|developmental stage:16ss|assay:RNA seq stranded|cellular comp1nt:nuclear|ribodepleted:ribodepleted|isolation method:InVivoBiotinylatedNuclei|strand:reverse", "GSM2386489", "GSM2386489: Sox10 RNASeq Nuclear 16ss 2; Danio rerio; RNA Seq", "GSM2386489", null, "1", "Nuclei isolation using biotin tagged outer nuclear envelope adapted from INTACT procedure. Polyribosome isolation using biotin tagged Rpl10 protein adapted from TRAP procedure. FACS procedure using cell specific fluorescent marker following gentle dissociation of embryonic tissue. ATAC procedure adapted from Buenostro et al. 2013 adapted for FACS sorted embryonic cells. RNA pools extracted using RNAqueous Micro Scale Total RNA Isolation Kit. Non directional sequencing libraries post polyA selection of RNA transcripts NEBNext\u00ae PolyA mRNA Magnetic Isolation Module NEB were built using NEBnext Ultra RNA library kit for Illumina NEB. Following ribodepletion using Ribo ZeroTM Magnetic Kit Epicentre directional RNA seq libraries were constructed using Stranded RNA Seq Library Preparation Kit KAPABiosystems.", "GEO Accession:GSM2386489", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP092952", null, null, "Sox10_RNASeq_Nuclear_16ss_2_R1.fastq.gz Sox10_RNASeq_Nuclear_16ss_2_R2.fastq.gz", "fastq fastq", 4329094914.0, 42442107.0, "GSM2386489 r1", "0:51 1:51", "A:1127420464;C:1030244600;G:1040492979;T:1129785099;N:1151772", 51, 51, null, null, 1127420464, 1030244600, 1040492979, 1129785099, 1151772, "SRX2337854", "SRS1791073", "SRA491940", "GEO", "Sauka-Spengler lab, University of Oxford, MRC Weatherall Institute of Molecular Medicine", 2, 0.83089, 0.83621, 0.48453, 0.48562, 0.6888, 0.68878, 0.47815, 0.47893, 51, 51, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "United Kingdom", "2016-11-08", "Undetermined", "Embryo", "Brain", "Nervous System"], [41544, "SRR5006025", "SRX2337853", "SRS1791072", "SRP092952", "PRJNA352869", "The Biotagging toolkit for analysis of specific cell populations in zebrafish reveals gene regulatory logic encoded in the nuclear transcriptome", "GSE89670", "Other", "Interrogation of gene regulatory circuits in complex organisms requires precise tools for the selection of individual cell types as well as robust methods for tissue specific labeling and biochemical profiling of target proteins. By exploiting multiple transgenesis strategies we have developed a tissue specific binary in vivo biotinylation system in zebrafish termed \"biotagging\" a versatile methodology that uses genetically encoded components to biotinylate target proteins enabling in depth genome wide analyses of their molecular interactions. Using tissue specific transgenic drivers and individual cell compartment effector lines from our \"biotagging\" toolkit we demonstrate the specificity of our approach at the biochemical cellular and transcriptional levels. By characterizing the in vivo transcriptional landscape of migratory neural crest and myocardial cells in two different cellular compartments ribosomes and nucleus we identify a comprehensive network of protein coding and non coding RNAs and uncover cis regulatory modules and regulatory logic conferring cell specific identity embedded in the complexity of the non coding nuclear transcriptomes. Our study demonstrates that \"biotagging\" eliminates background inherent to complex embryonic environments and allows analyses of molecular interactions in any cellular context at highest resolution. Overall design: Examination of RNA seq and ATAC seq using in vivo biotinylated nuclei and polysomes.", null, "pubmed:28402863", null, "Sox10 RNASeq Nuclear 16ss 1", "GSM2386488", null, "source name:Sox10 RNASeq Nuclear 16ss|strain/background:AB/TU|tissue:neural crest and otic|developmental stage:16ss|assay:RNA seq stranded|cellular comp1nt:nuclear|ribodepleted:ribodepleted|isolation method:InVivoBiotinylatedNuclei|strand:reverse", "Sox10 RNASeq Nuclear 16ss 1", "ATAC seq reads were trimmed for quality using sickle v 1.33 and mapped using bowtie v.1.0.0. Smoothened bigWig files were generated using an enhanced Perl script courtesy of Jim Hughes. RNA seq reads were mapped using STAR v.2.4.2a. BAM files incorporating reads belonging to either DNA strand were generated using custom python script. Genome build: danRer7 Zv9 Supplementary files format and content: bigWig files", "Sox10 RNASeq Nuclear 16ss", null, "Nuclei isolation using biotin tagged outer nuclear envelope adapted from INTACT procedure. Polyribosome isolation using biotin tagged Rpl10 protein adapted from TRAP procedure. FACS procedure using cell specific fluorescent marker following gentle dissociation of embryonic tissue. ATAC procedure adapted from Buenostro et al. 2013 adapted for FACS sorted embryonic cells. RNA pools extracted using RNAqueous Micro Scale Total RNA Isolation Kit. Non directional sequencing libraries post polyA selection of RNA transcripts NEBNext\u00ae PolyA mRNA Magnetic Isolation Module NEB were built using NEBnext Ultra RNA library kit for Illumina NEB. Following ribodepletion using Ribo ZeroTM Magnetic Kit Epicentre directional RNA seq libraries were constructed using Stranded RNA Seq Library Preparation Kit KAPABiosystems.", null, "strain/background:AB/TU|tissue:neural crest and otic|developmental stage:16ss|assay:RNA seq stranded|cellular comp1nt:nuclear|ribodepleted:ribodepleted|isolation method:InVivoBiotinylatedNuclei|strand:reverse", "GSM2386488", "GSM2386488: Sox10 RNASeq Nuclear 16ss 1; Danio rerio; RNA Seq", "GSM2386488", null, "1", "Nuclei isolation using biotin tagged outer nuclear envelope adapted from INTACT procedure. Polyribosome isolation using biotin tagged Rpl10 protein adapted from TRAP procedure. FACS procedure using cell specific fluorescent marker following gentle dissociation of embryonic tissue. ATAC procedure adapted from Buenostro et al. 2013 adapted for FACS sorted embryonic cells. RNA pools extracted using RNAqueous Micro Scale Total RNA Isolation Kit. Non directional sequencing libraries post polyA selection of RNA transcripts NEBNext\u00ae PolyA mRNA Magnetic Isolation Module NEB were built using NEBnext Ultra RNA library kit for Illumina NEB. Following ribodepletion using Ribo ZeroTM Magnetic Kit Epicentre directional RNA seq libraries were constructed using Stranded RNA Seq Library Preparation Kit KAPABiosystems.", "GEO Accession:GSM2386488", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP092952", null, null, "Sox10_RNASeq_Nuclear_16ss_1_R1.fastq.gz Sox10_RNASeq_Nuclear_16ss_1_R2.fastq.gz", "fastq fastq", 6105869838.0, 59861469.0, "GSM2386488 r1", "0:51 1:51", "A:1502965808;C:1526110440;G:1549725766;T:1515687223;N:11380601", 51, 51, null, null, 1502965808, 1526110440, 1549725766, 1515687223, 11380601, "SRX2337853", "SRS1791072", "SRA491940", "GEO", "Sauka-Spengler lab, University of Oxford, MRC Weatherall Institute of Molecular Medicine", 2, 0.83937, 0.84876, 0.37877, 0.38092, 0.69652, 0.69706, 0.47609, 0.47992, 51, 51, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "United Kingdom", "2016-11-08", "Undetermined", "Embryo", "Brain", "Nervous System"], [48097, "SRR7041789", "SRX3973827", "SRS3199286", "SRP141198", "PRJNA451019", "Potential role of gas6 in zebrafish hindbrain development", "GSE113396", "Transcriptome Analysis", "identification of differentially expressed genes in gas6 homozygous mutant hindbrain when compared to wildtype hindbrain in zebrafish Overall design: Total RNA was extracted from dissected hindbrain of gas6 homzygous mutants and wildtype embryos at 48hpf using the RNeasy Mini Kit Qiagen. Three libraries from wildtype embryos and three libraries from gas6 mutants were then generated from 3mg RNA using the TruSeq Stranded mRNA Library Prep Kit Illumina. All libraries were analyzed for quality on a bioanalyzer prior to sequencing Agilent 2100 BioAnalyzer.", "parent bioproject:PRJNA451178", "pubmed:29945667", null, "gas6 / mutant replicate 3 gas6mut", "GSM3105075", null, "source name:dissected hindbrain|developmental stage:48 hpf / mutant|tissue:hindbrain", "gas6 / mutant replicate 3 gas6mut", "reads quality check with FastQC alignment and read counts with RSEM v1.2.28 Normalized abundance measurements and identification of differentially expressed genes with DESeq2 Genome build: GRCz10/DanRer7 Supplementary files format and content: .tsv containing read count tmp values from each replicate adjusted p values and fold change compared to wildtype samples for all genes detected", "dissected hindbrain", null, "Total RNA was extracted from dissected hindbrain of gas6 homzygous mutants and wildtype embryos at 48hpf using the RNeasy Mini Kit Qiagen. Three libraries from wildtype embryos and three libraries from gas6 mutants were then generated from 3mg RNA using the TruSeq Stranded mRNA Library Prep Kit Illumina. All libraries were analyzed for quality on a bioanalyzer prior to sequencing Agilent 2100 BioAnalyzer.", "zebrafish egg water maintained at 28\u00b0C", "developmental stage:48 hpf / mutant|tissue:hindbrain", "GSM3105075", "GSM3105075: gas6 / mutant replicate 3 gas6mut; Danio rerio; RNA Seq", "GSM3105075", null, "1", "Total RNA was extracted from dissected hindbrain of gas6 homzygous mutants and wildtype embryos at 48hpf using the RNeasy Mini Kit Qiagen. Three libraries from wildtype embryos and three libraries from gas6 mutants were then generated from 3mg RNA using the TruSeq Stranded mRNA Library Prep Kit Illumina. All libraries were analyzed for quality on a bioanalyzer prior to sequencing Agilent 2100 BioAnalyzer.", "GEO Accession:GSM3105075", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP141198", null, null, "Mut3.fastq.gz", "fastq", 3795018900.0, 37950189.0, "GSM3105075 r1", "0:100", "A:918996199;C:928143353;G:923182529;T:1021402181;N:3294638", 100, null, null, null, 918996199, 928143353, 923182529, 1021402181, 3294638, "SRX3973827", "SRS3199286", "SRA693051", "GEO", "Biochemistry and Molecular Pharmacology, UMass Medical School", 1, 0.95946, null, 0.06073, null, 0.68235, null, 0.46562, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2018-04-19", "Hatching", "Embryo", "Brain", "Nervous System"], [48098, "SRR7041788", "SRX3973826", "SRS3199287", "SRP141198", "PRJNA451019", "Potential role of gas6 in zebrafish hindbrain development", "GSE113396", "Transcriptome Analysis", "identification of differentially expressed genes in gas6 homozygous mutant hindbrain when compared to wildtype hindbrain in zebrafish Overall design: Total RNA was extracted from dissected hindbrain of gas6 homzygous mutants and wildtype embryos at 48hpf using the RNeasy Mini Kit Qiagen. Three libraries from wildtype embryos and three libraries from gas6 mutants were then generated from 3mg RNA using the TruSeq Stranded mRNA Library Prep Kit Illumina. All libraries were analyzed for quality on a bioanalyzer prior to sequencing Agilent 2100 BioAnalyzer.", "parent bioproject:PRJNA451178", "pubmed:29945667", null, "gas6 / mutant replicate 2 gas6mut", "GSM3105074", null, "source name:dissected hindbrain|developmental stage:48 hpf / mutant|tissue:hindbrain", "gas6 / mutant replicate 2 gas6mut", "reads quality check with FastQC alignment and read counts with RSEM v1.2.28 Normalized abundance measurements and identification of differentially expressed genes with DESeq2 Genome build: GRCz10/DanRer7 Supplementary files format and content: .tsv containing read count tmp values from each replicate adjusted p values and fold change compared to wildtype samples for all genes detected", "dissected hindbrain", null, "Total RNA was extracted from dissected hindbrain of gas6 homzygous mutants and wildtype embryos at 48hpf using the RNeasy Mini Kit Qiagen. Three libraries from wildtype embryos and three libraries from gas6 mutants were then generated from 3mg RNA using the TruSeq Stranded mRNA Library Prep Kit Illumina. All libraries were analyzed for quality on a bioanalyzer prior to sequencing Agilent 2100 BioAnalyzer.", "zebrafish egg water maintained at 28\u00b0C", "developmental stage:48 hpf / mutant|tissue:hindbrain", "GSM3105074", "GSM3105074: gas6 / mutant replicate 2 gas6mut; Danio rerio; RNA Seq", "GSM3105074", null, "1", "Total RNA was extracted from dissected hindbrain of gas6 homzygous mutants and wildtype embryos at 48hpf using the RNeasy Mini Kit Qiagen. Three libraries from wildtype embryos and three libraries from gas6 mutants were then generated from 3mg RNA using the TruSeq Stranded mRNA Library Prep Kit Illumina. All libraries were analyzed for quality on a bioanalyzer prior to sequencing Agilent 2100 BioAnalyzer.", "GEO Accession:GSM3105074", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP141198", null, null, "Mut2.fastq.gz", "fastq", 3729663500.0, 37296635.0, "GSM3105074 r1", "0:100", "A:909818849;C:902636895;G:904978335;T:1008966488;N:3262933", 100, null, null, null, 909818849, 902636895, 904978335, 1008966488, 3262933, "SRX3973826", "SRS3199287", "SRA693051", "GEO", "Biochemistry and Molecular Pharmacology, UMass Medical School", 1, 0.95717, null, 0.06681, null, 0.68217, null, 0.46864, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2018-04-19", "Hatching", "Embryo", "Brain", "Nervous System"], [48099, "SRR7041787", "SRX3973825", "SRS3199285", "SRP141198", "PRJNA451019", "Potential role of gas6 in zebrafish hindbrain development", "GSE113396", "Transcriptome Analysis", "identification of differentially expressed genes in gas6 homozygous mutant hindbrain when compared to wildtype hindbrain in zebrafish Overall design: Total RNA was extracted from dissected hindbrain of gas6 homzygous mutants and wildtype embryos at 48hpf using the RNeasy Mini Kit Qiagen. Three libraries from wildtype embryos and three libraries from gas6 mutants were then generated from 3mg RNA using the TruSeq Stranded mRNA Library Prep Kit Illumina. All libraries were analyzed for quality on a bioanalyzer prior to sequencing Agilent 2100 BioAnalyzer.", "parent bioproject:PRJNA451178", "pubmed:29945667", null, "gas6 / mutant replicate 1 gas6mut", "GSM3105073", null, "source name:dissected hindbrain|developmental stage:48 hpf / mutant|tissue:hindbrain", "gas6 / mutant replicate 1 gas6mut", "reads quality check with FastQC alignment and read counts with RSEM v1.2.28 Normalized abundance measurements and identification of differentially expressed genes with DESeq2 Genome build: GRCz10/DanRer7 Supplementary files format and content: .tsv containing read count tmp values from each replicate adjusted p values and fold change compared to wildtype samples for all genes detected", "dissected hindbrain", null, "Total RNA was extracted from dissected hindbrain of gas6 homzygous mutants and wildtype embryos at 48hpf using the RNeasy Mini Kit Qiagen. Three libraries from wildtype embryos and three libraries from gas6 mutants were then generated from 3mg RNA using the TruSeq Stranded mRNA Library Prep Kit Illumina. All libraries were analyzed for quality on a bioanalyzer prior to sequencing Agilent 2100 BioAnalyzer.", "zebrafish egg water maintained at 28\u00b0C", "developmental stage:48 hpf / mutant|tissue:hindbrain", "GSM3105073", "GSM3105073: gas6 / mutant replicate 1 gas6mut; Danio rerio; RNA Seq", "GSM3105073", null, "1", "Total RNA was extracted from dissected hindbrain of gas6 homzygous mutants and wildtype embryos at 48hpf using the RNeasy Mini Kit Qiagen. Three libraries from wildtype embryos and three libraries from gas6 mutants were then generated from 3mg RNA using the TruSeq Stranded mRNA Library Prep Kit Illumina. All libraries were analyzed for quality on a bioanalyzer prior to sequencing Agilent 2100 BioAnalyzer.", "GEO Accession:GSM3105073", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP141198", null, null, "Mut1.fastq.gz", "fastq", 2554222700.0, 25542227.0, "GSM3105073 r1", "0:100", "A:629483819;C:619623433;G:604226674;T:698705739;N:2183035", 100, null, null, null, 629483819, 619623433, 604226674, 698705739, 2183035, "SRX3973825", "SRS3199285", "SRA693051", "GEO", "Biochemistry and Molecular Pharmacology, UMass Medical School", 1, 0.9561, null, 0.07094, null, 0.67838, null, 0.46772, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2018-04-19", "Hatching", "Embryo", "Brain", "Nervous System"], [48100, "SRR7041786", "SRX3973824", "SRS3199283", "SRP141198", "PRJNA451019", "Potential role of gas6 in zebrafish hindbrain development", "GSE113396", "Transcriptome Analysis", "identification of differentially expressed genes in gas6 homozygous mutant hindbrain when compared to wildtype hindbrain in zebrafish Overall design: Total RNA was extracted from dissected hindbrain of gas6 homzygous mutants and wildtype embryos at 48hpf using the RNeasy Mini Kit Qiagen. Three libraries from wildtype embryos and three libraries from gas6 mutants were then generated from 3mg RNA using the TruSeq Stranded mRNA Library Prep Kit Illumina. All libraries were analyzed for quality on a bioanalyzer prior to sequencing Agilent 2100 BioAnalyzer.", "parent bioproject:PRJNA451178", "pubmed:29945667", null, "wildtype control replicate 3 gas6mut", "GSM3105072", null, "source name:dissected hindbrain|developmental stage:48 hpf control|tissue:hindbrain", "wildtype control replicate 3 gas6mut", "reads quality check with FastQC alignment and read counts with RSEM v1.2.28 Normalized abundance measurements and identification of differentially expressed genes with DESeq2 Genome build: GRCz10/DanRer7 Supplementary files format and content: .tsv containing read count tmp values from each replicate adjusted p values and fold change compared to wildtype samples for all genes detected", "dissected hindbrain", null, "Total RNA was extracted from dissected hindbrain of gas6 homzygous mutants and wildtype embryos at 48hpf using the RNeasy Mini Kit Qiagen. Three libraries from wildtype embryos and three libraries from gas6 mutants were then generated from 3mg RNA using the TruSeq Stranded mRNA Library Prep Kit Illumina. All libraries were analyzed for quality on a bioanalyzer prior to sequencing Agilent 2100 BioAnalyzer.", "zebrafish egg water maintained at 28\u00b0C", "developmental stage:48 hpf control|tissue:hindbrain", "GSM3105072", "GSM3105072: wildtype control replicate 3 gas6mut; Danio rerio; RNA Seq", "GSM3105072", null, "1", "Total RNA was extracted from dissected hindbrain of gas6 homzygous mutants and wildtype embryos at 48hpf using the RNeasy Mini Kit Qiagen. Three libraries from wildtype embryos and three libraries from gas6 mutants were then generated from 3mg RNA using the TruSeq Stranded mRNA Library Prep Kit Illumina. All libraries were analyzed for quality on a bioanalyzer prior to sequencing Agilent 2100 BioAnalyzer.", "GEO Accession:GSM3105072", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP141198", null, null, "WT3.fastq.gz", "fastq", 3024416800.0, 30244168.0, "GSM3105072 r1", "0:100", "A:748173237;C:725813083;G:722763689;T:825021244;N:2645547", 100, null, null, null, 748173237, 725813083, 722763689, 825021244, 2645547, "SRX3973824", "SRS3199283", "SRA693051", "GEO", "Biochemistry and Molecular Pharmacology, UMass Medical School", 1, 0.95777, null, 0.0748, null, 0.69059, null, 0.46902, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2018-04-19", "Hatching", "Embryo", "Brain", "Nervous System"], [48101, "SRR7041785", "SRX3973823", "SRS3199284", "SRP141198", "PRJNA451019", "Potential role of gas6 in zebrafish hindbrain development", "GSE113396", "Transcriptome Analysis", "identification of differentially expressed genes in gas6 homozygous mutant hindbrain when compared to wildtype hindbrain in zebrafish Overall design: Total RNA was extracted from dissected hindbrain of gas6 homzygous mutants and wildtype embryos at 48hpf using the RNeasy Mini Kit Qiagen. Three libraries from wildtype embryos and three libraries from gas6 mutants were then generated from 3mg RNA using the TruSeq Stranded mRNA Library Prep Kit Illumina. All libraries were analyzed for quality on a bioanalyzer prior to sequencing Agilent 2100 BioAnalyzer.", "parent bioproject:PRJNA451178", "pubmed:29945667", null, "wildtype control replicate 2 gas6mut", "GSM3105071", null, "source name:dissected hindbrain|developmental stage:48 hpf control|tissue:hindbrain", "wildtype control replicate 2 gas6mut", "reads quality check with FastQC alignment and read counts with RSEM v1.2.28 Normalized abundance measurements and identification of differentially expressed genes with DESeq2 Genome build: GRCz10/DanRer7 Supplementary files format and content: .tsv containing read count tmp values from each replicate adjusted p values and fold change compared to wildtype samples for all genes detected", "dissected hindbrain", null, "Total RNA was extracted from dissected hindbrain of gas6 homzygous mutants and wildtype embryos at 48hpf using the RNeasy Mini Kit Qiagen. Three libraries from wildtype embryos and three libraries from gas6 mutants were then generated from 3mg RNA using the TruSeq Stranded mRNA Library Prep Kit Illumina. All libraries were analyzed for quality on a bioanalyzer prior to sequencing Agilent 2100 BioAnalyzer.", "zebrafish egg water maintained at 28\u00b0C", "developmental stage:48 hpf control|tissue:hindbrain", "GSM3105071", "GSM3105071: wildtype control replicate 2 gas6mut; Danio rerio; RNA Seq", "GSM3105071", null, "1", "Total RNA was extracted from dissected hindbrain of gas6 homzygous mutants and wildtype embryos at 48hpf using the RNeasy Mini Kit Qiagen. Three libraries from wildtype embryos and three libraries from gas6 mutants were then generated from 3mg RNA using the TruSeq Stranded mRNA Library Prep Kit Illumina. All libraries were analyzed for quality on a bioanalyzer prior to sequencing Agilent 2100 BioAnalyzer.", "GEO Accession:GSM3105071", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP141198", null, null, "WT2.fastq.gz", "fastq", 3358506900.0, 33585069.0, "GSM3105071 r1", "0:100", "A:816072735;C:817548352;G:813692655;T:908273519;N:2919639", 100, null, null, null, 816072735, 817548352, 813692655, 908273519, 2919639, "SRX3973823", "SRS3199284", "SRA693051", "GEO", "Biochemistry and Molecular Pharmacology, UMass Medical School", 1, 0.9596, null, 0.06574, null, 0.69197, null, 0.46749, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2018-04-19", "Hatching", "Embryo", "Brain", "Nervous System"], [48102, "SRR7041784", "SRX3973822", "SRS3199282", "SRP141198", "PRJNA451019", "Potential role of gas6 in zebrafish hindbrain development", "GSE113396", "Transcriptome Analysis", "identification of differentially expressed genes in gas6 homozygous mutant hindbrain when compared to wildtype hindbrain in zebrafish Overall design: Total RNA was extracted from dissected hindbrain of gas6 homzygous mutants and wildtype embryos at 48hpf using the RNeasy Mini Kit Qiagen. Three libraries from wildtype embryos and three libraries from gas6 mutants were then generated from 3mg RNA using the TruSeq Stranded mRNA Library Prep Kit Illumina. All libraries were analyzed for quality on a bioanalyzer prior to sequencing Agilent 2100 BioAnalyzer.", "parent bioproject:PRJNA451178", "pubmed:29945667", null, "wildtype control replicate 1 gas6mut", "GSM3105070", null, "source name:dissected hindbrain|developmental stage:48 hpf control|tissue:hindbrain", "wildtype control replicate 1 gas6mut", "reads quality check with FastQC alignment and read counts with RSEM v1.2.28 Normalized abundance measurements and identification of differentially expressed genes with DESeq2 Genome build: GRCz10/DanRer7 Supplementary files format and content: .tsv containing read count tmp values from each replicate adjusted p values and fold change compared to wildtype samples for all genes detected", "dissected hindbrain", null, "Total RNA was extracted from dissected hindbrain of gas6 homzygous mutants and wildtype embryos at 48hpf using the RNeasy Mini Kit Qiagen. Three libraries from wildtype embryos and three libraries from gas6 mutants were then generated from 3mg RNA using the TruSeq Stranded mRNA Library Prep Kit Illumina. All libraries were analyzed for quality on a bioanalyzer prior to sequencing Agilent 2100 BioAnalyzer.", "zebrafish egg water maintained at 28\u00b0C", "developmental stage:48 hpf control|tissue:hindbrain", "GSM3105070", "GSM3105070: wildtype control replicate 1 gas6mut; Danio rerio; RNA Seq", "GSM3105070", null, "1", "Total RNA was extracted from dissected hindbrain of gas6 homzygous mutants and wildtype embryos at 48hpf using the RNeasy Mini Kit Qiagen. Three libraries from wildtype embryos and three libraries from gas6 mutants were then generated from 3mg RNA using the TruSeq Stranded mRNA Library Prep Kit Illumina. All libraries were analyzed for quality on a bioanalyzer prior to sequencing Agilent 2100 BioAnalyzer.", "GEO Accession:GSM3105070", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP141198", null, null, "WT1.fastq.gz", "fastq", 3390648900.0, 33906489.0, "GSM3105070 r1", "0:100", "A:815584808;C:833592815;G:824903141;T:913622836;N:2945300", 100, null, null, null, 815584808, 833592815, 824903141, 913622836, 2945300, "SRX3973822", "SRS3199282", "SRA693051", "GEO", "Biochemistry and Molecular Pharmacology, UMass Medical School", 1, 0.96267, null, 0.05448, null, 0.69798, null, 0.46774, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2018-04-19", "Hatching", "Embryo", "Brain", "Nervous System"], [53003, "SRR9662036", "SRX6422912", "SRS5079701", "SRP213938", "PRJNA553572", "A map of cis regulatory elements and 3D genome structures in zebrafish", "GSE134055", "Other", "The zebrafish has been widely used for the study of human disease and development as 70% of the protein coding genes are conserved between the two species. Annotation of functional control elements of the zebrafish genome however has lagged behind that of other model systems such as mouse and Drosophila. Based on multi omics approaches taken in the ENCODE and Roadmap Epigenomics projects we performed RNA seq ATAC seq ChIP seq and Hi C experiments in ten adult and two embryonic tissues to generate a comprehensive map of transcriptomes and regulatory elements in the zebrafish Tuebingen reference strain. Overall we have identified 235 596 cis regulatory elements which potentially shape the tissue specific and developmental stage specific gene expression in zebrafish. A comparison of zebrafish human and mouse regulatory elements allowed us to identify both evolutionarily conserved and species specific regulatory sequences. Furthermore through the analysis of Hi C data in zebrafish brain and muscle we observed different levels of 3D genome organization including compartment topological associating domains TADs and chromatin loops in zebrafish. A subset of TADs are deeply conserved between zebrafish and human. This work provides an additional epigenomic anchor for the functional annotation of vertebrate genomes and the study of evolutionally conserved elements of 3D genome organization. Overall design: 13 tissues from adult and embryonic stage were examined using ChIP Seq H3K27ac and H3K4me3 RNA Seq 11 of them were examined using ATAC seq WGBS and ChIP seq H3K9me3 and H3K9me2 and one scATAC seq in brain. Additionally we performed HiC experiments in adult muscle and brain. Please note that for the samples GSM4661977 GSM4662088 [1] each processed data generated from both replicates is linked to the corresponding *rep1 sample records [2] the input sample used for each ChIP sample is indicated in the description field in the corresponding input sample records.", null, "pubmed:33239788;pubmed:35649578", null, "YueLab RNA Seq embryonic Brain rep2", "GSM3934904", null, "source name:Tissue|strain:Tuebingen|tissue:embryonic Brain", "YueLab RNA Seq embryonic Brain rep2", "RNA seq reads were aligned to zv10 genome assembly using STAR; ChIP seq and ATAC seq reads were aligned to zv10 genome assembly using BWA HiC reads were aligned to zv10 genome assembly using Bowtie2 The TPM value of gene expression was caculated using RSEM ChIP seq and ATAC seq peaks were called using MACS2 with the following setting: ChIP seq q value <10e 2 p value<10e 5 Change>1 FC>2. ATAC seq: q value<10e 2 and p value<10e 5 HiC matrix was generated using HiC Pro Genome build: zv10 Supplementary files format and content: tab delimited text files include TPM values for each Sample; the narrowPeak files included the peaks for each Sample; The .hic file were the matrix of Hi C for each Sample.**All replicates were merged", "Tissue", null, "For each RNA seq experiment the same tissues combined from at least two Tuebingen fish were used as one replicate. For embryonic trunk ten 1 dpf fish were dechorionated with pronase and trunk were cut off for RNA seq. For embryonic neuron green cells from TgHuc:Kaede cells were sorted by FACS and approxinately 20 000 cells were used for one replicate. The tissue RNA was extracted from Trizol\u00ae according to the protocol Invitrogen. The cDNA libraries were performed using SureSelect Strand Specific RNA Library Preparation Kit Agilent according to the manufacturer\u2019s protocol. Briefly polyA RNA was purified from 1000\u00a0ng of total RNA using oligo dT beads Invitrogen. Extracted RNA was first fragmented then followed by reverse transcription end repair adenylation adaptor ligation and subsequent PCR amplification. The final product was checked by size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit Agilent and Kapa Library Quantification Kit Kapa Biosystems and then followed by pair end 2X 50 bp high throughput sequencing using HiSeq 2500 Illumina.", "Embryonic and ault Tuebingen zebrafish were raised under standard laboratory conditions", "strain:Tuebingen|tissue:embryonic Brain", "GSM3934904", "GSM3934904: YueLab RNA Seq embryonic Brain rep2; Danio rerio; RNA Seq", "GSM3934904", null, "1", "For each RNA seq experiment the same tissues combined from at least two Tuebingen fish were used as one replicate. For embryonic trunk ten 1 dpf fish were dechorionated with pronase and trunk were cut off for RNA seq. For embryonic neuron green cells from TgHuc:Kaede cells were sorted by FACS and approxinately 20 000 cells were used for one replicate. The tissue RNA was extracted from Trizol\u00ae according to the protocol Invitrogen. The cDNA libraries were performed using SureSelect Strand Specific RNA Library Preparation Kit Agilent according to the manufacturer's protocol. Briefly polyA RNA was purified from 1000\u00a0ng of total RNA using oligo dT beads Invitrogen. Extracted RNA was first fragmented then followed by reverse transcription end repair adenylation adaptor ligation and subsequent PCR amplification. The final product was checked by size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit Agilent and Kapa Library Quantification Kit Kapa Biosystems and then followed by pair end 2X 50 bp high throughput sequencing using HiSeq 2500 Illumina.", "GEO Accession:GSM3934904", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina Genome Analyzer", null, "SRP213938", null, null, "YueLab-RNA-Seq-embryonic-Brain-rep2_1.fastq.gz YueLab-RNA-Seq-embryonic-Brain-rep2_2.fastq.gz", "fastq fastq", 4356185472.0, 21807597.0, "GSM3934904 r1", "0:99.63 1:100.13", "A:1230794981;C:931477391;G:940054394;T:1251750673;N:2108033", 99, 100, null, null, 1230794981, 931477391, 940054394, 1251750673, 2108033, "SRX6422912", "SRS5079701", "SRA919194", "GEO", "Feng Yue, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine", 2, 0.88944, 0.89191, 0.2053, 0.20664, 0.71242, 0.71394, 0.47557, 0.47724, 101, 101, "B", "B", "biological fallback assumption", "illumina", "early_illumina", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2019-07-09", "Pharyngula", "Embryo", "Brain", "Nervous System"], [53004, "SRR9662035", "SRX6422911", "SRS5079702", "SRP213938", "PRJNA553572", "A map of cis regulatory elements and 3D genome structures in zebrafish", "GSE134055", "Other", "The zebrafish has been widely used for the study of human disease and development as 70% of the protein coding genes are conserved between the two species. Annotation of functional control elements of the zebrafish genome however has lagged behind that of other model systems such as mouse and Drosophila. Based on multi omics approaches taken in the ENCODE and Roadmap Epigenomics projects we performed RNA seq ATAC seq ChIP seq and Hi C experiments in ten adult and two embryonic tissues to generate a comprehensive map of transcriptomes and regulatory elements in the zebrafish Tuebingen reference strain. Overall we have identified 235 596 cis regulatory elements which potentially shape the tissue specific and developmental stage specific gene expression in zebrafish. A comparison of zebrafish human and mouse regulatory elements allowed us to identify both evolutionarily conserved and species specific regulatory sequences. Furthermore through the analysis of Hi C data in zebrafish brain and muscle we observed different levels of 3D genome organization including compartment topological associating domains TADs and chromatin loops in zebrafish. A subset of TADs are deeply conserved between zebrafish and human. This work provides an additional epigenomic anchor for the functional annotation of vertebrate genomes and the study of evolutionally conserved elements of 3D genome organization. Overall design: 13 tissues from adult and embryonic stage were examined using ChIP Seq H3K27ac and H3K4me3 RNA Seq 11 of them were examined using ATAC seq WGBS and ChIP seq H3K9me3 and H3K9me2 and one scATAC seq in brain. Additionally we performed HiC experiments in adult muscle and brain. Please note that for the samples GSM4661977 GSM4662088 [1] each processed data generated from both replicates is linked to the corresponding *rep1 sample records [2] the input sample used for each ChIP sample is indicated in the description field in the corresponding input sample records.", null, "pubmed:33239788;pubmed:35649578", null, "YueLab RNA Seq embryonic Brain rep1", "GSM3934903", null, "source name:Tissue|strain:Tuebingen|tissue:embryonic Brain", "YueLab RNA Seq embryonic Brain rep1", "RNA seq reads were aligned to zv10 genome assembly using STAR; ChIP seq and ATAC seq reads were aligned to zv10 genome assembly using BWA HiC reads were aligned to zv10 genome assembly using Bowtie2 The TPM value of gene expression was caculated using RSEM ChIP seq and ATAC seq peaks were called using MACS2 with the following setting: ChIP seq q value <10e 2 p value<10e 5 Change>1 FC>2. ATAC seq: q value<10e 2 and p value<10e 5 HiC matrix was generated using HiC Pro Genome build: zv10 Supplementary files format and content: tab delimited text files include TPM values for each Sample; the narrowPeak files included the peaks for each Sample; The .hic file were the matrix of Hi C for each Sample.**All replicates were merged", "Tissue", null, "For each RNA seq experiment the same tissues combined from at least two Tuebingen fish were used as one replicate. For embryonic trunk ten 1 dpf fish were dechorionated with pronase and trunk were cut off for RNA seq. For embryonic neuron green cells from TgHuc:Kaede cells were sorted by FACS and approxinately 20 000 cells were used for one replicate. The tissue RNA was extracted from Trizol\u00ae according to the protocol Invitrogen. The cDNA libraries were performed using SureSelect Strand Specific RNA Library Preparation Kit Agilent according to the manufacturer\u2019s protocol. Briefly polyA RNA was purified from 1000\u00a0ng of total RNA using oligo dT beads Invitrogen. Extracted RNA was first fragmented then followed by reverse transcription end repair adenylation adaptor ligation and subsequent PCR amplification. The final product was checked by size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit Agilent and Kapa Library Quantification Kit Kapa Biosystems and then followed by pair end 2X 50 bp high throughput sequencing using HiSeq 2500 Illumina.", "Embryonic and ault Tuebingen zebrafish were raised under standard laboratory conditions", "strain:Tuebingen|tissue:embryonic Brain", "GSM3934903", "GSM3934903: YueLab RNA Seq embryonic Brain rep1; Danio rerio; RNA Seq", "GSM3934903", null, "1", "For each RNA seq experiment the same tissues combined from at least two Tuebingen fish were used as one replicate. For embryonic trunk ten 1 dpf fish were dechorionated with pronase and trunk were cut off for RNA seq. For embryonic neuron green cells from TgHuc:Kaede cells were sorted by FACS and approxinately 20 000 cells were used for one replicate. The tissue RNA was extracted from Trizol\u00ae according to the protocol Invitrogen. The cDNA libraries were performed using SureSelect Strand Specific RNA Library Preparation Kit Agilent according to the manufacturer's protocol. Briefly polyA RNA was purified from 1000\u00a0ng of total RNA using oligo dT beads Invitrogen. Extracted RNA was first fragmented then followed by reverse transcription end repair adenylation adaptor ligation and subsequent PCR amplification. The final product was checked by size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit Agilent and Kapa Library Quantification Kit Kapa Biosystems and then followed by pair end 2X 50 bp high throughput sequencing using HiSeq 2500 Illumina.", "GEO Accession:GSM3934903", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina Genome Analyzer", null, "SRP213938", null, null, "YueLab-RNA-Seq-embryonic-Brain-rep1_1.fastq.gz YueLab-RNA-Seq-embryonic-Brain-rep1_2.fastq.gz", "fastq fastq", 4952296956.0, 40592598.0, "GSM3934903 r1", "0:61 1:61", "A:1372792073;C:1100482364;G:1106380994;T:1368907195;N:3734330", 61, 61, null, null, 1372792073, 1100482364, 1106380994, 1368907195, 3734330, "SRX6422911", "SRS5079702", "SRA919194", "GEO", "Feng Yue, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine", 2, 0.8905, 0.89281, 0.09948, 0.10148, 0.7041, 0.7097, 0.46036, 0.45663, 61, 61, "B", "B", "biological fallback assumption", "illumina", "early_illumina", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2019-07-09", "Pharyngula", "Embryo", "Brain", "Nervous System"]], "truncated": false, "filtered_table_rows_count": 875, "expanded_columns": [], "expandable_columns": [], "columns": ["rowid", "run.accession", "experiment.accession", "sample.accession", "study.accession", "bioproject", "study.title", "study.alias", "study.type", "study.abstract", "study.attributes", "study.PMIDs", "sample.description", "sample.title", "sample.alias", "sample.centername", "sample.attributes", "GEOsample.title", "GEOsample.dataprocessing", "GEOsample.source", "GEOsample.treatmentprotocol", "GEOsample.extractprotocol", "GEOsample.growthprotocol", "GEOsample.characteristics", "GEOsample.accession", "experiment.title", "experiment.alias", "experiment.library_name", "experiment.design_description", "experiment.library_construction_protocol", "experiment.attributes", 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