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,experiment.library_strategy,experiment.library_source,experiment.library_selection,experiment.library_layout,experiment.platform,experiment.instrument_model,experiment.spot_descriptor,experiment.study_ref,run.title,run.attributes,run.filename,run.semantic_name,run.total_bases,run.total_spots,run.alias,run.read_lengths,run.base_counts,run.r1_length,run.r2_length,run.r3_length,run.r4_length,run.Acount,run.Ccount,run.Gcount,run.Tcount,run.Ncount,run.experiment,run.pool_member,submission.accession,submission.srasource,submission.bioprojectsource,seqdetective.n_mates,seqdetective.mapping_rate.mate1,seqdetective.mapping_rate.mate2,seqdetective.nofeature_rate.mate1,seqdetective.nofeature_rate.mate2,seqdetective.sparsity.mate1,seqdetective.sparsity.mate2,seqdetective.pos_strand_rate.mate1,seqdetective.pos_strand_rate.mate2,seqdetective.readlen.mate1,seqdetective.readlen.mate2,seqdetective.judgement.mate1,seqdetective.judgement.mate2,seqdetective.judgement.reason,platform_family,instrument_generation,read_bias,selection_class,prep_kit,sc_or_bulk,tech_class,technology,tech_variant,submission.bioprojectsource.country,earliest_date,devstage_curation,devstage_curation_coarse,tissue_curation,tissue_curation_coarse
5795,ERR1698352,ERX1767860,ERS1417534,ERP018188,PRJEB16335,RNA seq of the zebrafish danio rerio brain post developmental exposure to 17a ethinylestradiol,E-MTAB-5173,Transcriptome Analysis,17a ethinylestradiol EE2 is a synthetic estrogen commonly used as an active substance in oral contraceptives.  It is frequently found in waste water effluent and raise concern due to its persistent nature. EE2 binds to estrogen receptors with similar affinity to oestradiol and acts as one of the most potent hormone mimics found in the environment.  Estrogen is involved in many aspects of the development of the neuroendocrine system influencing both brain structure and behavior. We and others have reported a significant effect on non reproductive behaviors in adult fish and in recent studies we found that developmental exposure to EE2 resulted in an anxiogenic phenotype as adults even post a long remediation period.  In this study we aim to study possible mechanisms behind the behavior alterations of zebrafish developmentally exposed to EE2 by sequencing the whole brain transcriptome. Zebrafish embryos were exposed to 0  2.14 and 7.34 ng/L EE2 from 1 day to 80 dpf post the exposure period a remediation period of 120 days followed before the fish were sampled. 3 male brains from the control group 0 ng/L and the 2.14 ng/L group were sampled and 3 female brains from the control group 0 ng/L and 7.34 ng/L were sampled.,ENA FIRST PUBLIC:2017 10 02|ENA LAST UPDATE:2016 10 19|ArrayExpress:E MTAB 5173,,Protocols: RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich  Germany EE2 exposure. Fish exposed to 0  2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA,IonXpressRNA 012 up 058 12,SAMEA4518355,"School of Natural Science, Technology and Environmental Studies Sodertorn University",ENA first public:2017 10 02|ENA last update:2016 10 19|External Id:SAMEA4518355|INSDC center alias:School of Natural Science  Technology and Environmental Studies Sodertorn University|INSDC center name:School of Natural Science  Technology and Environmental Studies Sodertorn University|INSDC first public:2017 10 02T17:05:16Z|INSDC last update:2016 10 19T13:53:59Z|INSDC status:public|Submitter Id:E MTAB 5173:IonXpressRNA 012 up 058 12|age:200|broker name:ArrayExpress|common name:zebrafish|organism part:brain|sample name:E MTAB 5173:IonXpressRNA 012 up 058 12|sex:male,,,,,,,,,Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol,E MTAB 5173:IonXpressRNA 012 up 058 12 s,IonXpressRNA 012 up 058 12 s,RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol,RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich  Germany EE2 exposure. Fish exposed to 0  2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA,Experimental Factor: male:sex|Experimental Factor: 17 ethinylestradiol:compound|Experimental Factor: 2.14:dose,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP018188,Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol,ENA FIRST PUBLIC:2017 10 02|ENA LAST UPDATE:2018 11 16,IonXpressRNA_012_up_058_12.fastq.gz,fastq,2535299006.0,33956077.0,E MTAB 5173:IonXpressRNA 012 up 058 12,0:74.66,A:719061985;C:581906269;G:579932234;T:654398518;N:0,74,,,,719061985,581906269,579932234,654398518,0,ERX1767860,ERS1417534,ERA739176,"School of Natural Science, Technology and Environmental Studies Sodertorn University|European Nucleotide Archive","School of Natural Science, Technology and Environmental Studies Sodertorn University|European Nucleotide Archive",1,0.7343,,0.34119,,0.7359,,0.48406,,66,,B,,usable mapping rate,ion_torrent,ion_torrent,full_length,random_priming,ribozero,bulk,unknown,unknown,,Sweden,2016-10-19,Pharyngula,Embryo,Brain,Nervous System
5796,ERR1698351,ERX1767859,ERS1417533,ERP018188,PRJEB16335,RNA seq of the zebrafish danio rerio brain post developmental exposure to 17a ethinylestradiol,E-MTAB-5173,Transcriptome Analysis,17a ethinylestradiol EE2 is a synthetic estrogen commonly used as an active substance in oral contraceptives.  It is frequently found in waste water effluent and raise concern due to its persistent nature. EE2 binds to estrogen receptors with similar affinity to oestradiol and acts as one of the most potent hormone mimics found in the environment.  Estrogen is involved in many aspects of the development of the neuroendocrine system influencing both brain structure and behavior. We and others have reported a significant effect on non reproductive behaviors in adult fish and in recent studies we found that developmental exposure to EE2 resulted in an anxiogenic phenotype as adults even post a long remediation period.  In this study we aim to study possible mechanisms behind the behavior alterations of zebrafish developmentally exposed to EE2 by sequencing the whole brain transcriptome. Zebrafish embryos were exposed to 0  2.14 and 7.34 ng/L EE2 from 1 day to 80 dpf post the exposure period a remediation period of 120 days followed before the fish were sampled. 3 male brains from the control group 0 ng/L and the 2.14 ng/L group were sampled and 3 female brains from the control group 0 ng/L and 7.34 ng/L were sampled.,ENA FIRST PUBLIC:2017 10 02|ENA LAST UPDATE:2016 10 19|ArrayExpress:E MTAB 5173,,Protocols: RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich  Germany EE2 exposure. Fish exposed to 0  2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA,IonXpressRNA 011 up 058 11,SAMEA4518354,"School of Natural Science, Technology and Environmental Studies Sodertorn University",ENA first public:2017 10 02|ENA last update:2016 10 19|External Id:SAMEA4518354|INSDC center alias:School of Natural Science  Technology and Environmental Studies Sodertorn University|INSDC center name:School of Natural Science  Technology and Environmental Studies Sodertorn University|INSDC first public:2017 10 02T17:05:16Z|INSDC last update:2016 10 19T13:53:59Z|INSDC status:public|Submitter Id:E MTAB 5173:IonXpressRNA 011 up 058 11|age:200|broker name:ArrayExpress|common name:zebrafish|organism part:brain|sample name:E MTAB 5173:IonXpressRNA 011 up 058 11|sex:male,,,,,,,,,Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol,E MTAB 5173:IonXpressRNA 011 up 058 11 s,IonXpressRNA 011 up 058 11 s,RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol,RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich  Germany EE2 exposure. Fish exposed to 0  2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA,Experimental Factor: male:sex|Experimental Factor: 17 ethinylestradiol:compound|Experimental Factor: 2.14:dose,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP018188,Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol,ENA FIRST PUBLIC:2017 10 02|ENA LAST UPDATE:2018 11 16,IonXpressRNA_011_up_058_11.fastq.gz,fastq,3400774471.0,38709756.0,E MTAB 5173:IonXpressRNA 011 up 058 11,0:87.85,A:948991439;C:793389977;G:792539547;T:865853508;N:0,87,,,,948991439,793389977,792539547,865853508,0,ERX1767859,ERS1417533,ERA739176,"School of Natural Science, Technology and Environmental Studies Sodertorn University|European Nucleotide Archive","School of Natural Science, Technology and Environmental Studies Sodertorn University|European Nucleotide Archive",1,0.63968,,0.27033,,0.75213,,0.47966,,139,,B,,usable mapping rate,ion_torrent,ion_torrent,full_length,random_priming,ribozero,bulk,unknown,unknown,,Sweden,2016-10-19,Pharyngula,Embryo,Brain,Nervous System
5797,ERR1698350,ERX1767858,ERS1417532,ERP018188,PRJEB16335,RNA seq of the zebrafish danio rerio brain post developmental exposure to 17a ethinylestradiol,E-MTAB-5173,Transcriptome Analysis,17a ethinylestradiol EE2 is a synthetic estrogen commonly used as an active substance in oral contraceptives.  It is frequently found in waste water effluent and raise concern due to its persistent nature. EE2 binds to estrogen receptors with similar affinity to oestradiol and acts as one of the most potent hormone mimics found in the environment.  Estrogen is involved in many aspects of the development of the neuroendocrine system influencing both brain structure and behavior. We and others have reported a significant effect on non reproductive behaviors in adult fish and in recent studies we found that developmental exposure to EE2 resulted in an anxiogenic phenotype as adults even post a long remediation period.  In this study we aim to study possible mechanisms behind the behavior alterations of zebrafish developmentally exposed to EE2 by sequencing the whole brain transcriptome. Zebrafish embryos were exposed to 0  2.14 and 7.34 ng/L EE2 from 1 day to 80 dpf post the exposure period a remediation period of 120 days followed before the fish were sampled. 3 male brains from the control group 0 ng/L and the 2.14 ng/L group were sampled and 3 female brains from the control group 0 ng/L and 7.34 ng/L were sampled.,ENA FIRST PUBLIC:2017 10 02|ENA LAST UPDATE:2016 10 19|ArrayExpress:E MTAB 5173,,Protocols: RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich  Germany EE2 exposure. Fish exposed to 0  2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA,IonXpressRNA 010 up 058 10,SAMEA4518353,"School of Natural Science, Technology and Environmental Studies Sodertorn University",ENA first public:2017 10 02|ENA last update:2016 10 19|External Id:SAMEA4518353|INSDC center alias:School of Natural Science  Technology and Environmental Studies Sodertorn University|INSDC center name:School of Natural Science  Technology and Environmental Studies Sodertorn University|INSDC first public:2017 10 02T17:05:16Z|INSDC last update:2016 10 19T13:53:59Z|INSDC status:public|Submitter Id:E MTAB 5173:IonXpressRNA 010 up 058 10|age:200|broker name:ArrayExpress|common name:zebrafish|organism part:brain|sample name:E MTAB 5173:IonXpressRNA 010 up 058 10|sex:male,,,,,,,,,Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol,E MTAB 5173:IonXpressRNA 010 up 058 10 s,IonXpressRNA 010 up 058 10 s,RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol,RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich  Germany EE2 exposure. Fish exposed to 0  2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA,Experimental Factor: male:sex|Experimental Factor: 17 ethinylestradiol:compound|Experimental Factor: 2.14:dose,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP018188,Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol,ENA FIRST PUBLIC:2017 10 02|ENA LAST UPDATE:2018 11 16,IonXpressRNA_010_up_058_10.fastq.gz,fastq,3502667998.0,39204781.0,E MTAB 5173:IonXpressRNA 010 up 058 10,0:89.34,A:976977303;C:803330255;G:808731995;T:913628445;N:0,89,,,,976977303,803330255,808731995,913628445,0,ERX1767858,ERS1417532,ERA739176,"School of Natural Science, Technology and Environmental Studies Sodertorn University|European Nucleotide Archive","School of Natural Science, Technology and Environmental Studies Sodertorn University|European Nucleotide Archive",1,0.65846,,0.2815,,0.74028,,0.47784,,86,,B,,usable mapping rate,ion_torrent,ion_torrent,full_length,random_priming,ribozero,bulk,unknown,unknown,,Sweden,2016-10-19,Pharyngula,Embryo,Brain,Nervous System
5798,ERR1698349,ERX1767857,ERS1417531,ERP018188,PRJEB16335,RNA seq of the zebrafish danio rerio brain post developmental exposure to 17a ethinylestradiol,E-MTAB-5173,Transcriptome Analysis,17a ethinylestradiol EE2 is a synthetic estrogen commonly used as an active substance in oral contraceptives.  It is frequently found in waste water effluent and raise concern due to its persistent nature. EE2 binds to estrogen receptors with similar affinity to oestradiol and acts as one of the most potent hormone mimics found in the environment.  Estrogen is involved in many aspects of the development of the neuroendocrine system influencing both brain structure and behavior. We and others have reported a significant effect on non reproductive behaviors in adult fish and in recent studies we found that developmental exposure to EE2 resulted in an anxiogenic phenotype as adults even post a long remediation period.  In this study we aim to study possible mechanisms behind the behavior alterations of zebrafish developmentally exposed to EE2 by sequencing the whole brain transcriptome. Zebrafish embryos were exposed to 0  2.14 and 7.34 ng/L EE2 from 1 day to 80 dpf post the exposure period a remediation period of 120 days followed before the fish were sampled. 3 male brains from the control group 0 ng/L and the 2.14 ng/L group were sampled and 3 female brains from the control group 0 ng/L and 7.34 ng/L were sampled.,ENA FIRST PUBLIC:2017 10 02|ENA LAST UPDATE:2016 10 19|ArrayExpress:E MTAB 5173,,Protocols: RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich  Germany EE2 exposure. Fish exposed to 0  2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA,IonXpressRNA 009 up 058 9,SAMEA4518352,"School of Natural Science, Technology and Environmental Studies Sodertorn University",ENA first public:2017 10 02|ENA last update:2016 10 19|External Id:SAMEA4518352|INSDC center alias:School of Natural Science  Technology and Environmental Studies Sodertorn University|INSDC center name:School of Natural Science  Technology and Environmental Studies Sodertorn University|INSDC first public:2017 10 02T17:05:16Z|INSDC last update:2016 10 19T13:53:59Z|INSDC status:public|Submitter Id:E MTAB 5173:IonXpressRNA 009 up 058 9|age:200|broker name:ArrayExpress|common name:zebrafish|organism part:brain|sample name:E MTAB 5173:IonXpressRNA 009 up 058 9|sex:male,,,,,,,,,Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol,E MTAB 5173:IonXpressRNA 009 up 058 9 s,IonXpressRNA 009 up 058 9 s,RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol,RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich  Germany EE2 exposure. Fish exposed to 0  2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA,Experimental Factor: male:sex|Experimental Factor: n1:compound,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP018188,Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol,ENA FIRST PUBLIC:2017 10 02|ENA LAST UPDATE:2018 11 16,IonXpressRNA_009_up_058_9.fastq.gz,fastq,3575088264.0,39745481.0,E MTAB 5173:IonXpressRNA 009 up 058 9,0:89.95,A:1011474126;C:809896078;G:807471974;T:946246086;N:0,89,,,,1011474126,809896078,807471974,946246086,0,ERX1767857,ERS1417531,ERA739176,"School of Natural Science, Technology and Environmental Studies Sodertorn University|European Nucleotide Archive","School of Natural Science, Technology and Environmental Studies Sodertorn University|European Nucleotide Archive",1,0.65266,,0.30274,,0.75286,,0.48527,,94,,B,,usable mapping rate,ion_torrent,ion_torrent,full_length,random_priming,ribozero,bulk,unknown,unknown,,Sweden,2016-10-19,Pharyngula,Embryo,Brain,Nervous System
5799,ERR1698348,ERX1767856,ERS1417530,ERP018188,PRJEB16335,RNA seq of the zebrafish danio rerio brain post developmental exposure to 17a ethinylestradiol,E-MTAB-5173,Transcriptome Analysis,17a ethinylestradiol EE2 is a synthetic estrogen commonly used as an active substance in oral contraceptives.  It is frequently found in waste water effluent and raise concern due to its persistent nature. EE2 binds to estrogen receptors with similar affinity to oestradiol and acts as one of the most potent hormone mimics found in the environment.  Estrogen is involved in many aspects of the development of the neuroendocrine system influencing both brain structure and behavior. We and others have reported a significant effect on non reproductive behaviors in adult fish and in recent studies we found that developmental exposure to EE2 resulted in an anxiogenic phenotype as adults even post a long remediation period.  In this study we aim to study possible mechanisms behind the behavior alterations of zebrafish developmentally exposed to EE2 by sequencing the whole brain transcriptome. Zebrafish embryos were exposed to 0  2.14 and 7.34 ng/L EE2 from 1 day to 80 dpf post the exposure period a remediation period of 120 days followed before the fish were sampled. 3 male brains from the control group 0 ng/L and the 2.14 ng/L group were sampled and 3 female brains from the control group 0 ng/L and 7.34 ng/L were sampled.,ENA FIRST PUBLIC:2017 10 02|ENA LAST UPDATE:2016 10 19|ArrayExpress:E MTAB 5173,,Protocols: RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich  Germany EE2 exposure. Fish exposed to 0  2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA,IonXpressRNA 008 up 058 8,SAMEA4518351,"School of Natural Science, Technology and Environmental Studies Sodertorn University",ENA first public:2017 10 02|ENA last update:2016 10 19|External Id:SAMEA4518351|INSDC center alias:School of Natural Science  Technology and Environmental Studies Sodertorn University|INSDC center name:School of Natural Science  Technology and Environmental Studies Sodertorn University|INSDC first public:2017 10 02T17:05:16Z|INSDC last update:2016 10 19T13:53:59Z|INSDC status:public|Submitter Id:E MTAB 5173:IonXpressRNA 008 up 058 8|age:200|broker name:ArrayExpress|common name:zebrafish|organism part:brain|sample name:E MTAB 5173:IonXpressRNA 008 up 058 8|sex:male,,,,,,,,,Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol,E MTAB 5173:IonXpressRNA 008 up 058 8 s,IonXpressRNA 008 up 058 8 s,RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol,RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich  Germany EE2 exposure. Fish exposed to 0  2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA,Experimental Factor: male:sex|Experimental Factor: n1:compound,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP018188,Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol,ENA FIRST PUBLIC:2017 10 02|ENA LAST UPDATE:2018 11 16,IonXpressRNA_008_up_058_8.fastq.gz,fastq,3259710114.0,38530802.0,E MTAB 5173:IonXpressRNA 008 up 058 8,0:84.60,A:916053004;C:755694888;G:751125332;T:836836890;N:0,84,,,,916053004,755694888,751125332,836836890,0,ERX1767856,ERS1417530,ERA739176,"School of Natural Science, Technology and Environmental Studies Sodertorn University|European Nucleotide Archive","School of Natural Science, Technology and Environmental Studies Sodertorn University|European Nucleotide Archive",1,0.70995,,0.31365,,0.74781,,0.48846,,61,,B,,usable mapping rate,ion_torrent,ion_torrent,full_length,random_priming,ribozero,bulk,unknown,unknown,,Sweden,2016-10-19,Pharyngula,Embryo,Brain,Nervous System
5800,ERR1698347,ERX1767855,ERS1417529,ERP018188,PRJEB16335,RNA seq of the zebrafish danio rerio brain post developmental exposure to 17a ethinylestradiol,E-MTAB-5173,Transcriptome Analysis,17a ethinylestradiol EE2 is a synthetic estrogen commonly used as an active substance in oral contraceptives.  It is frequently found in waste water effluent and raise concern due to its persistent nature. EE2 binds to estrogen receptors with similar affinity to oestradiol and acts as one of the most potent hormone mimics found in the environment.  Estrogen is involved in many aspects of the development of the neuroendocrine system influencing both brain structure and behavior. We and others have reported a significant effect on non reproductive behaviors in adult fish and in recent studies we found that developmental exposure to EE2 resulted in an anxiogenic phenotype as adults even post a long remediation period.  In this study we aim to study possible mechanisms behind the behavior alterations of zebrafish developmentally exposed to EE2 by sequencing the whole brain transcriptome. Zebrafish embryos were exposed to 0  2.14 and 7.34 ng/L EE2 from 1 day to 80 dpf post the exposure period a remediation period of 120 days followed before the fish were sampled. 3 male brains from the control group 0 ng/L and the 2.14 ng/L group were sampled and 3 female brains from the control group 0 ng/L and 7.34 ng/L were sampled.,ENA FIRST PUBLIC:2017 10 02|ENA LAST UPDATE:2016 10 19|ArrayExpress:E MTAB 5173,,Protocols: RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich  Germany EE2 exposure. Fish exposed to 0  2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA,IonXpressRNA 007 up 058 7,SAMEA4518350,"School of Natural Science, Technology and Environmental Studies Sodertorn University",ENA first public:2017 10 02|ENA last update:2016 10 19|External Id:SAMEA4518350|INSDC center alias:School of Natural Science  Technology and Environmental Studies Sodertorn University|INSDC center name:School of Natural Science  Technology and Environmental Studies Sodertorn University|INSDC first public:2017 10 02T17:05:16Z|INSDC last update:2016 10 19T13:53:59Z|INSDC status:public|Submitter Id:E MTAB 5173:IonXpressRNA 007 up 058 7|age:200|broker name:ArrayExpress|common name:zebrafish|organism part:brain|sample name:E MTAB 5173:IonXpressRNA 007 up 058 7|sex:male,,,,,,,,,Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol,E MTAB 5173:IonXpressRNA 007 up 058 7 s,IonXpressRNA 007 up 058 7 s,RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol,RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich  Germany EE2 exposure. Fish exposed to 0  2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA,Experimental Factor: male:sex|Experimental Factor: n1:compound,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP018188,Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol,ENA FIRST PUBLIC:2017 10 02|ENA LAST UPDATE:2018 11 16,IonXpressRNA_007_up_058_7.fastq.gz,fastq,2307842164.0,28984666.0,E MTAB 5173:IonXpressRNA 007 up 058 7,0:79.62,A:634041732;C:548565089;G:545418985;T:579816358;N:0,79,,,,634041732,548565089,545418985,579816358,0,ERX1767855,ERS1417529,ERA739176,"School of Natural Science, Technology and Environmental Studies Sodertorn University|European Nucleotide Archive","School of Natural Science, Technology and Environmental Studies Sodertorn University|European Nucleotide Archive",1,0.67542,,0.2817,,0.74168,,0.47224,,37,,B,,usable mapping rate,ion_torrent,ion_torrent,full_length,random_priming,ribozero,bulk,unknown,unknown,,Sweden,2016-10-19,Pharyngula,Embryo,Brain,Nervous System
5801,ERR1698346,ERX1767854,ERS1417528,ERP018188,PRJEB16335,RNA seq of the zebrafish danio rerio brain post developmental exposure to 17a ethinylestradiol,E-MTAB-5173,Transcriptome Analysis,17a ethinylestradiol EE2 is a synthetic estrogen commonly used as an active substance in oral contraceptives.  It is frequently found in waste water effluent and raise concern due to its persistent nature. EE2 binds to estrogen receptors with similar affinity to oestradiol and acts as one of the most potent hormone mimics found in the environment.  Estrogen is involved in many aspects of the development of the neuroendocrine system influencing both brain structure and behavior. We and others have reported a significant effect on non reproductive behaviors in adult fish and in recent studies we found that developmental exposure to EE2 resulted in an anxiogenic phenotype as adults even post a long remediation period.  In this study we aim to study possible mechanisms behind the behavior alterations of zebrafish developmentally exposed to EE2 by sequencing the whole brain transcriptome. Zebrafish embryos were exposed to 0  2.14 and 7.34 ng/L EE2 from 1 day to 80 dpf post the exposure period a remediation period of 120 days followed before the fish were sampled. 3 male brains from the control group 0 ng/L and the 2.14 ng/L group were sampled and 3 female brains from the control group 0 ng/L and 7.34 ng/L were sampled.,ENA FIRST PUBLIC:2017 10 02|ENA LAST UPDATE:2016 10 19|ArrayExpress:E MTAB 5173,,Protocols: RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich  Germany EE2 exposure. Fish exposed to 0  2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA,IonXpressRNA 006 up 058 6,SAMEA4518349,"School of Natural Science, Technology and Environmental Studies Sodertorn University",ENA first public:2017 10 02|ENA last update:2016 10 19|External Id:SAMEA4518349|INSDC center alias:School of Natural Science  Technology and Environmental Studies Sodertorn University|INSDC center name:School of Natural Science  Technology and Environmental Studies Sodertorn University|INSDC first public:2017 10 02T17:05:16Z|INSDC last update:2016 10 19T13:53:59Z|INSDC status:public|Submitter Id:E MTAB 5173:IonXpressRNA 006 up 058 6|age:200|broker name:ArrayExpress|common name:zebrafish|organism part:brain|sample name:E MTAB 5173:IonXpressRNA 006 up 058 6|sex:female,,,,,,,,,Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol,E MTAB 5173:IonXpressRNA 006 up 058 6 s,IonXpressRNA 006 up 058 6 s,RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol,RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich  Germany EE2 exposure. Fish exposed to 0  2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA,Experimental Factor: female:sex|Experimental Factor: 17 ethinylestradiol:compound|Experimental Factor: 7.34:dose,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP018188,Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol,ENA FIRST PUBLIC:2017 10 02|ENA LAST UPDATE:2018 11 16,IonXpressRNA_006_up_058_6.fastq.gz,fastq,2239484857.0,27021234.0,E MTAB 5173:IonXpressRNA 006 up 058 6,0:82.88,A:637326624;C:506830056;G:503508207;T:591819970;N:0,82,,,,637326624,506830056,503508207,591819970,0,ERX1767854,ERS1417528,ERA739176,"School of Natural Science, Technology and Environmental Studies Sodertorn University|European Nucleotide Archive","School of Natural Science, Technology and Environmental Studies Sodertorn University|European Nucleotide Archive",1,0.66441,,0.31904,,0.74905,,0.47154,,122,,B,,usable mapping rate,ion_torrent,ion_torrent,full_length,random_priming,ribozero,bulk,unknown,unknown,,Sweden,2016-10-19,Pharyngula,Embryo,Brain,Nervous System
5802,ERR1698345,ERX1767853,ERS1417527,ERP018188,PRJEB16335,RNA seq of the zebrafish danio rerio brain post developmental exposure to 17a ethinylestradiol,E-MTAB-5173,Transcriptome Analysis,17a ethinylestradiol EE2 is a synthetic estrogen commonly used as an active substance in oral contraceptives.  It is frequently found in waste water effluent and raise concern due to its persistent nature. EE2 binds to estrogen receptors with similar affinity to oestradiol and acts as one of the most potent hormone mimics found in the environment.  Estrogen is involved in many aspects of the development of the neuroendocrine system influencing both brain structure and behavior. We and others have reported a significant effect on non reproductive behaviors in adult fish and in recent studies we found that developmental exposure to EE2 resulted in an anxiogenic phenotype as adults even post a long remediation period.  In this study we aim to study possible mechanisms behind the behavior alterations of zebrafish developmentally exposed to EE2 by sequencing the whole brain transcriptome. Zebrafish embryos were exposed to 0  2.14 and 7.34 ng/L EE2 from 1 day to 80 dpf post the exposure period a remediation period of 120 days followed before the fish were sampled. 3 male brains from the control group 0 ng/L and the 2.14 ng/L group were sampled and 3 female brains from the control group 0 ng/L and 7.34 ng/L were sampled.,ENA FIRST PUBLIC:2017 10 02|ENA LAST UPDATE:2016 10 19|ArrayExpress:E MTAB 5173,,Protocols: RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich  Germany EE2 exposure. Fish exposed to 0  2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA,IonXpressRNA 005 up 058 5,SAMEA4518348,"School of Natural Science, Technology and Environmental Studies Sodertorn University",ENA first public:2017 10 02|ENA last update:2016 10 19|External Id:SAMEA4518348|INSDC center alias:School of Natural Science  Technology and Environmental Studies Sodertorn University|INSDC center name:School of Natural Science  Technology and Environmental Studies Sodertorn University|INSDC first public:2017 10 02T17:05:16Z|INSDC last update:2016 10 19T13:53:59Z|INSDC status:public|Submitter Id:E MTAB 5173:IonXpressRNA 005 up 058 5|age:200|broker name:ArrayExpress|common name:zebrafish|organism part:brain|sample name:E MTAB 5173:IonXpressRNA 005 up 058 5|sex:female,,,,,,,,,Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol,E MTAB 5173:IonXpressRNA 005 up 058 5 s,IonXpressRNA 005 up 058 5 s,RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol,RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich  Germany EE2 exposure. Fish exposed to 0  2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA,Experimental Factor: female:sex|Experimental Factor: 17 ethinylestradiol:compound|Experimental Factor: 7.34:dose,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP018188,Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol,ENA FIRST PUBLIC:2017 10 02|ENA LAST UPDATE:2018 11 16,IonXpressRNA_005_up_058_5.fastq.gz,fastq,2920608487.0,39573075.0,E MTAB 5173:IonXpressRNA 005 up 058 5,0:73.80,A:814851327;C:678116994;G:691911192;T:735728974;N:0,73,,,,814851327,678116994,691911192,735728974,0,ERX1767853,ERS1417527,ERA739176,"School of Natural Science, Technology and Environmental Studies Sodertorn University|European Nucleotide Archive","School of Natural Science, Technology and Environmental Studies Sodertorn University|European Nucleotide Archive",1,0.60005,,0.25542,,0.76481,,0.4886,,12,,B,,usable mapping rate,ion_torrent,ion_torrent,full_length,random_priming,ribozero,bulk,unknown,unknown,,Sweden,2016-10-19,Pharyngula,Embryo,Brain,Nervous System
5803,ERR1698344,ERX1767852,ERS1417526,ERP018188,PRJEB16335,RNA seq of the zebrafish danio rerio brain post developmental exposure to 17a ethinylestradiol,E-MTAB-5173,Transcriptome Analysis,17a ethinylestradiol EE2 is a synthetic estrogen commonly used as an active substance in oral contraceptives.  It is frequently found in waste water effluent and raise concern due to its persistent nature. EE2 binds to estrogen receptors with similar affinity to oestradiol and acts as one of the most potent hormone mimics found in the environment.  Estrogen is involved in many aspects of the development of the neuroendocrine system influencing both brain structure and behavior. We and others have reported a significant effect on non reproductive behaviors in adult fish and in recent studies we found that developmental exposure to EE2 resulted in an anxiogenic phenotype as adults even post a long remediation period.  In this study we aim to study possible mechanisms behind the behavior alterations of zebrafish developmentally exposed to EE2 by sequencing the whole brain transcriptome. Zebrafish embryos were exposed to 0  2.14 and 7.34 ng/L EE2 from 1 day to 80 dpf post the exposure period a remediation period of 120 days followed before the fish were sampled. 3 male brains from the control group 0 ng/L and the 2.14 ng/L group were sampled and 3 female brains from the control group 0 ng/L and 7.34 ng/L were sampled.,ENA FIRST PUBLIC:2017 10 02|ENA LAST UPDATE:2016 10 19|ArrayExpress:E MTAB 5173,,Protocols: RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich  Germany EE2 exposure. Fish exposed to 0  2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA,IonXpressRNA 004 up 058 4,SAMEA4518347,"School of Natural Science, Technology and Environmental Studies Sodertorn University",ENA first public:2017 10 02|ENA last update:2016 10 19|External Id:SAMEA4518347|INSDC center alias:School of Natural Science  Technology and Environmental Studies Sodertorn University|INSDC center name:School of Natural Science  Technology and Environmental Studies Sodertorn University|INSDC first public:2017 10 02T17:05:16Z|INSDC last update:2016 10 19T13:53:59Z|INSDC status:public|Submitter Id:E MTAB 5173:IonXpressRNA 004 up 058 4|age:200|broker name:ArrayExpress|common name:zebrafish|organism part:brain|sample name:E MTAB 5173:IonXpressRNA 004 up 058 4|sex:female,,,,,,,,,Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol,E MTAB 5173:IonXpressRNA 004 up 058 4 s,IonXpressRNA 004 up 058 4 s,RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol,RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich  Germany EE2 exposure. Fish exposed to 0  2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA,Experimental Factor: female:sex|Experimental Factor: 17 ethinylestradiol:compound|Experimental Factor: 7.34:dose,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP018188,Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol,ENA FIRST PUBLIC:2017 10 02|ENA LAST UPDATE:2018 11 16,IonXpressRNA_004_up_058_4.fastq.gz,fastq,2989727396.0,37953454.0,E MTAB 5173:IonXpressRNA 004 up 058 4,0:78.77,A:802963810;C:722434772;G:742850530;T:721478284;N:0,78,,,,802963810,722434772,742850530,721478284,0,ERX1767852,ERS1417526,ERA739176,"School of Natural Science, Technology and Environmental Studies Sodertorn University|European Nucleotide Archive","School of Natural Science, Technology and Environmental Studies Sodertorn University|European Nucleotide Archive",1,0.76402,,0.32503,,0.74241,,0.4815,,128,,B,,usable mapping rate,ion_torrent,ion_torrent,full_length,random_priming,ribozero,bulk,unknown,unknown,,Sweden,2016-10-19,Pharyngula,Embryo,Brain,Nervous System
5804,ERR1698343,ERX1767851,ERS1417525,ERP018188,PRJEB16335,RNA seq of the zebrafish danio rerio brain post developmental exposure to 17a ethinylestradiol,E-MTAB-5173,Transcriptome Analysis,17a ethinylestradiol EE2 is a synthetic estrogen commonly used as an active substance in oral contraceptives.  It is frequently found in waste water effluent and raise concern due to its persistent nature. EE2 binds to estrogen receptors with similar affinity to oestradiol and acts as one of the most potent hormone mimics found in the environment.  Estrogen is involved in many aspects of the development of the neuroendocrine system influencing both brain structure and behavior. We and others have reported a significant effect on non reproductive behaviors in adult fish and in recent studies we found that developmental exposure to EE2 resulted in an anxiogenic phenotype as adults even post a long remediation period.  In this study we aim to study possible mechanisms behind the behavior alterations of zebrafish developmentally exposed to EE2 by sequencing the whole brain transcriptome. Zebrafish embryos were exposed to 0  2.14 and 7.34 ng/L EE2 from 1 day to 80 dpf post the exposure period a remediation period of 120 days followed before the fish were sampled. 3 male brains from the control group 0 ng/L and the 2.14 ng/L group were sampled and 3 female brains from the control group 0 ng/L and 7.34 ng/L were sampled.,ENA FIRST PUBLIC:2017 10 02|ENA LAST UPDATE:2016 10 19|ArrayExpress:E MTAB 5173,,Protocols: RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich  Germany EE2 exposure. Fish exposed to 0  2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA,IonXpressRNA 003 up 058 3,SAMEA4518346,"School of Natural Science, Technology and Environmental Studies Sodertorn University",ENA first public:2017 10 02|ENA last update:2016 10 19|External Id:SAMEA4518346|INSDC center alias:School of Natural Science  Technology and Environmental Studies Sodertorn University|INSDC center name:School of Natural Science  Technology and Environmental Studies Sodertorn University|INSDC first public:2017 10 02T17:05:16Z|INSDC last update:2016 10 19T13:53:59Z|INSDC status:public|Submitter Id:E MTAB 5173:IonXpressRNA 003 up 058 3|age:200|broker name:ArrayExpress|common name:zebrafish|organism part:brain|sample name:E MTAB 5173:IonXpressRNA 003 up 058 3|sex:female,,,,,,,,,Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol,E MTAB 5173:IonXpressRNA 003 up 058 3 s,IonXpressRNA 003 up 058 3 s,RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol,RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich  Germany EE2 exposure. Fish exposed to 0  2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA,Experimental Factor: female:sex|Experimental Factor: n1:compound,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP018188,Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol,ENA FIRST PUBLIC:2017 10 02|ENA LAST UPDATE:2018 11 16,IonXpressRNA_003_up_058_3.fastq.gz,fastq,4068383115.0,41996847.0,E MTAB 5173:IonXpressRNA 003 up 058 3,0:96.87,A:1133167706;C:944306379;G:948626944;T:1042282086;N:0,96,,,,1133167706,944306379,948626944,1042282086,0,ERX1767851,ERS1417525,ERA739176,"School of Natural Science, Technology and Environmental Studies Sodertorn University|European Nucleotide Archive","School of Natural Science, Technology and Environmental Studies Sodertorn University|European Nucleotide Archive",1,0.54804,,0.22334,,0.76353,,0.49163,,93,,B,,usable mapping rate,ion_torrent,ion_torrent,full_length,random_priming,ribozero,bulk,unknown,unknown,,Sweden,2016-10-19,Pharyngula,Embryo,Brain,Nervous System
5805,ERR1698342,ERX1767850,ERS1417524,ERP018188,PRJEB16335,RNA seq of the zebrafish danio rerio brain post developmental exposure to 17a ethinylestradiol,E-MTAB-5173,Transcriptome Analysis,17a ethinylestradiol EE2 is a synthetic estrogen commonly used as an active substance in oral contraceptives.  It is frequently found in waste water effluent and raise concern due to its persistent nature. EE2 binds to estrogen receptors with similar affinity to oestradiol and acts as one of the most potent hormone mimics found in the environment.  Estrogen is involved in many aspects of the development of the neuroendocrine system influencing both brain structure and behavior. We and others have reported a significant effect on non reproductive behaviors in adult fish and in recent studies we found that developmental exposure to EE2 resulted in an anxiogenic phenotype as adults even post a long remediation period.  In this study we aim to study possible mechanisms behind the behavior alterations of zebrafish developmentally exposed to EE2 by sequencing the whole brain transcriptome. Zebrafish embryos were exposed to 0  2.14 and 7.34 ng/L EE2 from 1 day to 80 dpf post the exposure period a remediation period of 120 days followed before the fish were sampled. 3 male brains from the control group 0 ng/L and the 2.14 ng/L group were sampled and 3 female brains from the control group 0 ng/L and 7.34 ng/L were sampled.,ENA FIRST PUBLIC:2017 10 02|ENA LAST UPDATE:2016 10 19|ArrayExpress:E MTAB 5173,,Protocols: RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich  Germany EE2 exposure. Fish exposed to 0  2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA,IonXpressRNA 002 up 058 2,SAMEA4518345,"School of Natural Science, Technology and Environmental Studies Sodertorn University",ENA first public:2017 10 02|ENA last update:2016 10 19|External Id:SAMEA4518345|INSDC center alias:School of Natural Science  Technology and Environmental Studies Sodertorn University|INSDC center name:School of Natural Science  Technology and Environmental Studies Sodertorn University|INSDC first public:2017 10 02T17:05:16Z|INSDC last update:2016 10 19T13:53:59Z|INSDC status:public|Submitter Id:E MTAB 5173:IonXpressRNA 002 up 058 2|age:200|broker name:ArrayExpress|common name:zebrafish|organism part:brain|sample name:E MTAB 5173:IonXpressRNA 002 up 058 2|sex:female,,,,,,,,,Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol,E MTAB 5173:IonXpressRNA 002 up 058 2 s,IonXpressRNA 002 up 058 2 s,RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol,RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich  Germany EE2 exposure. Fish exposed to 0  2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA,Experimental Factor: female:sex|Experimental Factor: n1:compound,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP018188,Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol,ENA FIRST PUBLIC:2017 10 02|ENA LAST UPDATE:2018 11 16,IonXpressRNA_002_up_058_2.fastq.gz,fastq,2679963893.0,33552723.0,E MTAB 5173:IonXpressRNA 002 up 058 2,0:79.87,A:709092431;C:635329399;G:670478210;T:665063853;N:0,79,,,,709092431,635329399,670478210,665063853,0,ERX1767850,ERS1417524,ERA739176,"School of Natural Science, Technology and Environmental Studies Sodertorn University|European Nucleotide Archive","School of Natural Science, Technology and Environmental Studies Sodertorn University|European Nucleotide Archive",1,0.43283,,0.18649,,0.81178,,0.52885,,116,,B,,usable mapping rate,ion_torrent,ion_torrent,full_length,random_priming,ribozero,bulk,unknown,unknown,,Sweden,2016-10-19,Pharyngula,Embryo,Brain,Nervous System
5806,ERR1698341,ERX1767849,ERS1417523,ERP018188,PRJEB16335,RNA seq of the zebrafish danio rerio brain post developmental exposure to 17a ethinylestradiol,E-MTAB-5173,Transcriptome Analysis,17a ethinylestradiol EE2 is a synthetic estrogen commonly used as an active substance in oral contraceptives.  It is frequently found in waste water effluent and raise concern due to its persistent nature. EE2 binds to estrogen receptors with similar affinity to oestradiol and acts as one of the most potent hormone mimics found in the environment.  Estrogen is involved in many aspects of the development of the neuroendocrine system influencing both brain structure and behavior. We and others have reported a significant effect on non reproductive behaviors in adult fish and in recent studies we found that developmental exposure to EE2 resulted in an anxiogenic phenotype as adults even post a long remediation period.  In this study we aim to study possible mechanisms behind the behavior alterations of zebrafish developmentally exposed to EE2 by sequencing the whole brain transcriptome. Zebrafish embryos were exposed to 0  2.14 and 7.34 ng/L EE2 from 1 day to 80 dpf post the exposure period a remediation period of 120 days followed before the fish were sampled. 3 male brains from the control group 0 ng/L and the 2.14 ng/L group were sampled and 3 female brains from the control group 0 ng/L and 7.34 ng/L were sampled.,ENA FIRST PUBLIC:2017 10 02|ENA LAST UPDATE:2016 10 19|ArrayExpress:E MTAB 5173,,Protocols: RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich  Germany EE2 exposure. Fish exposed to 0  2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA,IonXpressRNA 001 up 058 1,SAMEA4518344,"School of Natural Science, Technology and Environmental Studies Sodertorn University",ENA first public:2017 10 02|ENA last update:2016 10 19|External Id:SAMEA4518344|INSDC center alias:School of Natural Science  Technology and Environmental Studies Sodertorn University|INSDC center name:School of Natural Science  Technology and Environmental Studies Sodertorn University|INSDC first public:2017 10 02T17:05:16Z|INSDC last update:2016 10 19T13:53:59Z|INSDC status:public|Submitter Id:E MTAB 5173:IonXpressRNA 001 up 058 1|age:200|broker name:ArrayExpress|common name:zebrafish|organism part:brain|sample name:E MTAB 5173:IonXpressRNA 001 up 058 1|sex:female,,,,,,,,,Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol,E MTAB 5173:IonXpressRNA 001 up 058 1 s,IonXpressRNA 001 up 058 1 s,RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol,RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich  Germany EE2 exposure. Fish exposed to 0  2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA,Experimental Factor: female:sex|Experimental Factor: n1:compound,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP018188,Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol,ENA FIRST PUBLIC:2017 10 02|ENA LAST UPDATE:2018 11 16,IonXpressRNA_001_up_058_1.fastq.gz,fastq,3358902499.0,39857024.0,E MTAB 5173:IonXpressRNA 001 up 058 1,0:84.27,A:933405205;C:784111716;G:780404241;T:860981337;N:0,84,,,,933405205,784111716,780404241,860981337,0,ERX1767849,ERS1417523,ERA739176,"School of Natural Science, Technology and Environmental Studies Sodertorn University|European Nucleotide Archive","School of Natural Science, Technology and Environmental Studies Sodertorn University|European Nucleotide Archive",1,0.71789,,0.33159,,0.76619,,0.514,,56,,B,,usable mapping rate,ion_torrent,ion_torrent,full_length,random_priming,ribozero,bulk,unknown,unknown,,Sweden,2016-10-19,Pharyngula,Embryo,Brain,Nervous System
11240,ERR10782553,ERX10233130,ERS14439195,ERP144048,PRJEB58983,RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling,E-MTAB-12503,Transcriptome Analysis,Defects in blood development are a major contributor to complex congenital anomalies. Thrombocytopenia Absent Radius TAR Syndrome is a rare congenital disease presenting with reduced blood platelets megakaryocytic thrombocytopenia and forelimb anomalies  concurrent with variable heart and kidney defects caused by hypomorphic RBM8A/Y14 gene function. RBM8A encodes a component of the ubiquitous exon junction complex involved in mRNA splicing  transport  and nonsense mediated decay. How perturbing a general mRNA processing factor causes the distinct phenotypes of TAR Syndrome remains unknown. Here  we connect zebrafish rbm8a perturbation to early hematopoiesis defects via attenuated planar cell polarity PCP signaling involved in controlling developmental cell arrangements. Combining different genetic means to reduce rbm8a function  we find a significant reduction of cd41 positive thrombocytes in hypomorphic rbm8a larvae. Transcriptomics analysis documents rbm8a mutant zebrafish embryos already post gastrulation accumulate mRNAs with erroneously included introns  a hallmark of defective nonsense mediated decay. Affected mRNAs include transcripts encoding components of the non canonical Wnt pathway involved in PCP signaling  and rbm8a mutant embryos show hallmarks of Wnt/PCP dependent  early convergent extension defects. We establish that reduced rbm8a function synergizes with perturbations in Wnt/PCP pathway genes including wnt5b  wnt11f2  fzd7a  and vangl2. Following axis formation  rbm8a perturbation impairs the migration and architecture of the lateral plate mesoderm LPM  that forms the hematopoietic  cardiovascular  kidney  and forelimb skeleton progenitors. Subsequently  rbm8a perturbation impairs expression of early hematopoietic/endothelial genes including runx1a  kdrl  sox7  and the megakaryocyte regulator gfi1aa. Lastly  we document similar hematopoietic defects upon loss of vangl2. Together  our data link reduced rbm8a function to LPM migration and hematopoietic defects via attenuated Wnt/PCP signaling. Our findings establish a developmental framework that connects the complex TAR Syndrome phenotypes to a potential LPM origin.,ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31,,Protocols: Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined  pooled embryos by Trizol LS extraction as per manufacturer’s guidelines Invitrogen  with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.,Sample 2,E MTAB 12503:Sample 2,,strain:mixed AB and Tubingen|ENA FIRST PUBLIC:2023 03 31|individual:20170530.A 2|organism:Danio rerio|organism:Danio rerio|ENA LAST UPDATE:2023 03 31|scientific name:Danio rerio|common name:zebrafish|organism part:embryo|age:24|developmental stage:pharyngula prim 5|genotype:wild type genotype|ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling,E MTAB 12503:Sample 2 p,Sample 2 p,RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling,Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined  pooled embryos by Trizol LS extraction as per manufacturer’s guidelines Invitrogen  with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.,Experimental Factor: developmental stage:pharyngula prim 5|Experimental Factor: genotype:wild type genotype,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP144048,Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling,ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31,20170530.A-2_R1.fastq.gz 20170530.A-2_R2.fastq.gz,fastq fastq,16267571562.0,53866131.0,E MTAB 12503:20170530.A 2 R,0:151 1:151,A:4395815325;C:3765428574;G:3780844712;T:4310729283;N:14753668,151,151,,,4395815325,3765428574,3780844712,4310729283,14753668,ERX10233130,ERS14439195,ERA20162442,University of Zurich|European Nucleotide Archive,University of Zurich|European Nucleotide Archive,2,0.86977,0.8727,0.28497,0.28427,0.70763,0.72301,0.47478,0.47986,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,sc,unknown,unknown,,Switzerland,2023-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
11241,ERR10782552,ERX10233129,ERS14439194,ERP144048,PRJEB58983,RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling,E-MTAB-12503,Transcriptome Analysis,Defects in blood development are a major contributor to complex congenital anomalies. Thrombocytopenia Absent Radius TAR Syndrome is a rare congenital disease presenting with reduced blood platelets megakaryocytic thrombocytopenia and forelimb anomalies  concurrent with variable heart and kidney defects caused by hypomorphic RBM8A/Y14 gene function. RBM8A encodes a component of the ubiquitous exon junction complex involved in mRNA splicing  transport  and nonsense mediated decay. How perturbing a general mRNA processing factor causes the distinct phenotypes of TAR Syndrome remains unknown. Here  we connect zebrafish rbm8a perturbation to early hematopoiesis defects via attenuated planar cell polarity PCP signaling involved in controlling developmental cell arrangements. Combining different genetic means to reduce rbm8a function  we find a significant reduction of cd41 positive thrombocytes in hypomorphic rbm8a larvae. Transcriptomics analysis documents rbm8a mutant zebrafish embryos already post gastrulation accumulate mRNAs with erroneously included introns  a hallmark of defective nonsense mediated decay. Affected mRNAs include transcripts encoding components of the non canonical Wnt pathway involved in PCP signaling  and rbm8a mutant embryos show hallmarks of Wnt/PCP dependent  early convergent extension defects. We establish that reduced rbm8a function synergizes with perturbations in Wnt/PCP pathway genes including wnt5b  wnt11f2  fzd7a  and vangl2. Following axis formation  rbm8a perturbation impairs the migration and architecture of the lateral plate mesoderm LPM  that forms the hematopoietic  cardiovascular  kidney  and forelimb skeleton progenitors. Subsequently  rbm8a perturbation impairs expression of early hematopoietic/endothelial genes including runx1a  kdrl  sox7  and the megakaryocyte regulator gfi1aa. Lastly  we document similar hematopoietic defects upon loss of vangl2. Together  our data link reduced rbm8a function to LPM migration and hematopoietic defects via attenuated Wnt/PCP signaling. Our findings establish a developmental framework that connects the complex TAR Syndrome phenotypes to a potential LPM origin.,ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31,,Protocols: Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined  pooled embryos by Trizol LS extraction as per manufacturer’s guidelines Invitrogen  with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.,Sample 1,E MTAB 12503:Sample 1,,strain:mixed AB and Tubingen|ENA FIRST PUBLIC:2023 03 31|individual:20170530.A 1|organism:Danio rerio|organism:Danio rerio|ENA LAST UPDATE:2023 03 31|scientific name:Danio rerio|common name:zebrafish|organism part:embryo|age:24|developmental stage:pharyngula prim 5|genotype:wild type genotype|ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling,E MTAB 12503:Sample 1 p,Sample 1 p,RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling,Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined  pooled embryos by Trizol LS extraction as per manufacturer’s guidelines Invitrogen  with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.,Experimental Factor: developmental stage:pharyngula prim 5|Experimental Factor: genotype:wild type genotype,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP144048,Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling,ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31,20170530.A-1_R1.fastq.gz 20170530.A-1_R2.fastq.gz,fastq fastq,15446599662.0,51147681.0,E MTAB 12503:20170530.A 1 R,0:151 1:151,A:4289931639;C:3451135010;G:3474244788;T:4217248893;N:14039332,151,151,,,4289931639,3451135010,3474244788,4217248893,14039332,ERX10233129,ERS14439194,ERA20162442,University of Zurich|European Nucleotide Archive,University of Zurich|European Nucleotide Archive,2,0.90114,0.90507,0.32128,0.32127,0.70232,0.71956,0.47336,0.47528,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,sc,unknown,unknown,,Switzerland,2023-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
11243,ERR10782550,ERX10233127,ERS14439192,ERP144048,PRJEB58983,RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling,E-MTAB-12503,Transcriptome Analysis,Defects in blood development are a major contributor to complex congenital anomalies. Thrombocytopenia Absent Radius TAR Syndrome is a rare congenital disease presenting with reduced blood platelets megakaryocytic thrombocytopenia and forelimb anomalies  concurrent with variable heart and kidney defects caused by hypomorphic RBM8A/Y14 gene function. RBM8A encodes a component of the ubiquitous exon junction complex involved in mRNA splicing  transport  and nonsense mediated decay. How perturbing a general mRNA processing factor causes the distinct phenotypes of TAR Syndrome remains unknown. Here  we connect zebrafish rbm8a perturbation to early hematopoiesis defects via attenuated planar cell polarity PCP signaling involved in controlling developmental cell arrangements. Combining different genetic means to reduce rbm8a function  we find a significant reduction of cd41 positive thrombocytes in hypomorphic rbm8a larvae. Transcriptomics analysis documents rbm8a mutant zebrafish embryos already post gastrulation accumulate mRNAs with erroneously included introns  a hallmark of defective nonsense mediated decay. Affected mRNAs include transcripts encoding components of the non canonical Wnt pathway involved in PCP signaling  and rbm8a mutant embryos show hallmarks of Wnt/PCP dependent  early convergent extension defects. We establish that reduced rbm8a function synergizes with perturbations in Wnt/PCP pathway genes including wnt5b  wnt11f2  fzd7a  and vangl2. Following axis formation  rbm8a perturbation impairs the migration and architecture of the lateral plate mesoderm LPM  that forms the hematopoietic  cardiovascular  kidney  and forelimb skeleton progenitors. Subsequently  rbm8a perturbation impairs expression of early hematopoietic/endothelial genes including runx1a  kdrl  sox7  and the megakaryocyte regulator gfi1aa. Lastly  we document similar hematopoietic defects upon loss of vangl2. Together  our data link reduced rbm8a function to LPM migration and hematopoietic defects via attenuated Wnt/PCP signaling. Our findings establish a developmental framework that connects the complex TAR Syndrome phenotypes to a potential LPM origin.,ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31,,Protocols: Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined  pooled embryos by Trizol LS extraction as per manufacturer’s guidelines Invitrogen  with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.,Sample 4,E MTAB 12503:Sample 4,,strain:mixed AB and Tubingen|ENA FIRST PUBLIC:2023 03 31|individual:20170530.A 4|organism:Danio rerio|organism:Danio rerio|ENA LAST UPDATE:2023 03 31|scientific name:Danio rerio|common name:zebrafish|organism part:embryo|age:24|developmental stage:pharyngula prim 5|genotype:rbm8a d5/d5|ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling,E MTAB 12503:Sample 4 p,Sample 4 p,RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling,Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined  pooled embryos by Trizol LS extraction as per manufacturer’s guidelines Invitrogen  with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.,Experimental Factor: developmental stage:pharyngula prim 5|Experimental Factor: genotype:rbm8a d5/d5,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP144048,Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling,ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31,20170530.A-4_R1.fastq.gz 20170530.A-4_R2.fastq.gz,fastq fastq,15697575554.0,51978727.0,E MTAB 12503:20170530.A 4 R,0:151 1:151,A:4256444510;C:3622485921;G:3650190489;T:4154211501;N:14243133,151,151,,,4256444510,3622485921,3650190489,4154211501,14243133,ERX10233127,ERS14439192,ERA20162442,University of Zurich|European Nucleotide Archive,University of Zurich|European Nucleotide Archive,2,0.87714,0.88071,0.29319,0.29235,0.69844,0.7164,0.47594,0.47385,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,sc,unknown,unknown,,Switzerland,2023-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
11244,ERR10782549,ERX10233126,ERS14439191,ERP144048,PRJEB58983,RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling,E-MTAB-12503,Transcriptome Analysis,Defects in blood development are a major contributor to complex congenital anomalies. Thrombocytopenia Absent Radius TAR Syndrome is a rare congenital disease presenting with reduced blood platelets megakaryocytic thrombocytopenia and forelimb anomalies  concurrent with variable heart and kidney defects caused by hypomorphic RBM8A/Y14 gene function. RBM8A encodes a component of the ubiquitous exon junction complex involved in mRNA splicing  transport  and nonsense mediated decay. How perturbing a general mRNA processing factor causes the distinct phenotypes of TAR Syndrome remains unknown. Here  we connect zebrafish rbm8a perturbation to early hematopoiesis defects via attenuated planar cell polarity PCP signaling involved in controlling developmental cell arrangements. Combining different genetic means to reduce rbm8a function  we find a significant reduction of cd41 positive thrombocytes in hypomorphic rbm8a larvae. Transcriptomics analysis documents rbm8a mutant zebrafish embryos already post gastrulation accumulate mRNAs with erroneously included introns  a hallmark of defective nonsense mediated decay. Affected mRNAs include transcripts encoding components of the non canonical Wnt pathway involved in PCP signaling  and rbm8a mutant embryos show hallmarks of Wnt/PCP dependent  early convergent extension defects. We establish that reduced rbm8a function synergizes with perturbations in Wnt/PCP pathway genes including wnt5b  wnt11f2  fzd7a  and vangl2. Following axis formation  rbm8a perturbation impairs the migration and architecture of the lateral plate mesoderm LPM  that forms the hematopoietic  cardiovascular  kidney  and forelimb skeleton progenitors. Subsequently  rbm8a perturbation impairs expression of early hematopoietic/endothelial genes including runx1a  kdrl  sox7  and the megakaryocyte regulator gfi1aa. Lastly  we document similar hematopoietic defects upon loss of vangl2. Together  our data link reduced rbm8a function to LPM migration and hematopoietic defects via attenuated Wnt/PCP signaling. Our findings establish a developmental framework that connects the complex TAR Syndrome phenotypes to a potential LPM origin.,ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31,,Protocols: Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined  pooled embryos by Trizol LS extraction as per manufacturer’s guidelines Invitrogen  with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.,Sample 3,E MTAB 12503:Sample 3,,strain:mixed AB and Tubingen|ENA FIRST PUBLIC:2023 03 31|individual:20170530.A 3|organism:Danio rerio|organism:Danio rerio|ENA LAST UPDATE:2023 03 31|scientific name:Danio rerio|common name:zebrafish|organism part:embryo|age:24|developmental stage:pharyngula prim 5|genotype:rbm8a d5/d5|ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling,E MTAB 12503:Sample 3 p,Sample 3 p,RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling,Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined  pooled embryos by Trizol LS extraction as per manufacturer’s guidelines Invitrogen  with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.,Experimental Factor: developmental stage:pharyngula prim 5|Experimental Factor: genotype:rbm8a d5/d5,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP144048,Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling,ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31,20170530.A-3_R1.fastq.gz 20170530.A-3_R2.fastq.gz,fastq fastq,13839085674.0,45824787.0,E MTAB 12503:20170530.A 3 R,0:151 1:151,A:3812423011;C:3120168590;G:3163957945;T:3729983766;N:12552362,151,151,,,3812423011,3120168590,3163957945,3729983766,12552362,ERX10233126,ERS14439191,ERA20162442,University of Zurich|European Nucleotide Archive,University of Zurich|European Nucleotide Archive,2,0.88987,0.74432,0.33651,0.27875,0.69229,0.72934,0.46981,0.46116,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,sc,unknown,unknown,,Switzerland,2023-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
19098,ERR13822110,ERX13224862,ERS21098697,ERP164534,PRJEB80557,RNAseq of Danio Rerio Photoreceptors  Amacrine  and Horizontal cells  collected 38  48  and 58 hpf,e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed,Other,This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs  during the retinal lamination. We dissected retinae from three different developmental stages  corresponding to different stages in HCs lamination process  and separated HCs  PRs and HCs  based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed  converted to cDNA sequenced using the SMART SEQ2 protocol.,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,,retinal neurons,38PR2 S2 R1 001.fastq.gz,38 PR2,,organism:Danio rerio|collection date:2021 11 30|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:38 hpf type:retina|geographic location country and/or sea:Portugal,,,,,,,,,Raw reads: 38 PR2,webin reads 38 PR2,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,ERP164534,Raw reads: 38 PR2,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,38PR2_S2_R1_001.fastq.gz,fastq,3463281109.0,34821985.0,webin reads 38 PR2,0:99.46,A:969862466;C:733798241;G:755135957;T:1004440555;N:43890,99,,,,969862466,733798241,755135957,1004440555,43890,ERX13224862,ERS21098697,ERA30879238,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,Belgium,2025-01-01,Pharyngula,Embryo,Eye,Sensory System
19099,ERR13822784,ERX13225536,ERS21098706,ERP164534,PRJEB80557,RNAseq of Danio Rerio Photoreceptors  Amacrine  and Horizontal cells  collected 38  48  and 58 hpf,e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed,Other,This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs  during the retinal lamination. We dissected retinae from three different developmental stages  corresponding to different stages in HCs lamination process  and separated HCs  PRs and HCs  based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed  converted to cDNA sequenced using the SMART SEQ2 protocol.,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,,retinal neurons,38HC3 S11 R1 001.fastq.gz,38 HC3,,organism:Danio rerio|collection date:2021 12 07|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:38 hpf type:retina|geographic location country and/or sea:Portugal,,,,,,,,,Raw reads: 38 HC3,webin reads 38 HC3,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,ERP164534,Raw reads: 38 HC3,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,38HC3_S11_R1_001.fastq.gz,fastq,4360921873.0,44107486.0,webin reads 38 HC3,0:98.87,A:1222778761;C:918257887;G:948838973;T:1270939370;N:106882,98,,,,1222778761,918257887,948838973,1270939370,106882,ERX13225536,ERS21098706,ERA30879613,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,Belgium,2025-01-01,Pharyngula,Embryo,Eye,Sensory System
19103,ERR13822197,ERX13224949,ERS21098704,ERP164534,PRJEB80557,RNAseq of Danio Rerio Photoreceptors  Amacrine  and Horizontal cells  collected 38  48  and 58 hpf,e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed,Other,This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs  during the retinal lamination. We dissected retinae from three different developmental stages  corresponding to different stages in HCs lamination process  and separated HCs  PRs and HCs  based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed  converted to cDNA sequenced using the SMART SEQ2 protocol.,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,,retinal neurons,38HC1 S9 R1 001.fastq.gz,SAMEA116100624,GIMM,ENA first public:2024 01 01|INSDC center name:GIMM|INSDC status:public|Submitter Id:38 HC1|collected by:Jaakko Lehtimaki|collection date:2021 11 30|common name:zebrafish|dev stage:38 hpf location country and/or sea:Portugal|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|sample name:38 HC1|scientific name:Danio rerio|tissue type:retina,,,,,,,,,Raw reads: 38 HC1,webin reads 38 HC1,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,ERP164534,Raw reads: 38 HC1,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,38HC1_S9_R1_001.fastq.gz,fastq,3784641498.0,38331162.0,webin reads 38 HC1,0:98.74,A:1064199311;C:791310791;G:818910597;T:1110118632;N:102167,98,,,,1064199311,791310791,818910597,1110118632,102167,ERX13224949,ERS21098704,ERA30879548,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,Belgium,2024-01-01,Pharyngula,Embryo,Eye,Sensory System
19106,ERR13822131,ERX13224883,ERS21098700,ERP164534,PRJEB80557,RNAseq of Danio Rerio Photoreceptors  Amacrine  and Horizontal cells  collected 38  48  and 58 hpf,e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed,Other,This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs  during the retinal lamination. We dissected retinae from three different developmental stages  corresponding to different stages in HCs lamination process  and separated HCs  PRs and HCs  based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed  converted to cDNA sequenced using the SMART SEQ2 protocol.,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,,retinal neurons,38AC1 S5 R1 001.fastq.gz,SAMEA116100620,GIMM,ENA first public:2024 01 01|INSDC center name:GIMM|INSDC status:public|Submitter Id:38 AC1|collected by:Jaakko Lehtimaki|collection date:2021 11 30|common name:zebrafish|dev stage:38 hpf location country and/or sea:Portugal|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|sample name:38 AC1|scientific name:Danio rerio|tissue type:retina,,,,,,,,,Raw reads: 38 AC1,webin reads 38 AC1,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,ERP164534,Raw reads: 38 AC1,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,38AC1_S5_R1_001.fastq.gz,fastq,3836921113.0,38702139.0,webin reads 38 AC1,0:99.14,A:1066720805;C:818958589;G:843762182;T:1107403844;N:75693,99,,,,1066720805,818958589,843762182,1107403844,75693,ERX13224883,ERS21098700,ERA30879356,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,Belgium,2024-01-01,Pharyngula,Embryo,Eye,Sensory System
19107,ERR13822143,ERX13224895,ERS21098702,ERP164534,PRJEB80557,RNAseq of Danio Rerio Photoreceptors  Amacrine  and Horizontal cells  collected 38  48  and 58 hpf,e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed,Other,This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs  during the retinal lamination. We dissected retinae from three different developmental stages  corresponding to different stages in HCs lamination process  and separated HCs  PRs and HCs  based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed  converted to cDNA sequenced using the SMART SEQ2 protocol.,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,,retinal neurons,38AC3 S7 R1 001.fastq.gz,38 AC3,,organism:Danio rerio|collection date:2021 12 07|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:38 hpf type:retina|geographic location country and/or sea:Portugal,,,,,,,,,Raw reads: 38 AC3,webin reads 38 AC3,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,ERP164534,Raw reads: 38 AC3,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,38AC3_S7_R1_001.fastq.gz,fastq,3452707377.0,34902410.0,webin reads 38 AC3,0:98.92,A:970868997;C:726795179;G:750560378;T:1004408693;N:74130,98,,,,970868997,726795179,750560378,1004408693,74130,ERX13224895,ERS21098702,ERA30879451,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,Belgium,2025-01-01,Pharyngula,Embryo,Eye,Sensory System
19109,ERR13822153,ERX13224905,ERS21098703,ERP164534,PRJEB80557,RNAseq of Danio Rerio Photoreceptors  Amacrine  and Horizontal cells  collected 38  48  and 58 hpf,e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed,Other,This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs  during the retinal lamination. We dissected retinae from three different developmental stages  corresponding to different stages in HCs lamination process  and separated HCs  PRs and HCs  based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed  converted to cDNA sequenced using the SMART SEQ2 protocol.,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,,retinal neurons,38AC4 S8 R1 001.fastq.gz,38 AC4,,organism:Danio rerio|collection date:2021 12 07|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:38 hpf type:retina|geographic location country and/or sea:Portugal,,,,,,,,,Raw reads: 38 AC4,webin reads 38 AC4,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,ERP164534,Raw reads: 38 AC4,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,38AC4_S8_R1_001.fastq.gz,fastq,4130629624.0,41794865.0,webin reads 38 AC4,0:98.83,A:1156746387;C:877063962;G:905379690;T:1191264308;N:175277,98,,,,1156746387,877063962,905379690,1191264308,175277,ERX13224905,ERS21098703,ERA30879532,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,Belgium,2025-01-01,Pharyngula,Embryo,Eye,Sensory System
19110,ERR13822201,ERX13224953,ERS21098705,ERP164534,PRJEB80557,RNAseq of Danio Rerio Photoreceptors  Amacrine  and Horizontal cells  collected 38  48  and 58 hpf,e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed,Other,This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs  during the retinal lamination. We dissected retinae from three different developmental stages  corresponding to different stages in HCs lamination process  and separated HCs  PRs and HCs  based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed  converted to cDNA sequenced using the SMART SEQ2 protocol.,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,,retinal neurons,38HC2 S10 R1 001.fastq.gz,38 HC2,,organism:Danio rerio|collection date:2021 11 30|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:38 hpf type:retina|geographic location country and/or sea:Portugal,,,,,,,,,Raw reads: 38 HC2,webin reads 38 HC2,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,ERP164534,Raw reads: 38 HC2,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,38HC2_S10_R1_001.fastq.gz,fastq,4221340137.0,42584743.0,webin reads 38 HC2,0:99.13,A:1195817135;C:879958039;G:908085464;T:1237394738;N:84761,99,,,,1195817135,879958039,908085464,1237394738,84761,ERX13224953,ERS21098705,ERA30879582,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,Belgium,2025-01-01,Pharyngula,Embryo,Eye,Sensory System
19111,ERR13822114,ERX13224866,ERS21098698,ERP164534,PRJEB80557,RNAseq of Danio Rerio Photoreceptors  Amacrine  and Horizontal cells  collected 38  48  and 58 hpf,e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed,Other,This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs  during the retinal lamination. We dissected retinae from three different developmental stages  corresponding to different stages in HCs lamination process  and separated HCs  PRs and HCs  based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed  converted to cDNA sequenced using the SMART SEQ2 protocol.,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,,retinal neurons,38PR3 S3 R1 001.fastq.gz,SAMEA116100618,GIMM,ENA first public:2024 01 01|INSDC center name:GIMM|INSDC status:public|Submitter Id:38 PR3|collected by:Jaakko Lehtimaki|collection date:2021 12 07|common name:zebrafish|dev stage:38 hpf location country and/or sea:Portugal|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|sample name:38 PR3|scientific name:Danio rerio|tissue type:retina,,,,,,,,,Raw reads: 38 PR3,webin reads 38 PR3,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,ERP164534,Raw reads: 38 PR3,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,38PR3_S3_R1_001.fastq.gz,fastq,3894010106.0,39196855.0,webin reads 38 PR3,0:99.34,A:1093221995;C:818047738;G:843661747;T:1138957138;N:121488,99,,,,1093221995,818047738,843661747,1138957138,121488,ERX13224866,ERS21098698,ERA30879273,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,Belgium,2024-01-01,Pharyngula,Embryo,Eye,Sensory System
19112,ERR13822135,ERX13224887,ERS21098701,ERP164534,PRJEB80557,RNAseq of Danio Rerio Photoreceptors  Amacrine  and Horizontal cells  collected 38  48  and 58 hpf,e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed,Other,This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs  during the retinal lamination. We dissected retinae from three different developmental stages  corresponding to different stages in HCs lamination process  and separated HCs  PRs and HCs  based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed  converted to cDNA sequenced using the SMART SEQ2 protocol.,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,,retinal neurons,38AC2 S6 R1 001.fastq.gz,38 AC2,,organism:Danio rerio|collection date:2021 11 30|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:38 hpf type:retina|geographic location country and/or sea:Portugal,,,,,,,,,Raw reads: 38 AC2,webin reads 38 AC2,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,ERP164534,Raw reads: 38 AC2,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,38AC2_S6_R1_001.fastq.gz,fastq,3913343007.0,39682834.0,webin reads 38 AC2,0:98.62,A:1089960083;C:827936673;G:855955684;T:1139372607;N:117960,98,,,,1089960083,827936673,855955684,1139372607,117960,ERX13224887,ERS21098701,ERA30879382,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,Belgium,2025-01-01,Pharyngula,Embryo,Eye,Sensory System
19115,ERR13822099,ERX13224851,ERS21098696,ERP164534,PRJEB80557,RNAseq of Danio Rerio Photoreceptors  Amacrine  and Horizontal cells  collected 38  48  and 58 hpf,e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed,Other,This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs  during the retinal lamination. We dissected retinae from three different developmental stages  corresponding to different stages in HCs lamination process  and separated HCs  PRs and HCs  based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed  converted to cDNA sequenced using the SMART SEQ2 protocol.,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,,retinal neurons,38PR1 S1 R1 001.fastq.gz,38 PR1,,organism:Danio rerio|collection date:2021 11 30|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:38 hpf type:retina|geographic location country and/or sea:Portugal,,,,,,,,,Raw reads: 38 PR1,webin reads 38 PR1,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,ERP164534,Raw reads: 38 PR1,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,38PR1_S1_R1_001.fastq.gz,fastq,4256158288.0,42658127.0,webin reads 38 PR1,0:99.77,A:1193880575;C:899261652;G:926114030;T:1236860186;N:41845,99,,,,1193880575,899261652,926114030,1236860186,41845,ERX13224851,ERS21098696,ERA30879152,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,Belgium,2025-01-01,Pharyngula,Embryo,Eye,Sensory System
19116,ERR13822119,ERX13224871,ERS21098699,ERP164534,PRJEB80557,RNAseq of Danio Rerio Photoreceptors  Amacrine  and Horizontal cells  collected 38  48  and 58 hpf,e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed,Other,This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs  during the retinal lamination. We dissected retinae from three different developmental stages  corresponding to different stages in HCs lamination process  and separated HCs  PRs and HCs  based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed  converted to cDNA sequenced using the SMART SEQ2 protocol.,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,,retinal neurons,38PR4 S4 R1 001.fastq.gz,38 PR4,,organism:Danio rerio|collection date:2021 12 07|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:38 hpf type:retina|geographic location country and/or sea:Portugal,,,,,,,,,Raw reads: 38 PR4,webin reads 38 PR4,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,ERP164534,Raw reads: 38 PR4,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,38PR4_S4_R1_001.fastq.gz,fastq,3726308046.0,37591038.0,webin reads 38 PR4,0:99.13,A:1043231302;C:789255840;G:812957881;T:1080801843;N:61180,99,,,,1043231302,789255840,812957881,1080801843,61180,ERX13224871,ERS21098699,ERA30879302,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,Belgium,2025-01-01,Pharyngula,Embryo,Eye,Sensory System
19120,ERR13822788,ERX13225540,ERS21098707,ERP164534,PRJEB80557,RNAseq of Danio Rerio Photoreceptors  Amacrine  and Horizontal cells  collected 38  48  and 58 hpf,e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed,Other,This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs  during the retinal lamination. We dissected retinae from three different developmental stages  corresponding to different stages in HCs lamination process  and separated HCs  PRs and HCs  based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed  converted to cDNA sequenced using the SMART SEQ2 protocol.,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,,retinal neurons,38HC4 S12 R1 001.fastq.gz,38 HC4,,organism:Danio rerio|collection date:2021 12 07|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:38 hpf type:retina|geographic location country and/or sea:Portugal,,,,,,,,,Raw reads: 38 HC4,webin reads 38 HC4,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,ERP164534,Raw reads: 38 HC4,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,38HC4_S12_R1_001.fastq.gz,fastq,3353994440.0,33744828.0,webin reads 38 HC4,0:99.39,A:939537209;C:709367668;G:731849729;T:973193819;N:46015,99,,,,939537209,709367668,731849729,973193819,46015,ERX13225540,ERS21098707,ERA30879650,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,Belgium,2025-01-01,Pharyngula,Embryo,Eye,Sensory System
39827,SRR2441454,SRX1321833,SRS1109642,SRP062493,PRJNA293106,Danio rerio Raw sequence reads,PRJNA293106,Metagenomics,Zebrafish Hypoxia RNAseq,,,RNAseq at 24hpf following hypoxia,,24hpf hypoxia,,strain:TU|age:24hpf|sex:not determined|tissue:brain|treatment:hypoxia|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample       24hpf hypoxia,24hpf.hypoxia.3.10329X21,24hpf.hypoxia.3.10329X21,We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition.  For hypoxia  we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected.  We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages.  At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation.  RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer.  The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides  single end  stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer  providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP062493,,,10329X21_130822_SN141_0719_AD2CK5ACXX_7.txt.gz,fastq,1205447950.0,24108959.0,24hpf.hypoxia.3.10329X21,0:50,A:299680333;C:267717935;G:264833481;T:357936794;N:15279407,50,,,,299680333,267717935,264833481,357936794,15279407,SRX1321833,SRS1109642,SRA289450,University of Utah|Bonkowsky,University of Utah,1,0.87455,,0.24266,,0.74121,,0.57777,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United States,2015-10-10,Pharyngula,Embryo,Brain,Nervous System
39829,SRR2434699,SRX1321831,SRS1109642,SRP062493,PRJNA293106,Danio rerio Raw sequence reads,PRJNA293106,Metagenomics,Zebrafish Hypoxia RNAseq,,,RNAseq at 24hpf following hypoxia,,24hpf hypoxia,,strain:TU|age:24hpf|sex:not determined|tissue:brain|treatment:hypoxia|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample       24hpf hypoxia,24hpf.hypoxia.2.10329X11,24hpf.hypoxia.2.10329X11,We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition.  For hypoxia  we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected.  We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages.  At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation.  RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer.  The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides  single end  stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer  providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP062493,,,10329X11_130822_SN141_0719_AD2CK5ACXX_5.txt.gz,fastq,1227682750.0,24553655.0,24hpf.hypoxia.2.10329X11,0:50,A:299759613;C:292757497;G:281904026;T:353193075;N:68539,50,,,,299759613,292757497,281904026,353193075,68539,SRX1321831,SRS1109642,SRA289450,University of Utah|Bonkowsky,University of Utah,1,0.94855,,0.27579,,0.73298,,0.58307,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United States,2015-10-07,Pharyngula,Embryo,Brain,Nervous System
39831,SRR2426760,SRX1321829,SRS1109645,SRP062493,PRJNA293106,Danio rerio Raw sequence reads,PRJNA293106,Metagenomics,Zebrafish Hypoxia RNAseq,,,RNAseq at 36hpf following hypoxia,,36hpf hypoxia,,strain:TU|age:36hpf|sex:not determined|tissue:brain|treatment:hypoxia|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample       36hpf hypoxia,36hpf.hypoxia.1.10329X4,36hpf.hypoxia.1.10329X4,We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition.  For hypoxia  we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected.  We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages.  At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation.  RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer.  The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides  single end  stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer  providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP062493,,,10329X4_130822_SN141_0719_AD2CK5ACXX_4.txt.gz,fastq,1604107450.0,32082149.0,36hpf.hypoxia.1.10329X4,0:50,A:395786409;C:358263833;G:358391489;T:491601452;N:64267,50,,,,395786409,358263833,358391489,491601452,64267,SRX1321829,SRS1109645,SRA289450,University of Utah|Bonkowsky,University of Utah,1,0.95408,,0.28965,,0.69593,,0.54826,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United States,2015-10-10,Pharyngula,Embryo,Brain,Nervous System
39834,SRR2400601,SRX1321826,SRS1109642,SRP062493,PRJNA293106,Danio rerio Raw sequence reads,PRJNA293106,Metagenomics,Zebrafish Hypoxia RNAseq,,,RNAseq at 24hpf following hypoxia,,24hpf hypoxia,,strain:TU|age:24hpf|sex:not determined|tissue:brain|treatment:hypoxia|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample       24hpf hypoxia,24hpf.hypoxia.1.10329X2,24hpf.hypoxia.1.10329X2,We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition.  For hypoxia  we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected.  We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages.  At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation.  RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer.  The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides  single end  stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer  providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP062493,,,10329X2_130822_SN141_0719_AD2CK5ACXX_4.txt.gz,fastq,1249046350.0,24980927.0,24hpf.hypoxia.1.10329X2,0:50,A:309098695;C:281875016;G:278706888;T:379315616;N:50135,50,,,,309098695,281875016,278706888,379315616,50135,SRX1321826,SRS1109642,SRA289450,University of Utah|Bonkowsky,University of Utah,1,0.95443,,0.27405,,0.69747,,0.40987,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United States,2015-10-10,Pharyngula,Embryo,Brain,Nervous System
39839,SRR2340149,SRX1321821,SRS1109650,SRP062493,PRJNA293106,Danio rerio Raw sequence reads,PRJNA293106,Metagenomics,Zebrafish Hypoxia RNAseq,,,RNAseq at 36hpf following normoxia,,36hpf normoxia,,strain:TU|age:36hpf|sex:not determined|tissue:brain|treatment:normoxia|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample       36hpf normoxia,36hpf.normoxia.3.10329X24,36hpf.normoxia.3.10329X24,We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition.  For hypoxia  we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected.  We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages.  At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation.  RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer.  The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides  single end  stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer  providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP062493,,,10329X24_130822_SN141_0719_AD2CK5ACXX_7.txt.gz,fastq,1588630750.0,31772615.0,36hpf.normoxia.3.10329X24,0:50,A:404319446;C:349459823;G:346545846;T:468209953;N:20095682,50,,,,404319446,349459823,346545846,468209953,20095682,SRX1321821,SRS1109650,SRA289450,University of Utah|Bonkowsky,University of Utah,1,0.8739,,0.32489,,0.71701,,0.51646,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United States,2015-10-10,Pharyngula,Embryo,Brain,Nervous System
39840,SRR2245887,SRX1321820,SRS1109645,SRP062493,PRJNA293106,Danio rerio Raw sequence reads,PRJNA293106,Metagenomics,Zebrafish Hypoxia RNAseq,,,RNAseq at 36hpf following hypoxia,,36hpf hypoxia,,strain:TU|age:36hpf|sex:not determined|tissue:brain|treatment:hypoxia|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample       36hpf hypoxia,36hpf.hypoxia.3.10329X23,36hpf.hypoxia.3.10329X23,We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition.  For hypoxia  we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected.  We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages.  At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation.  RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer.  The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides  single end  stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer  providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP062493,,,10329X23_130822_SN141_0719_AD2CK5ACXX_7.txt.gz,fastq,1207331350.0,24146627.0,36hpf.hypoxia.3.10329X23,0:50,A:305628501;C:266059461;G:259888045;T:360487730;N:15267613,50,,,,305628501,266059461,259888045,360487730,15267613,SRX1321820,SRS1109645,SRA289450,University of Utah|Bonkowsky,University of Utah,1,0.87814,,0.27249,,0.72853,,0.53527,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United States,2015-10-10,Pharyngula,Embryo,Brain,Nervous System
39841,SRR2245257,SRX1321819,SRS1109651,SRP062493,PRJNA293106,Danio rerio Raw sequence reads,PRJNA293106,Metagenomics,Zebrafish Hypoxia RNAseq,,,RNAseq at 24hpf following normoxia,,24hpf normoxia,,strain:TU|age:24hpf|sex:not determined|tissue:brain|treatment:normoxia|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample       24hpf normoxia,24hpf.normoxia.3.10329X22,24hpf.normoxia.3.10329X22,We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition.  For hypoxia  we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected.  We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages.  At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation.  RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer.  The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides  single end  stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer  providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP062493,,,10329X22_130822_SN141_0719_AD2CK5ACXX_7.txt.gz,fastq,1257159050.0,25143181.0,24hpf.normoxia.3.10329X22,0:50,A:320558638;C:275312235;G:271710647;T:373637690;N:15939840,50,,,,320558638,275312235,271710647,373637690,15939840,SRX1321819,SRS1109651,SRA289450,University of Utah|Bonkowsky,University of Utah,1,0.87634,,0.30298,,0.71356,,0.54673,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United States,2015-10-10,Pharyngula,Embryo,Brain,Nervous System
39847,SRR2239772,SRX1321813,SRS1109650,SRP062493,PRJNA293106,Danio rerio Raw sequence reads,PRJNA293106,Metagenomics,Zebrafish Hypoxia RNAseq,,,RNAseq at 36hpf following normoxia,,36hpf normoxia,,strain:TU|age:36hpf|sex:not determined|tissue:brain|treatment:normoxia|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample       36hpf normoxia,36hpf.normoxia.2.10329X14,36hpf.normoxia.2.10329X14,We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition.  For hypoxia  we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected.  We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages.  At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation.  RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer.  The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides  single end  stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer  providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP062493,,,10329X14_130822_SN141_0719_AD2CK5ACXX_6.txt.gz,fastq,1533885200.0,30677704.0,36hpf.normoxia.2.10329X14,0:50,A:392813056;C:354469675;G:348871622;T:437692730;N:38117,50,,,,392813056,354469675,348871622,437692730,38117,SRX1321813,SRS1109650,SRA289450,University of Utah|Bonkowsky,University of Utah,1,0.91439,,0.31812,,0.70863,,0.51667,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United States,2015-10-10,Pharyngula,Embryo,Brain,Nervous System
39848,SRR2232685,SRX1321812,SRS1109645,SRP062493,PRJNA293106,Danio rerio Raw sequence reads,PRJNA293106,Metagenomics,Zebrafish Hypoxia RNAseq,,,RNAseq at 36hpf following hypoxia,,36hpf hypoxia,,strain:TU|age:36hpf|sex:not determined|tissue:brain|treatment:hypoxia|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample       36hpf hypoxia,36hpf.hypoxia.2.10329X13,36hpf.hypoxia.2.10329X13,We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition.  For hypoxia  we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected.  We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages.  At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation.  RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer.  The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides  single end  stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer  providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP062493,,,10329X13_130822_SN141_0719_AD2CK5ACXX_6.txt.gz,fastq,1112846200.0,22256924.0,36hpf.hypoxia.2.10329X13,0:50,A:279147206;C:259582122;G:249642505;T:324452965;N:21402,50,,,,279147206,259582122,249642505,324452965,21402,SRX1321812,SRS1109645,SRA289450,University of Utah|Bonkowsky,University of Utah,1,0.94469,,0.25952,,0.72243,,0.52701,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United States,2015-10-10,Pharyngula,Embryo,Brain,Nervous System
39849,SRR2227658,SRX1321811,SRS1109651,SRP062493,PRJNA293106,Danio rerio Raw sequence reads,PRJNA293106,Metagenomics,Zebrafish Hypoxia RNAseq,,,RNAseq at 24hpf following normoxia,,24hpf normoxia,,strain:TU|age:24hpf|sex:not determined|tissue:brain|treatment:normoxia|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample       24hpf normoxia,24hpf.normoxia.2.10329X12,24hpf.normoxia.2.10329X12,We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition.  For hypoxia  we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected.  We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages.  At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation.  RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer.  The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides  single end  stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer  providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP062493,,,10329X12_130822_SN141_0719_AD2CK5ACXX_5.txt.gz,fastq,1243623750.0,24872475.0,24hpf.normoxia.2.10329X12,0:50,A:317179221;C:285081899;G:274648790;T:366643275;N:70565,50,,,,317179221,285081899,274648790,366643275,70565,SRX1321811,SRS1109651,SRA289450,University of Utah|Bonkowsky,University of Utah,1,0.95045,,0.27525,,0.69688,,0.53555,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United States,2015-09-01,Pharyngula,Embryo,Brain,Nervous System
39854,SRR2225675,SRX1321806,SRS1109650,SRP062493,PRJNA293106,Danio rerio Raw sequence reads,PRJNA293106,Metagenomics,Zebrafish Hypoxia RNAseq,,,RNAseq at 36hpf following normoxia,,36hpf normoxia,,strain:TU|age:36hpf|sex:not determined|tissue:brain|treatment:normoxia|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample       36hpf normoxia,36hpf.normoxia.1.10329X5,36hpf.normoxia.1.10329X5,We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition.  For hypoxia  we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected.  We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages.  At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation.  RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer.  The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides  single end  stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer  providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP062493,,,10329X5_130822_SN141_0719_AD2CK5ACXX_4.txt.gz,fastq,1244744700.0,24894894.0,36hpf.normoxia.1.10329X5,0:50,A:301597123;C:287750990;G:281194881;T:374152417;N:49289,50,,,,301597123,287750990,281194881,374152417,49289,SRX1321806,SRS1109650,SRA289450,University of Utah|Bonkowsky,University of Utah,1,0.95571,,0.22791,,0.71177,,0.53801,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United States,2015-10-10,Pharyngula,Embryo,Brain,Nervous System
39855,SRR2225572,SRX1321805,SRS1109651,SRP062493,PRJNA293106,Danio rerio Raw sequence reads,PRJNA293106,Metagenomics,Zebrafish Hypoxia RNAseq,,,RNAseq at 24hpf following normoxia,,24hpf normoxia,,strain:TU|age:24hpf|sex:not determined|tissue:brain|treatment:normoxia|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample       24hpf normoxia,24hpf.normoxia.1.10329X3,24hpf.normoxia.1.10329X3,We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition.  For hypoxia  we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected.  We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages.  At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation.  RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer.  The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides  single end  stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer  providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP062493,,,10329X3_130822_SN141_0719_AD2CK5ACXX_4.txt.gz,fastq,1293605500.0,25872110.0,24hpf.normoxia.1.10329X3,0:50,A:310265067;C:296406990;G:295054246;T:391826687;N:52510,50,,,,310265067,296406990,295054246,391826687,52510,SRX1321805,SRS1109651,SRA289450,University of Utah|Bonkowsky,University of Utah,1,0.95596,,0.21907,,0.71512,,0.39029,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United States,2015-09-01,Pharyngula,Embryo,Brain,Nervous System
42097,SRR5483549,SRX2766898,SRS2151000,SRP105338,PRJNA381309,Danio rerio strain:AB Raw sequence reads,PRJNA381309,Whole Genome Sequencing,RNA seq data from control and MCT8 morphant zebrafish embryos at 25hpf,,,,C1 CGATGT L001 R1 001,C1,,strain:AB|dev stage:25hpf|sex:not applicable|tissue:Whole embryo|death date:25 hpf type:ReplicateC1L1R1|treatment:CTR morpholino|BioSampleModel:Model organism or animal,,,,,,,,,Pair end L1R1,C1 CGATGT L001,C1 CGATGT L001,Total RNA was extrated from pools of 50 embryos using EZNA total RNA extraction kit I and Dnased with Ambion turbo Dnase kit.Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries following Illumina's standard procedures,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 1000,,SRP105338,,loader:fastq load.py,C1_CGATGT_L001_R1_001.fastq C1_CGATGT_L001_R2_001.fastq C1_CGATGT_L002_R1_001.fastq C1_CGATGT_L002_R2_001.fastq,fastq fastq fastq fastq,1411679200.0,14356543.0,C1 CGATGT L001 R2 001.fastq,,A:371472311;C:327400140;G:335224751;T:377147836;N:434162,,,,,371472311,327400140,335224751,377147836,434162,SRX2766898,SRS2151000,SRA557338,Centro Ciencias do Mar|Comparative Endocrinology and Integrative Biology,Centro Ciencias do Mar,2,0.93533,0.94243,0.07183,0.07215,0.72111,0.72251,0.46894,0.47065,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,Portugal,2017-09-19,Pharyngula,Embryo,Whole Organism,All anatomical structures
42098,SRR5483548,SRX2766897,SRS2150999,SRP105338,PRJNA381309,Danio rerio strain:AB Raw sequence reads,PRJNA381309,Whole Genome Sequencing,RNA seq data from control and MCT8 morphant zebrafish embryos at 25hpf,,,,C2 CGATGT L001 R1 001,C2,,strain:AB|dev stage:25hpf|sex:not applicable|tissue:Whole embryo|death date:25 hpf type:ReplicateC2L1R1|treatment:CTR morpholino|BioSampleModel:Model organism or animal,,,,,,,,,Pair end L1R1,C2 CGATGT L001,C2 CGATGT L001,Total RNA was extrated from pools of 50 embryos using EZNA total RNA extraction kit I and Dnased with Ambion turbo Dnase kit.Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries following Illumina's standard procedures,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 1000,,SRP105338,,loader:fastq load.py,C2_TGACCA_L001_R1_001.fastq C2_TGACCA_L001_R2_001.fastq C2_TGACCA_L002_R1_001.fastq C2_TGACCA_L002_R2_001.fastq,fastq fastq fastq fastq,1242565800.0,12898403.0,C2 TGACCA L001 R1 001.fastq,,A:326022462;C:289113775;G:293830205;T:333244455;N:354903,,,,,326022462,289113775,293830205,333244455,354903,SRX2766897,SRS2150999,SRA557338,Centro Ciencias do Mar|Comparative Endocrinology and Integrative Biology,Centro Ciencias do Mar,2,0.93498,0.94161,0.07112,0.0695,0.72693,0.72717,0.46957,0.48109,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,Portugal,2017-09-18,Pharyngula,Embryo,Whole Organism,All anatomical structures
42099,SRR5483547,SRX2766896,SRS2150998,SRP105338,PRJNA381309,Danio rerio strain:AB Raw sequence reads,PRJNA381309,Whole Genome Sequencing,RNA seq data from control and MCT8 morphant zebrafish embryos at 25hpf,,,,C4 CGATGT L001 R1 001,C4,,strain:AB|dev stage:25hpf|sex:not applicable|tissue:Whole embryo|death date:25 hpf type:ReplicateC4L1R1|treatment:CTR morpholino|BioSampleModel:Model organism or animal,,,,,,,,,Pair end L1R1,C4 CGATGT L001,C4 CGATGT L001,Total RNA was extrated from pools of 50 embryos using EZNA total RNA extraction kit I and Dnased with Ambion turbo Dnase kit.Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries following Illumina's standard procedures,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 1000,,SRP105338,,loader:fastq load.py,C4_GCCAAT_L001_R1_001.fastq C4_GCCAAT_L001_R2_001.fastq C4_GCCAAT_L002_R1_001.fastq C4_GCCAAT_L002_R2_001.fastq,fastq fastq fastq fastq,1185823950.0,12152845.0,C4 GCCAAT L001 R2 001.fastq,,A:314615152;C:271806853;G:280914266;T:318186592;N:301087,,,,,314615152,271806853,280914266,318186592,301087,SRX2766896,SRS2150998,SRA557338,Centro Ciencias do Mar|Comparative Endocrinology and Integrative Biology,Centro Ciencias do Mar,2,0.93274,0.94146,0.07722,0.07634,0.7223,0.72358,0.48559,0.48318,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,Portugal,2017-09-18,Pharyngula,Embryo,Whole Organism,All anatomical structures
42100,SRR5483546,SRX2766895,SRS2150996,SRP105338,PRJNA381309,Danio rerio strain:AB Raw sequence reads,PRJNA381309,Whole Genome Sequencing,RNA seq data from control and MCT8 morphant zebrafish embryos at 25hpf,,,,C5 CGATGT L001 R1 001,C5,,strain:AB|dev stage:25hpf|sex:not applicable|tissue:Whole embryo|death date:25 hpf type:ReplicateC5L1R1|treatment:CTR morpholino|BioSampleModel:Model organism or animal,,,,,,,,,Pair end L1R1,C5 CGATGT L001,C5 CGATGT L001,Total RNA was extrated from pools of 50 embryos using EZNA total RNA extraction kit I and Dnased with Ambion turbo Dnase kit.Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries following Illumina's standard procedures,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 1000,,SRP105338,,loader:fastq load.py,C5_ACTTGA_L001_R1_001.fastq C5_ACTTGA_L001_R2_001.fastq C5_ACTTGA_L002_R1_001.fastq C5_ACTTGA_L002_R2_001.fastq,fastq fastq fastq fastq,1107911114.0,11470347.0,C5 ACTTGA L001 R1 001.fastq,,A:291142814;C:256111405;G:262122909;T:298258834;N:275152,,,,,291142814,256111405,262122909,298258834,275152,SRX2766895,SRS2150996,SRA557338,Centro Ciencias do Mar|Comparative Endocrinology and Integrative Biology,Centro Ciencias do Mar,2,0.93423,0.94182,0.07555,0.07453,0.72344,0.72579,0.47773,0.47732,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,Portugal,2017-09-18,Pharyngula,Embryo,Whole Organism,All anatomical structures
42101,SRR5483545,SRX2766894,SRS2150997,SRP105338,PRJNA381309,Danio rerio strain:AB Raw sequence reads,PRJNA381309,Whole Genome Sequencing,RNA seq data from control and MCT8 morphant zebrafish embryos at 25hpf,,,,C6 CGATGT L001 R1 001,C6,,strain:AB|dev stage:25hpf|sex:not applicable|tissue:Whole embryo|death date:25 hpf type:ReplicateC6L1R1|treatment:CTR morpholino|BioSampleModel:Model organism or animal,,,,,,,,,Pair end L1R1,C6 CGATGT L001,C6 CGATGT L001,Total RNA was extrated from pools of 50 embryos using EZNA total RNA extraction kit I and Dnased with Ambion turbo Dnase kit.Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries following Illumina's standard procedures,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 1000,,SRP105338,,loader:fastq load.py,C6_TAGCTT_L001_R1_001.fastq C6_TAGCTT_L002_R1_001.fastq C6_TAGCTT_L002_R2_001.fastq C6_TAGCTT_L001_R2_001.fastq,fastq fastq fastq fastq,1083109717.0,10884377.0,C6 TAGCTT L001 R2 001.fastq,,A:285687095;C:248867355;G:257309681;T:290972966;N:272620,,,,,285687095,248867355,257309681,290972966,272620,SRX2766894,SRS2150997,SRA557338,Centro Ciencias do Mar|Comparative Endocrinology and Integrative Biology,Centro Ciencias do Mar,2,0.9312,0.94054,0.07791,0.07785,0.72056,0.72131,0.47439,0.47662,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,Portugal,2017-09-18,Pharyngula,Embryo,Whole Organism,All anatomical structures
42102,SRR5483544,SRX2766893,SRS2150995,SRP105338,PRJNA381309,Danio rerio strain:AB Raw sequence reads,PRJNA381309,Whole Genome Sequencing,RNA seq data from control and MCT8 morphant zebrafish embryos at 25hpf,,,,C7 CGATGT L001 R1 001,C7,,strain:AB|dev stage:25hpf|sex:not applicable|tissue:Whole embryo|death date:25 hpf type:ReplicateC7L1R1|treatment:CTR morpholino|BioSampleModel:Model organism or animal,,,,,,,,,Pair end L1R1,C7 CGATGT L001,C7 CGATGT L001,Total RNA was extrated from pools of 50 embryos using EZNA total RNA extraction kit I and Dnased with Ambion turbo Dnase kit.Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries following Illumina's standard procedures,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 1000,,SRP105338,,loader:fastq load.py,C7_CTTGTA_L001_R1_001.fastq C7_CTTGTA_L001_R2_001.fastq C7_CTTGTA_L002_R1_001.fastq C7_CTTGTA_L002_R2_001.fastq,fastq fastq fastq fastq,1085918450.0,11100560.0,C7 CTTGTA L002 R2 001.fastq,,A:285918868;C:249635769;G:259725006;T:290324468;N:314339,,,,,285918868,249635769,259725006,290324468,314339,SRX2766893,SRS2150995,SRA557338,Centro Ciencias do Mar|Comparative Endocrinology and Integrative Biology,Centro Ciencias do Mar,2,0.93539,0.94346,0.06947,0.06884,0.72421,0.72502,0.4671,0.48382,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,Portugal,2017-09-18,Pharyngula,Embryo,Whole Organism,All anatomical structures
42103,SRR5483543,SRX2766892,SRS2150994,SRP105338,PRJNA381309,Danio rerio strain:AB Raw sequence reads,PRJNA381309,Whole Genome Sequencing,RNA seq data from control and MCT8 morphant zebrafish embryos at 25hpf,,,,C8 CGATGT L001 R1 001,C8,,strain:AB|dev stage:25hpf|sex:not applicable|tissue:Whole embryo|death date:25 hpf type:ReplicateC8L1R1|treatment:CTR morpholino|BioSampleModel:Model organism or animal,,,,,,,,,Pair end L1R1,C8 CGATGT L001,C8 CGATGT L001,Total RNA was extrated from pools of 50 embryos using EZNA total RNA extraction kit I and Dnased with Ambion turbo Dnase kit.Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries following Illumina's standard procedures,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 1000,,SRP105338,,loader:fastq load.py,C8_AGTTCC_L001_R1_001.fastq C8_AGTTCC_L001_R2_001.fastq C8_AGTTCC_L002_R1_001.fastq C8_AGTTCC_L002_R2_001.fastq,fastq fastq fastq fastq,1073608497.0,11267084.0,C8 AGTTCC L001 R1 001.fastq,,A:281312906;C:246954741;G:257647783;T:287433153;N:259914,,,,,281312906,246954741,257647783,287433153,259914,SRX2766892,SRS2150994,SRA557338,Centro Ciencias do Mar|Comparative Endocrinology and Integrative Biology,Centro Ciencias do Mar,2,0.93523,0.94416,0.0757,0.07511,0.72868,0.72924,0.45926,0.48524,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,Portugal,2017-09-18,Pharyngula,Embryo,Whole Organism,All anatomical structures
42104,SRR5483542,SRX2766891,SRS2150993,SRP105338,PRJNA381309,Danio rerio strain:AB Raw sequence reads,PRJNA381309,Whole Genome Sequencing,RNA seq data from control and MCT8 morphant zebrafish embryos at 25hpf,,,,M1 CGATGT L001 R1 001,M1,,strain:AB|dev stage:25hpf|sex:not applicable|tissue:Whole embryo|death date:25 hpf type:ReplicateM1L1R1|treatment:MCT8 morpholino|BioSampleModel:Model organism or animal,,,,,,,,,Pair end L1R1,M1 CGATGT L001,M1 CGATGT L001,Total RNA was extrated from pools of 50 embryos using EZNA total RNA extraction kit I and Dnased with Ambion turbo Dnase kit.Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries following Illumina's standard procedures,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 1000,,SRP105338,,loader:fastq load.py,M1_ATCACG_L001_R1_001.fastq M1_ATCACG_L001_R2_001.fastq M1_ATCACG_L002_R1_001.fastq M1_ATCACG_L002_R2_001.fastq,fastq fastq fastq fastq,1076263104.0,11250362.0,M1 ATCACG L001 R1 001.fastq,,A:283920293;C:247496404;G:257418630;T:287117906;N:309871,,,,,283920293,247496404,257418630,287117906,309871,SRX2766891,SRS2150993,SRA557338,Centro Ciencias do Mar|Comparative Endocrinology and Integrative Biology,Centro Ciencias do Mar,2,0.93089,0.93777,0.07725,0.07679,0.72519,0.7264,0.47634,0.48399,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,Portugal,2017-09-18,Pharyngula,Embryo,Whole Organism,All anatomical structures
42105,SRR5483541,SRX2766890,SRS2150992,SRP105338,PRJNA381309,Danio rerio strain:AB Raw sequence reads,PRJNA381309,Whole Genome Sequencing,RNA seq data from control and MCT8 morphant zebrafish embryos at 25hpf,,,,M2 CGATGT L001 R1 001,M2,,strain:AB|dev stage:25hpf|sex:not applicable|tissue:Whole embryo|death date:25 hpf type:ReplicateM2L1R1|treatment:MCT8 morpholino|BioSampleModel:Model organism or animal,,,,,,,,,Pair end L1R1,M2 CGATGT L001,M2 CGATGT L001,Total RNA was extrated from pools of 50 embryos using EZNA total RNA extraction kit I and Dnased with Ambion turbo Dnase kit.Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries following Illumina's standard procedures,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 1000,,SRP105338,,loader:fastq load.py,M2_TTAGGC_L001_R1_001.fastq M2_TTAGGC_L001_R2_001.fastq M2_TTAGGC_L002_R1_001.fastq M2_TTAGGC_L002_R2_001.fastq,fastq fastq fastq fastq,1044313397.0,10967496.0,M2 TTAGGC L002 R2 001.fastq,,A:276052785;C:238107857;G:247363631;T:282542437;N:246687,,,,,276052785,238107857,247363631,282542437,246687,SRX2766890,SRS2150992,SRA557338,Centro Ciencias do Mar|Comparative Endocrinology and Integrative Biology,Centro Ciencias do Mar,2,0.93066,0.93744,0.08494,0.08454,0.71835,0.72119,0.47424,0.47546,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,Portugal,2017-09-18,Pharyngula,Embryo,Whole Organism,All anatomical structures
42106,SRR5483540,SRX2766889,SRS2150991,SRP105338,PRJNA381309,Danio rerio strain:AB Raw sequence reads,PRJNA381309,Whole Genome Sequencing,RNA seq data from control and MCT8 morphant zebrafish embryos at 25hpf,,,,M4 CGATGT L001 R1 001,M4,,strain:AB|dev stage:25hpf|sex:not applicable|tissue:Whole embryo|death date:25 hpf type:ReplicateM4L1R1|treatment:MCT8 morpholino|BioSampleModel:Model organism or animal,,,,,,,,,Pair end L1R1,M4 CGATGT L001,M4 CGATGT L001,Total RNA was extrated from pools of 50 embryos using EZNA total RNA extraction kit I and Dnased with Ambion turbo Dnase kit.Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries following Illumina's standard procedures,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 1000,,SRP105338,,loader:fastq load.py,M4_ACAGTG_L001_R1_001.fastq M4_ACAGTG_L001_R2_001.fastq M4_ACAGTG_L002_R1_001.fastq M4_ACAGTG_L002_R2_001.fastq,fastq fastq fastq fastq,1040309805.0,10467987.0,M4 ACAGTG L001 R1 001.fastq,,A:274887463;C:239206759;G:246059361;T:279869834;N:286388,,,,,274887463,239206759,246059361,279869834,286388,SRX2766889,SRS2150991,SRA557338,Centro Ciencias do Mar|Comparative Endocrinology and Integrative Biology,Centro Ciencias do Mar,2,0.92883,0.9367,0.07702,0.07622,0.71723,0.72054,0.47154,0.47398,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,Portugal,2017-09-18,Pharyngula,Embryo,Whole Organism,All anatomical structures
42107,SRR5483538,SRX2766888,SRS2150990,SRP105338,PRJNA381309,Danio rerio strain:AB Raw sequence reads,PRJNA381309,Whole Genome Sequencing,RNA seq data from control and MCT8 morphant zebrafish embryos at 25hpf,,,,M5 CGATGT L001 R1 001,M5,,strain:AB|dev stage:25hpf|sex:not applicable|tissue:Whole embryo|death date:25 hpf type:ReplicateM5L1R1|treatment:MCT8 morpholino|BioSampleModel:Model organism or animal,,,,,,,,,Pair end L1R1,M5 CGATGT L001,M5 CGATGT L001,Total RNA was extrated from pools of 50 embryos using EZNA total RNA extraction kit I and Dnased with Ambion turbo Dnase kit.Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries following Illumina's standard procedures,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 1000,,SRP105338,,loader:fastq load.py,M5_CAGATC_L001_R1_001.fastq M5_CAGATC_L001_R2_001.fastq M5_CAGATC_L002_R1_001.fastq M5_CAGATC_L002_R2_001.fastq,fastq fastq fastq fastq,1042489285.0,10734591.0,M5 CAGATC L002 R1 001.fastq,,A:274701145;C:240814745;G:247900443;T:278809711;N:263241,,,,,274701145,240814745,247900443,278809711,263241,SRX2766888,SRS2150990,SRA557338,Centro Ciencias do Mar|Comparative Endocrinology and Integrative Biology,Centro Ciencias do Mar,2,0.93334,0.94159,0.07462,0.07419,0.7247,0.726,0.46897,0.47065,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,Portugal,2017-09-18,Pharyngula,Embryo,Whole Organism,All anatomical structures
42108,SRR5483537,SRX2766887,SRS2150989,SRP105338,PRJNA381309,Danio rerio strain:AB Raw sequence reads,PRJNA381309,Whole Genome Sequencing,RNA seq data from control and MCT8 morphant zebrafish embryos at 25hpf,,,,M6 CGATGT L001 R1 001,M6,,strain:AB|dev stage:25hpf|sex:not applicable|tissue:Whole embryo|death date:25 hpf type:ReplicateM6L1R1|treatment:MCT8 morpholino|BioSampleModel:Model organism or animal,,,,,,,,,Pair end L1R1,M6 CGATGT L001,M6 CGATGT L001,Total RNA was extrated from pools of 50 embryos using EZNA total RNA extraction kit I and Dnased with Ambion turbo Dnase kit.Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries following Illumina's standard procedures,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 1000,,SRP105338,,loader:fastq load.py,M6_GATCAG_L001_R1_001.fastq M6_GATCAG_L001_R2_001.fastq M6_GATCAG_L002_R1_001.fastq M6_GATCAG_L002_R2_001.fastq,fastq fastq fastq fastq,1031478329.0,10597728.0,M6 GATCAG L001 R1 001.fastq,,A:271373993;C:237256959;G:245402803;T:277169379;N:275195,,,,,271373993,237256959,245402803,277169379,275195,SRX2766887,SRS2150989,SRA557338,Centro Ciencias do Mar|Comparative Endocrinology and Integrative Biology,Centro Ciencias do Mar,2,0.93278,0.93984,0.0768,0.07622,0.72261,0.72494,0.46732,0.48412,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,Portugal,2017-09-18,Pharyngula,Embryo,Whole Organism,All anatomical structures
42109,SRR5483536,SRX2766886,SRS2150987,SRP105338,PRJNA381309,Danio rerio strain:AB Raw sequence reads,PRJNA381309,Whole Genome Sequencing,RNA seq data from control and MCT8 morphant zebrafish embryos at 25hpf,,,,M7 CGATGT L001 R1 001,M7,,strain:AB|dev stage:25hpf|sex:not applicable|tissue:Whole embryo|death date:25 hpf type:ReplicateM7L1R1|treatment:MCT8 morpholino|BioSampleModel:Model organism or animal,,,,,,,,,Pair end L1R1,M7 CGATGT L001,M7 CGATGT L001,Total RNA was extrated from pools of 50 embryos using EZNA total RNA extraction kit I and Dnased with Ambion turbo Dnase kit.Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries following Illumina's standard procedures,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 1000,,SRP105338,,loader:fastq load.py,M7_GGCTAC_L001_R1_001.fastq M7_GGCTAC_L001_R2_001.fastq M7_GGCTAC_L002_R1_001.fastq M7_GGCTAC_L002_R2_001.fastq,fastq fastq fastq fastq,1029672796.0,10581444.0,M7 GGCTAC L001 R2 001.fastq,,A:272134982;C:235882853;G:243458535;T:277945711;N:250715,,,,,272134982,235882853,243458535,277945711,250715,SRX2766886,SRS2150987,SRA557338,Centro Ciencias do Mar|Comparative Endocrinology and Integrative Biology,Centro Ciencias do Mar,2,0.93095,0.93916,0.07906,0.07917,0.72208,0.72376,0.4638,0.47021,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,Portugal,2017-09-18,Pharyngula,Embryo,Whole Organism,All anatomical structures
42110,SRR5483535,SRX2766885,SRS2150988,SRP105338,PRJNA381309,Danio rerio strain:AB Raw sequence reads,PRJNA381309,Whole Genome Sequencing,RNA seq data from control and MCT8 morphant zebrafish embryos at 25hpf,,,,M8 CGATGT L001 R1 001,M8,,strain:AB|dev stage:25hpf|sex:not applicable|tissue:Whole embryo|death date:25 hpf type:ReplicateM8L1R1|treatment:MCT8 morpholino|BioSampleModel:Model organism or animal,,,,,,,,,Pair end L1R1,M8 CGATGT L001,M8 CGATGT L001,Total RNA was extrated from pools of 50 embryos using EZNA total RNA extraction kit I and Dnased with Ambion turbo Dnase kit.Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries following Illumina's standard procedures,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 1000,,SRP105338,,loader:fastq load.py,M8_AGTCAA_L001_R1_001.fastq M8_AGTCAA_L002_R2_001.fastq M8_AGTCAA_L002_R1_001.fastq M8_AGTCAA_L001_R2_001.fastq,fastq fastq fastq fastq,1043646073.0,10637865.0,M8 AGTCAA L002 R2 001.fastq,,A:276074388;C:238813481;G:248854024;T:279639163;N:265017,,,,,276074388,238813481,248854024,279639163,265017,SRX2766885,SRS2150988,SRA557338,Centro Ciencias do Mar|Comparative Endocrinology and Integrative Biology,Centro Ciencias do Mar,2,0.93291,0.94231,0.07997,0.07941,0.73156,0.73594,0.49984,0.50182,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,Portugal,2017-09-18,Pharyngula,Embryo,Whole Organism,All anatomical structures
51271,SRR8663332,SRX5460029,SRS4433919,SRP187415,PRJNA525392,Whole transcriptome bisufilte sequencing for multiple species [Zebrafish],GSE127779,Other,We applied a robust experimental and computational framework to identify mRNA m5C sites with high specificity in multiple species. Overall design: RNA BS seq of mRNA for multiple species.,parent bioproject:PRJNA525389,pubmed:35513466,,ZF 24hpf rep2,GSM3638673,,source name:embryo|tissue:embryo|developmental stage:24 hpf|strain:wild type AB fish,ZF 24hpf rep2,Basecalls performed using illumina bcl2fastq 2.17. Adapters were trimmed with cutadapt. Adapter trimmed reads were quality trimmed with Trimmomatic. Clean reads were firstly mapped to the genome and then transcriptome with hisat2 2.10 Pileup was performed using samtools API pysam. Customized scripts were used to call m5C sites from samples Genome build: Zv9.78 Supplementary files format and content: CSV files recording the coverage  m5C level  P value for m5C sites,embryo,,For the embryonic stages  200 embryos were collected and for the larval stage 150 larvae were collected.  Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit  NEB. The fragmented RNA was then used for library construction  following the manufacturer’s protocol NEBNext Ultra II Directional RNA Library Prep Kit  NEB.,Embryos were reared at 28.5 °C and all experiments and observations were performed as close to this temperature as possible.,tissue:embryo|developmental stage:24 hpf|strain:wild type AB fish,GSM3638673,GSM3638673: ZF 24hpf rep2; Danio rerio; Bisulfite Seq,GSM3638673,,1,For the embryonic stages  200 embryos were collected and for the larval stage 150 larvae were collected.  Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit  NEB. The fragmented RNA was then used for library construction  following the manufacturer's protocol NEBNext Ultra II Directional RNA Library Prep Kit  NEB.,GEO Accession:GSM3638673,Bisulfite-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP187415,,,,,21961409700.0,73204699.0,GSM3638673 r1,0:150 1:150,A:7568027843;C:3406881222;G:3795216487;T:7190249641;N:1034507,150,150,,,7568027843,3406881222,3795216487,7190249641,1034507,SRX5460029,SRS4433919,SRA855736,GEO,Sun Yat-sen University,2,0.00082,0.0007,0.00032,0.00023,0.99945,0.99947,0.65517,0.65,150,150,T,T,mates < 9% mapping rate,illumina,hiseq_era,full_length,random_priming,nebnext,bulk,unknown,unknown,,China,2019-03-04,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
51272,SRR8663331,SRX5460028,SRS4433918,SRP187415,PRJNA525392,Whole transcriptome bisufilte sequencing for multiple species [Zebrafish],GSE127779,Other,We applied a robust experimental and computational framework to identify mRNA m5C sites with high specificity in multiple species. Overall design: RNA BS seq of mRNA for multiple species.,parent bioproject:PRJNA525389,pubmed:35513466,,ZF 24hpf rep1,GSM3638672,,source name:embryo|tissue:embryo|developmental stage:24 hpf|strain:wild type AB fish,ZF 24hpf rep1,Basecalls performed using illumina bcl2fastq 2.17. Adapters were trimmed with cutadapt. Adapter trimmed reads were quality trimmed with Trimmomatic. Clean reads were firstly mapped to the genome and then transcriptome with hisat2 2.10 Pileup was performed using samtools API pysam. Customized scripts were used to call m5C sites from samples Genome build: Zv9.78 Supplementary files format and content: CSV files recording the coverage  m5C level  P value for m5C sites,embryo,,For the embryonic stages  200 embryos were collected and for the larval stage 150 larvae were collected.  Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit  NEB. The fragmented RNA was then used for library construction  following the manufacturer’s protocol NEBNext Ultra II Directional RNA Library Prep Kit  NEB.,Embryos were reared at 28.5 °C and all experiments and observations were performed as close to this temperature as possible.,tissue:embryo|developmental stage:24 hpf|strain:wild type AB fish,GSM3638672,GSM3638672: ZF 24hpf rep1; Danio rerio; Bisulfite Seq,GSM3638672,,1,For the embryonic stages  200 embryos were collected and for the larval stage 150 larvae were collected.  Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit  NEB. The fragmented RNA was then used for library construction  following the manufacturer's protocol NEBNext Ultra II Directional RNA Library Prep Kit  NEB.,GEO Accession:GSM3638672,Bisulfite-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP187415,,,,,22998615300.0,76662051.0,GSM3638672 r1,0:150 1:150,A:7938674920;C:3553518327;G:3950127781;T:7555207157;N:1087115,150,150,,,7938674920,3553518327,3950127781,7555207157,1087115,SRX5460028,SRS4433918,SRA855736,GEO,Sun Yat-sen University,2,0.00076,0.00067,0.00027,0.00021,0.99926,0.99937,0.53658,0.58666,150,150,T,T,mates < 9% mapping rate,illumina,hiseq_era,full_length,random_priming,nebnext,bulk,unknown,unknown,,China,2019-03-04,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
51812,SRR8862072,SRX5649486,SRS4594851,SRP191202,PRJNA531242,Zebrafish Otolith Biomineralization Requires Polyketide Synthase,PRJNA531242,Other,RNA seq analysis of nco no content zebrafish embryos at 24 hpf,,,,,Wild type,,strain:AB|age:24hpf|sex:pooled male and female|tissue:Whole embryo lysate|genotype:WT|phenotype:WT|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of 24hpf Danio rerio WT,WT,WT,Expression profiling by high throughput sequencing,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP191202,,,WT_accepted_hits.bam,bam,4678276912.0,46627860.0,WT accepted hits.bam,0:100.33,A:1220754988;C:1121942916;G:1099337627;T:1236237181;N:4200,100,,,,1220754988,1121942916,1099337627,1236237181,4200,SRX5649486,SRS4594851,SRA870334,Creighton University|Biomedical Sciences,Creighton University,1,0.99199,,0.07435,,0.69587,,0.47078,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,United States,2019-04-06,Pharyngula,Embryo,Whole Organism,All anatomical structures
51813,SRR8862073,SRX5649485,SRS4594850,SRP191202,PRJNA531242,Zebrafish Otolith Biomineralization Requires Polyketide Synthase,PRJNA531242,Other,RNA seq analysis of nco no content zebrafish embryos at 24 hpf,,,,,nco mutant,,strain:AB|age:24hpf|sex:pooled male and female|tissue:Whole embryo lysate|genotype:nco|phenotype:otolith agenesis|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of 24hpf Danio rerio nco,nco,nco,Expression profiling by high throughput sequencing,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP191202,,,MUT_accepted_hits.bam,bam,4123578221.0,41065807.0,MUT accepted hits.bam,0:100.41,A:1067146358;C:996426621;G:980020305;T:1079981310;N:3627,100,,,,1067146358,996426621,980020305,1079981310,3627,SRX5649485,SRS4594850,SRA870334,Creighton University|Biomedical Sciences,Creighton University,1,0.9923,,0.06787,,0.69901,,0.46967,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,United States,2019-04-06,Pharyngula,Embryo,Whole Organism,All anatomical structures
53390,SRR9849853,SRX6604475,SRS5169415,SRP216580,PRJNA556992,Global identification of circular RNAs during zebrafish embryogenesis,PRJNA556992,Other,Fertilization and embryo development guarantee the activation of totipotent zygote and tissues formation. Over past few yrs  thousands of circRNAs have been identified in various animals representing a ubiquitous set of non coding RNA and conserved mechanism as essential biological functions. We sequenced RNA time series of stages with RNase R treated approach during zebrafish development in the present.,,,,,40h,,cultivar:Danio rerio|age:40hpf stage:pharyngula|sex:not determined|tissue:not applicable|BioSampleModel:Model organism or animal,,,,,,,,,circRNA 40h 2,40h 2,40h 2,circRNA sequence using embryo from zebrafish 40 hpf,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP216580,,,40h-1_Clean_1.fq.gz 40h-1_Clean_2.fq.gz,fastq fastq,13039776756.0,43496055.0,40h 1 Clean 1.fq.gz,0:149.90 1:149.90,A:3288491359;C:3163780126;G:3276849759;T:3309186789;N:1468723,149,149,,,3288491359,3163780126,3276849759,3309186789,1468723,SRX6604475,SRS5169415,SRA927972,Guangxi Academy of Fishery Sciences|Guangxi Academy of Fishery Sciences,Guangxi Academy of Fishery Sciences,2,0.7816,0.78295,0.30782,0.30455,0.81148,0.82091,0.45266,0.46863,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2019-07-27,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
53393,SRR9849856,SRX6604472,SRS5169415,SRP216580,PRJNA556992,Global identification of circular RNAs during zebrafish embryogenesis,PRJNA556992,Other,Fertilization and embryo development guarantee the activation of totipotent zygote and tissues formation. Over past few yrs  thousands of circRNAs have been identified in various animals representing a ubiquitous set of non coding RNA and conserved mechanism as essential biological functions. We sequenced RNA time series of stages with RNase R treated approach during zebrafish development in the present.,,,,,40h,,cultivar:Danio rerio|age:40hpf stage:pharyngula|sex:not determined|tissue:not applicable|BioSampleModel:Model organism or animal,,,,,,,,,circRNA 40h 1,40h 1,40h 1,circRNA sequence using embryo from zebrafish 40 hpf,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP216580,,,BN2-435_L4_7005.R1.clean.fastq.gz BN2-435_L4_7005.R2.clean.fastq.gz,fastq fastq,7253248500.0,24177495.0,BN2 435 L4 7005.R1.clean.fastq.gz,0:150 1:150,A:1410890545;C:2084999879;G:2163487041;T:1593413760;N:457275,150,150,,,1410890545,2084999879,2163487041,1593413760,457275,SRX6604472,SRS5169415,SRA927972,Guangxi Academy of Fishery Sciences|Guangxi Academy of Fishery Sciences,Guangxi Academy of Fishery Sciences,2,0.87864,0.86461,0.70089,0.69415,0.94899,0.95221,0.45413,0.48608,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2019-07-27,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
55846,SRR10862988,SRX7533081,SRS5972268,SRP241074,PRJNA597223,Danio rerio primordial germ cell expression pofiling,PRJNA597223,Whole Genome Sequencing,Primordial germ cells PGCs are the precursors of germ cells  which migrate to the genital ridge during early development. Relatively little is known about PGCs post their migration. We studied this post migratory stage using microscopy and sequencing techniques. We found that many PGC specific genes  including genes known to induce PGC fate in the mouse  are only activated several days post migration. At this same timepoint  PGC nuclei become extremely gyrated  displaying general opening of chromatin and high levels of transcription. This is accompanied by changes in nuage morphology and expression of large loci  named PERLs  enriched for retro transposons and piRNAs. piRNA biogenesis signatures rise in this same period. Interestingly  no nuclear Piwi protein could be detected  indicating that the zebrafish piRNA pathway is fully cytoplasmic. Our data show that the post migratory stage of zebrafish PGCs holds many cues to both germ cell fate establishment and piRNA pathway activation.,,,The vasa:eGFP line Krøvel and Olsen  2002 was used to FACS sort PGCs at different timepoints. Embryos were collected and incubated with TrypLETM Express for 40 to 70 minutes  killed on ice and gently pippeted up and down with a glass pipet and/or a 200µl low retention pipet tip. post visual inspection  cell suspension was separated from trunks using a 100 µm siev. Following another 5 15 minutes of digestion  FCS was added to 10% of total volume. Cells were spun down at 500g for 5min at RT  washed with PBS  resuspended in PBS with 2% FCS  put on Ice and immediately subjected to FACS using a 85µm nozzle on a BD FACSAria III SORP Becton Dickinson. 1000 to 2500 cells were sorted directly into Trizol. RNA from sorted PGCs and whole embryos was extracted with Trizol and stored in MQ at  80°C until library preparation was done.,,wt PGCs 1dpf rep3,,strain:vasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:1dpf|dev stage:Pharyngula period|sex:not applicable|tissue:germline|biological replicate:replicate 3|BioSampleModel:Model organism or animal,,,,,,,,,totalRNA of Zebrafish: PGCs 1dpf,wt PGCs 1dpf rep3 totalRNA,wt PGCs 1dpf rep3 totalRNA,NGS library prep was performed with NuGen Ovation SoLo RNA Seq System following NuGen`s standard protocol M01406v2. Libraries were prepared with a starting amount of 1 ng and amplified in 14 PCR cycles. Libraries were profiled in a High Sensitivity DNA on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit  in a Qubit 2.0 Fluorometer Life technologies. Samples were pooled in equimolar ratio and sequenced PE for 2x 75 cycles plus 16 cycles for the index read. Small RNA sequencing,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,NextSeq 550,,SRP241074,,,09072018-wt_PGCs_1dpf_rep3_totalRNA.R1.fastq.gz 14022018-wt_PGCs_1dpf_rep3_totalRNA.R2.fastq.gz 14022018-wt_PGCs_1dpf_rep3_totalRNA.R1.fastq.gz 09072018-wt_PGCs_1dpf_rep3_totalRNA.R2.fastq.gz,fastq fastq fastq fastq,3082887936.0,21408944.0,09072018 wt PGCs 1dpf rep3 totalRNA.R1.fastq.gz,0:72 1:72,A:855717326;C:671894681;G:694821062;T:859704799;N:750068,72,72,,,855717326,671894681,694821062,859704799,750068,SRX7533081,SRS5972268,SRA1023320,Rene Ketting group|Ketting Lab,Rene Ketting group,2,0.91419,0.90389,0.26055,0.25953,0.68331,0.68968,0.69151,0.69054,72,72,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,bulk,unknown,unknown,,Germany,2020-01-10,Pharyngula,Embryo,Whole Organism,All anatomical structures
55847,SRR10862989,SRX7533080,SRS5972267,SRP241074,PRJNA597223,Danio rerio primordial germ cell expression pofiling,PRJNA597223,Whole Genome Sequencing,Primordial germ cells PGCs are the precursors of germ cells  which migrate to the genital ridge during early development. Relatively little is known about PGCs post their migration. We studied this post migratory stage using microscopy and sequencing techniques. We found that many PGC specific genes  including genes known to induce PGC fate in the mouse  are only activated several days post migration. At this same timepoint  PGC nuclei become extremely gyrated  displaying general opening of chromatin and high levels of transcription. This is accompanied by changes in nuage morphology and expression of large loci  named PERLs  enriched for retro transposons and piRNAs. piRNA biogenesis signatures rise in this same period. Interestingly  no nuclear Piwi protein could be detected  indicating that the zebrafish piRNA pathway is fully cytoplasmic. Our data show that the post migratory stage of zebrafish PGCs holds many cues to both germ cell fate establishment and piRNA pathway activation.,,,The vasa:eGFP line Krøvel and Olsen  2002 was used to FACS sort PGCs at different timepoints. Embryos were collected and incubated with TrypLETM Express for 40 to 70 minutes  killed on ice and gently pippeted up and down with a glass pipet and/or a 200µl low retention pipet tip. post visual inspection  cell suspension was separated from trunks using a 100 µm siev. Following another 5 15 minutes of digestion  FCS was added to 10% of total volume. Cells were spun down at 500g for 5min at RT  washed with PBS  resuspended in PBS with 2% FCS  put on Ice and immediately subjected to FACS using a 85µm nozzle on a BD FACSAria III SORP Becton Dickinson. 1000 to 2500 cells were sorted directly into Trizol. RNA from sorted PGCs and whole embryos was extracted with Trizol and stored in MQ at  80°C until library preparation was done.,,wt PGCs 1dpf rep2,,strain:vasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:1dpf|dev stage:Pharyngula period|sex:not applicable|tissue:germline|biological replicate:replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,totalRNA of Zebrafish: PGCs 1dpf,wt PGCs 1dpf rep2 totalRNA,wt PGCs 1dpf rep2 totalRNA,NGS library prep was performed with NuGen Ovation SoLo RNA Seq System following NuGen`s standard protocol M01406v2. Libraries were prepared with a starting amount of 1 ng and amplified in 14 PCR cycles. Libraries were profiled in a High Sensitivity DNA on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit  in a Qubit 2.0 Fluorometer Life technologies. Samples were pooled in equimolar ratio and sequenced PE for 2x 75 cycles plus 16 cycles for the index read. Small RNA sequencing,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,NextSeq 550,,SRP241074,,,29032017-wt_PGCs_1dpf_rep2_totalRNA.R2.fastq.gz 29032017-wt_PGCs_1dpf_rep2_totalRNA.R1.fastq.gz 14022018-wt_PGCs_1dpf_rep2_totalRNA.R2.fastq.gz 14022018-wt_PGCs_1dpf_rep2_totalRNA.R1.fastq.gz 09072018-wt_PGCs_1dpf_rep2_totalRNA.R2.fastq.gz 09072018-wt_PGCs_1dpf_rep2_totalRNA.R1.fastq.gz,fastq fastq fastq fastq fastq fastq,6561306720.0,45564630.0,09072018 wt PGCs 1dpf rep2 totalRNA.R1.fastq.gz,0:72 1:72,A:1861196009;C:1391214649;G:1438814631;T:1867812823;N:2268608,72,72,,,1861196009,1391214649,1438814631,1867812823,2268608,SRX7533080,SRS5972267,SRA1023320,Rene Ketting group|Ketting Lab,Rene Ketting group,2,0.8998,0.89346,0.31823,0.31875,0.67752,0.68629,0.65395,0.65402,72,72,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,bulk,unknown,unknown,,Germany,2020-01-10,Pharyngula,Embryo,Whole Organism,All anatomical structures
55848,SRR10862990,SRX7533079,SRS5972265,SRP241074,PRJNA597223,Danio rerio primordial germ cell expression pofiling,PRJNA597223,Whole Genome Sequencing,Primordial germ cells PGCs are the precursors of germ cells  which migrate to the genital ridge during early development. Relatively little is known about PGCs post their migration. We studied this post migratory stage using microscopy and sequencing techniques. We found that many PGC specific genes  including genes known to induce PGC fate in the mouse  are only activated several days post migration. At this same timepoint  PGC nuclei become extremely gyrated  displaying general opening of chromatin and high levels of transcription. This is accompanied by changes in nuage morphology and expression of large loci  named PERLs  enriched for retro transposons and piRNAs. piRNA biogenesis signatures rise in this same period. Interestingly  no nuclear Piwi protein could be detected  indicating that the zebrafish piRNA pathway is fully cytoplasmic. Our data show that the post migratory stage of zebrafish PGCs holds many cues to both germ cell fate establishment and piRNA pathway activation.,,,The vasa:eGFP line Krøvel and Olsen  2002 was used to FACS sort PGCs at different timepoints. Embryos were collected and incubated with TrypLETM Express for 40 to 70 minutes  killed on ice and gently pippeted up and down with a glass pipet and/or a 200µl low retention pipet tip. post visual inspection  cell suspension was separated from trunks using a 100 µm siev. Following another 5 15 minutes of digestion  FCS was added to 10% of total volume. Cells were spun down at 500g for 5min at RT  washed with PBS  resuspended in PBS with 2% FCS  put on Ice and immediately subjected to FACS using a 85µm nozzle on a BD FACSAria III SORP Becton Dickinson. 1000 to 2500 cells were sorted directly into Trizol. RNA from sorted PGCs and whole embryos was extracted with Trizol and stored in MQ at  80°C until library preparation was done.,,wt PGCs 1dpf rep1,,strain:vasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:1dpf|dev stage:Pharyngula period|sex:not applicable|tissue:germline|biological replicate:replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,totalRNA of Zebrafish: PGCs 1dpf,wt PGCs 1dpf rep1 totalRNA,wt PGCs 1dpf rep1 totalRNA,NGS library prep was performed with NuGen Ovation SoLo RNA Seq System following NuGen`s standard protocol M01406v2. Libraries were prepared with a starting amount of 1 ng and amplified in 14 PCR cycles. Libraries were profiled in a High Sensitivity DNA on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit  in a Qubit 2.0 Fluorometer Life technologies. Samples were pooled in equimolar ratio and sequenced PE for 2x 75 cycles plus 16 cycles for the index read. Small RNA sequencing,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,NextSeq 550,,SRP241074,,,29032017-wt_PGCs_1dpf_rep1_totalRNA.R2.fastq.gz 29032017-wt_PGCs_1dpf_rep1_totalRNA.R1.fastq.gz 14022018-wt_PGCs_1dpf_rep1_totalRNA.R2.fastq.gz 14022018-wt_PGCs_1dpf_rep1_totalRNA.R1.fastq.gz 09072018-wt_PGCs_1dpf_rep1_totalRNA.R2.fastq.gz 09072018-wt_PGCs_1dpf_rep1_totalRNA.R1.fastq.gz,fastq fastq fastq fastq fastq fastq,6485869872.0,45040763.0,09072018 wt PGCs 1dpf rep1 totalRNA.R1.fastq.gz,0:72 1:72,A:1841554858;C:1374245433;G:1421963334;T:1845879023;N:2227224,72,72,,,1841554858,1374245433,1421963334,1845879023,2227224,SRX7533079,SRS5972265,SRA1023320,Rene Ketting group|Ketting Lab,Rene Ketting group,2,0.90135,0.89658,0.31596,0.31688,0.67969,0.68523,0.65921,0.55484,72,72,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,bulk,unknown,unknown,,Germany,2020-01-10,Pharyngula,Embryo,Whole Organism,All anatomical structures
55858,SRR10862999,SRX7533069,SRS5972257,SRP241074,PRJNA597223,Danio rerio primordial germ cell expression pofiling,PRJNA597223,Whole Genome Sequencing,Primordial germ cells PGCs are the precursors of germ cells  which migrate to the genital ridge during early development. Relatively little is known about PGCs post their migration. We studied this post migratory stage using microscopy and sequencing techniques. We found that many PGC specific genes  including genes known to induce PGC fate in the mouse  are only activated several days post migration. At this same timepoint  PGC nuclei become extremely gyrated  displaying general opening of chromatin and high levels of transcription. This is accompanied by changes in nuage morphology and expression of large loci  named PERLs  enriched for retro transposons and piRNAs. piRNA biogenesis signatures rise in this same period. Interestingly  no nuclear Piwi protein could be detected  indicating that the zebrafish piRNA pathway is fully cytoplasmic. Our data show that the post migratory stage of zebrafish PGCs holds many cues to both germ cell fate establishment and piRNA pathway activation.,,,The vasa:eGFP line Krøvel and Olsen  2002 was used to FACS sort PGCs at different timepoints. Embryos were collected and incubated with TrypLETM Express for 40 to 70 minutes  killed on ice and gently pippeted up and down with a glass pipet and/or a 200µl low retention pipet tip. post visual inspection  cell suspension was separated from trunks using a 100 µm siev. Following another 5 15 minutes of digestion  FCS was added to 10% of total volume. Cells were spun down at 500g for 5min at RT  washed with PBS  resuspended in PBS with 2% FCS  put on Ice and immediately subjected to FACS using a 85µm nozzle on a BD FACSAria III SORP Becton Dickinson. 1000 to 2500 cells were sorted directly into Trizol. RNA from sorted PGCs and whole embryos was extracted with Trizol and stored in MQ at  80°C until library preparation was done.,,wt Fish 1dpf rep2,,strain:vasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:1dpf|dev stage:Pharyngula period|sex:not applicable|tissue:whole embryo|biological replicate:replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,totalRNA of Zebrafish: Fish 1dpf,wt Fish 1dpf rep2 totalRNA,wt Fish 1dpf rep2 totalRNA,NGS library prep was performed with NuGen Ovation SoLo RNA Seq System following NuGen`s standard protocol M01406v2. Libraries were prepared with a starting amount of 1 ng and amplified in 14 PCR cycles. Libraries were profiled in a High Sensitivity DNA on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit  in a Qubit 2.0 Fluorometer Life technologies. Samples were pooled in equimolar ratio and sequenced PE for 2x 75 cycles plus 16 cycles for the index read. Small RNA sequencing,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,NextSeq 550,,SRP241074,,,14022018-wt_Fish_1dpf_rep2_totalRNA.R1.fastq.gz 14022018-wt_Fish_1dpf_rep2_totalRNA.R2.fastq.gz,fastq fastq,2343087648.0,16271442.0,14022018 wt Fish 1dpf rep2 totalRNA.R1.fastq.gz,0:72 1:72,A:662555166;C:497989417;G:513684948;T:668079451;N:778666,72,72,,,662555166,497989417,513684948,668079451,778666,SRX7533069,SRS5972257,SRA1023320,Rene Ketting group|Ketting Lab,Rene Ketting group,2,0.89129,0.88116,0.31577,0.31548,0.73018,0.7374,0.61911,0.61959,72,72,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,bulk,unknown,unknown,,Germany,2020-01-10,Pharyngula,Embryo,Whole Organism,All anatomical structures
55859,SRR10863000,SRX7533068,SRS5972256,SRP241074,PRJNA597223,Danio rerio primordial germ cell expression pofiling,PRJNA597223,Whole Genome Sequencing,Primordial germ cells PGCs are the precursors of germ cells  which migrate to the genital ridge during early development. Relatively little is known about PGCs post their migration. We studied this post migratory stage using microscopy and sequencing techniques. We found that many PGC specific genes  including genes known to induce PGC fate in the mouse  are only activated several days post migration. At this same timepoint  PGC nuclei become extremely gyrated  displaying general opening of chromatin and high levels of transcription. This is accompanied by changes in nuage morphology and expression of large loci  named PERLs  enriched for retro transposons and piRNAs. piRNA biogenesis signatures rise in this same period. Interestingly  no nuclear Piwi protein could be detected  indicating that the zebrafish piRNA pathway is fully cytoplasmic. Our data show that the post migratory stage of zebrafish PGCs holds many cues to both germ cell fate establishment and piRNA pathway activation.,,,The vasa:eGFP line Krøvel and Olsen  2002 was used to FACS sort PGCs at different timepoints. Embryos were collected and incubated with TrypLETM Express for 40 to 70 minutes  killed on ice and gently pippeted up and down with a glass pipet and/or a 200µl low retention pipet tip. post visual inspection  cell suspension was separated from trunks using a 100 µm siev. Following another 5 15 minutes of digestion  FCS was added to 10% of total volume. Cells were spun down at 500g for 5min at RT  washed with PBS  resuspended in PBS with 2% FCS  put on Ice and immediately subjected to FACS using a 85µm nozzle on a BD FACSAria III SORP Becton Dickinson. 1000 to 2500 cells were sorted directly into Trizol. RNA from sorted PGCs and whole embryos was extracted with Trizol and stored in MQ at  80°C until library preparation was done.,,wt Fish 1dpf rep1,,strain:vasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:1dpf|dev stage:Pharyngula period|sex:not applicable|tissue:whole embryo|biological replicate:replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,totalRNA of Zebrafish: Fish 1dpf,wt Fish 1dpf rep1 totalRNA,wt Fish 1dpf rep1 totalRNA,NGS library prep was performed with NuGen Ovation SoLo RNA Seq System following NuGen`s standard protocol M01406v2. Libraries were prepared with a starting amount of 1 ng and amplified in 14 PCR cycles. Libraries were profiled in a High Sensitivity DNA on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit  in a Qubit 2.0 Fluorometer Life technologies. Samples were pooled in equimolar ratio and sequenced PE for 2x 75 cycles plus 16 cycles for the index read. Small RNA sequencing,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,NextSeq 550,,SRP241074,,,14022018-wt_Fish_1dpf_rep1_totalRNA.R1.fastq.gz 14022018-wt_Fish_1dpf_rep1_totalRNA.R2.fastq.gz,fastq fastq,2254756752.0,15658033.0,14022018 wt Fish 1dpf rep1 totalRNA.R1.fastq.gz,0:72 1:72,A:641405677;C:476851816;G:490910356;T:644833255;N:755648,72,72,,,641405677,476851816,490910356,644833255,755648,SRX7533068,SRS5972256,SRA1023320,Rene Ketting group|Ketting Lab,Rene Ketting group,2,0.90882,0.8984,0.32945,0.3281,0.72411,0.72985,0.61805,0.60813,72,72,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,bulk,unknown,unknown,,Germany,2020-01-10,Pharyngula,Embryo,Whole Organism,All anatomical structures
69472,SRR18712321,SRX14812930,SRS12569573,SRP369458,PRJNA825495,Regulation of retina microexons by srrm3 in zebrafish,PRJNA825495,Other,To investigate the role of srrm3 as a regulator of retina microexons RetMICs we have sequenced heads from WT animals at 24 hpf and enucleated eyes from 48 hpf  60 hpf  and 72 hpf larvae WT and KO for srrm3.,,,,,Head 24hpf WT b,,strain:WT|dev stage:24 hpf|sex:NA|tissue:Head|BioSampleModel:Model organism or animal,,,,,,,,,Heads from 24 hpf larvae WT for the eMIC domain of srrm3.,Head 24hpf WT,Head 24hpf WT,WT and srrm3 mutant zebrafish were grown at  28C 14h light/10h dark cycle. Extract protocol: 24 hpf WT fish heads were removed and pulled for RNA extraction using RNA RNeasy Mini kit QIAGEN. Larvae eyes were removed and from twenty to sixty eyes per genotype were pulled for RNA extraction using RNA RNeasy Micro kit QIAGENLibrary preparation: RNA libraries were prepared for sequencing using standard Illumina protocols; polyA selected stranded RNA seq,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP369458,,,Head_24hpf_WT_b_R1-125.fq.gz Head_24hpf_WT_b_R2-125.fq.gz,fastq fastq,16050157000.0,64200628.0,Head 24hpf WT b R1 125.fq.gz,0:125 1:125,A:4076433263;C:3955246853;G:3964617037;T:4044497256;N:9362591,125,125,,,4076433263,3955246853,3964617037,4044497256,9362591,SRX14812930,SRS12569573,SRA1402039,Centre for Genomic Regulation|Systems Biology,Centre for Genomic Regulation|Systems Biology,2,0.97774,0.97918,0.03623,0.03592,0.71035,0.71474,0.46304,0.46994,125,125,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,Spain,2022-04-11,Pharyngula,Embryo,Head,Nervous System