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203 rows where experiment.library_layout = "SINGLE", experiment.library_selection = "RANDOM" and experiment.library_source = "TRANSCRIPTOMIC"

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tissue_curation >10

devstage_curation >10

devstage_curation_coarse 6

experiment.platform 5

experiment.library_strategy 3

technology 2

experiment.library_source 1

  • TRANSCRIPTOMIC · 203 ✖

experiment.library_selection 1

  • RANDOM · 203 ✖

experiment.library_layout 1

  • SINGLE · 203 ✖
Link rowid ▼ run.accession experiment.accession sample.accession study.accession bioproject study.title study.alias study.type study.abstract study.attributes study.PMIDs sample.description sample.title sample.alias sample.centername sample.attributes 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
32 32 DRR408242 DRX393848 DRS407006 DRP012035 PRJDB14274 Zebrafish Gut RNA seq. DRP012035 Transcriptome Analysis A project to find differential expressed genes between larval and adult zebrafish gut. We dissected guts of wild type AB line and prepared three duplicates for each of larval and adult gut. Libraries for NGS are prepared using illumina TruSeq standard mRNA sample prep kit.     zebrafish wild type AB adult gut replicate 3 zebrafish adult gut replicate 3 SAMD00529462   sample name:zebrafish adult gut replicate 3|biological replicate:adult 3|strain:AB                 Illumina HiSeq 1500 sequencing of SAMD00529462 DRX393848 AR019 gut 6 adult 1 1   RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 1500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>126</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> DRP012035 Illumina HiSeq 1500 sequencing of SAMD00529462       3546347364.0 28145614.0 DRR408242 0:126 1:0 A:919466631;C:829424335;G:818581155;T:978810217;N:65026 126 0     919466631 829424335 818581155 978810217 65026 DRX393848 DRS407006 DRA014885 NIBB|NIBB core research facilities, National Institute for Basic Biology University of Hyogo                       B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   Japan 2024-09-20 Adult Adult Gut Digestive System
33 33 DRR408241 DRX393847 DRS407005 DRP012035 PRJDB14274 Zebrafish Gut RNA seq. DRP012035 Transcriptome Analysis A project to find differential expressed genes between larval and adult zebrafish gut. We dissected guts of wild type AB line and prepared three duplicates for each of larval and adult gut. Libraries for NGS are prepared using illumina TruSeq standard mRNA sample prep kit.     zebrafish wild type AB adult gut replicate 2 zebrafish adult gut replicate 2 SAMD00529461   sample name:zebrafish adult gut replicate 2|biological replicate:adult 2|strain:AB                 Illumina HiSeq 1500 sequencing of SAMD00529461 DRX393847 AR006 gut 4 adult 1 1   RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 1500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>126</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> DRP012035 Illumina HiSeq 1500 sequencing of SAMD00529461       3671973648.0 29142648.0 DRR408241 0:126 1:0 A:942167543;C:859431290;G:852661772;T:1017643011;N:70032 126 0     942167543 859431290 852661772 1017643011 70032 DRX393847 DRS407005 DRA014885 NIBB|NIBB core research facilities, National Institute for Basic Biology University of Hyogo                       B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   Japan 2024-09-20 Adult Adult Gut Digestive System
34 34 DRR408240 DRX393846 DRS407004 DRP012035 PRJDB14274 Zebrafish Gut RNA seq. DRP012035 Transcriptome Analysis A project to find differential expressed genes between larval and adult zebrafish gut. We dissected guts of wild type AB line and prepared three duplicates for each of larval and adult gut. Libraries for NGS are prepared using illumina TruSeq standard mRNA sample prep kit.     zebrafish wild type AB adult gut replicate 1 zebrafish adult gut replicate 1 SAMD00529460   sample name:zebrafish adult gut replicate 1|biological replicate:adult 1|strain:AB                 Illumina HiSeq 1500 sequencing of SAMD00529460 DRX393846 AR004 gut 2 adult 1 1   RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 1500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>126</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> DRP012035 Illumina HiSeq 1500 sequencing of SAMD00529460       3480523704.0 27623204.0 DRR408240 0:126 1:0 A:898051986;C:827557593;G:816541244;T:938307607;N:65274 126 0     898051986 827557593 816541244 938307607 65274 DRX393846 DRS407004 DRA014885 NIBB|NIBB core research facilities, National Institute for Basic Biology University of Hyogo                       B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   Japan 2024-09-20 Adult Adult Gut Digestive System
35 35 DRR408239 DRX393845 DRS407003 DRP012035 PRJDB14274 Zebrafish Gut RNA seq. DRP012035 Transcriptome Analysis A project to find differential expressed genes between larval and adult zebrafish gut. We dissected guts of wild type AB line and prepared three duplicates for each of larval and adult gut. Libraries for NGS are prepared using illumina TruSeq standard mRNA sample prep kit.     zebrafish wild type AB larval gut replicate 3 zebrafish larval gut replicate 3 SAMD00529459   sample name:zebrafish larval gut replicate 3|biological replicate:larval 3|strain:AB                 Illumina HiSeq 1500 sequencing of SAMD00529459 DRX393845 AR012 gut 5 5 dpf 6 dpf larvae 1 1   RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 1500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>126</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> DRP012035 Illumina HiSeq 1500 sequencing of SAMD00529459       3463982046.0 27491921.0 DRR408239 0:126 1:0 A:842552557;C:849757648;G:837664725;T:933942026;N:65090 126 0     842552557 849757648 837664725 933942026 65090 DRX393845 DRS407003 DRA014885 NIBB|NIBB core research facilities, National Institute for Basic Biology University of Hyogo                       B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   Japan 2024-09-20 Larval Larval Gut Digestive System
36 36 DRR408238 DRX393844 DRS407002 DRP012035 PRJDB14274 Zebrafish Gut RNA seq. DRP012035 Transcriptome Analysis A project to find differential expressed genes between larval and adult zebrafish gut. We dissected guts of wild type AB line and prepared three duplicates for each of larval and adult gut. Libraries for NGS are prepared using illumina TruSeq standard mRNA sample prep kit.     zebrafish wild type AB larval gut replicate 2 zebrafish larval gut replicate 2 SAMD00529458   sample name:zebrafish larval gut replicate 2|biological replicate:larval 2|strain:AB                 Illumina HiSeq 1500 sequencing of SAMD00529458 DRX393844 AR005 gut 3 5 dpf 6 dpf larvae 1 1   RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 1500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>126</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> DRP012035 Illumina HiSeq 1500 sequencing of SAMD00529458       3782320416.0 30018416.0 DRR408238 0:126 1:0 A:930337206;C:920645770;G:906559955;T:1024704277;N:73208 126 0     930337206 920645770 906559955 1024704277 73208 DRX393844 DRS407002 DRA014885 NIBB|NIBB core research facilities, National Institute for Basic Biology University of Hyogo                       B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   Japan 2024-09-20 Larval Larval Gut Digestive System
37 37 DRR408237 DRX393843 DRS407001 DRP012035 PRJDB14274 Zebrafish Gut RNA seq. DRP012035 Transcriptome Analysis A project to find differential expressed genes between larval and adult zebrafish gut. We dissected guts of wild type AB line and prepared three duplicates for each of larval and adult gut. Libraries for NGS are prepared using illumina TruSeq standard mRNA sample prep kit.     zebrafish wild type AB larval gut replicate 1 zebrafish larval gut replicate 1 SAMD00529457   sample name:zebrafish larval gut replicate 1|biological replicate:larval 1|strain:AB                 Illumina HiSeq 1500 sequencing of SAMD00529457 DRX393843 AR002 gut 1 5 dpf 6 dpf larvae 1 1   RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 1500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>126</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> DRP012035 Illumina HiSeq 1500 sequencing of SAMD00529457       3606885828.0 28626078.0 DRR408237 0:126 1:0 A:879148446;C:885673723;G:870330963;T:971663212;N:69484 126 0     879148446 885673723 870330963 971663212 69484 DRX393843 DRS407001 DRA014885 NIBB|NIBB core research facilities, National Institute for Basic Biology University of Hyogo                       B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   Japan 2024-09-20 Larval Larval Gut Digestive System
5795 5795 ERR1698352 ERX1767860 ERS1417534 ERP018188 PRJEB16335 RNA seq of the zebrafish danio rerio brain post developmental exposure to 17a ethinylestradiol E-MTAB-5173 Transcriptome Analysis 17a ethinylestradiol EE2 is a synthetic estrogen commonly used as an active substance in oral contraceptives. It is frequently found in waste water effluent and raise concern due to its persistent nature. EE2 binds to estrogen receptors with similar affinity to oestradiol and acts as one of the most potent hormone mimics found in the environment. Estrogen is involved in many aspects of the development of the neuroendocrine system influencing both brain structure and behavior. We and others have reported a significant effect on non reproductive behaviors in adult fish and in recent studies we found that developmental exposure to EE2 resulted in an anxiogenic phenotype as adults even post a long remediation period. In this study we aim to study possible mechanisms behind the behavior alterations of zebrafish developmentally exposed to EE2 by sequencing the whole brain transcriptome. Zebrafish embryos were exposed to 0 2.14 and 7.34 ng/L EE2 from 1 day to 80 dpf post the exposure period a remediation period of 120 days followed before the fish were sampled. 3 male brains from the control group 0 ng/L and the 2.14 ng/L group were sampled and 3 female brains from the control group 0 ng/L and 7.34 ng/L were sampled. ENA FIRST PUBLIC:2017 10 02|ENA LAST UPDATE:2016 10 19|ArrayExpress:E MTAB 5173   Protocols: RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich Germany EE2 exposure. Fish exposed to 0 2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA IonXpressRNA 012 up 058 12 SAMEA4518355 School of Natural Science, Technology and Environmental Studies Sodertorn University ENA first public:2017 10 02|ENA last update:2016 10 19|External Id:SAMEA4518355|INSDC center alias:School of Natural Science Technology and Environmental Studies Sodertorn University|INSDC center name:School of Natural Science Technology and Environmental Studies Sodertorn University|INSDC first public:2017 10 02T17:05:16Z|INSDC last update:2016 10 19T13:53:59Z|INSDC status:public|Submitter Id:E MTAB 5173:IonXpressRNA 012 up 058 12|age:200|broker name:ArrayExpress|common name:zebrafish|organism part:brain|sample name:E MTAB 5173:IonXpressRNA 012 up 058 12|sex:male                 Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol E MTAB 5173:IonXpressRNA 012 up 058 12 s IonXpressRNA 012 up 058 12 s RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich Germany EE2 exposure. Fish exposed to 0 2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA Experimental Factor: male:sex|Experimental Factor: 17 ethinylestradiol:compound|Experimental Factor: 2.14:dose RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ION_TORRENT Ion Torrent Proton   ERP018188 Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 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 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 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 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 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 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 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 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 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 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 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 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
8088 8088 ERR034127 ERX012653 ERS032268 ERP000635 PRJEB2512 The Zebrafish transcriptome during early development KI-BN-JKE-DRERIO-RNASEQ-2011 Transcriptome Analysis Background: Zebrafish Danio rerio is an important model for the study of early vertebrate development. The transition from fertilized egg to embryo is accompanied by a multitude of changes in gene expression and the transcriptional events that underlie these processes have not been fully characterized. In this study we use RNA Seq to characterize and compare the transcriptome of four early developmental stages in zebrafish on a global scale. Results: An average of 79M total reads were detected from the different stages. Out of the total number of reads 65% 73% reads were successfully mapped to the zebrafish genome and 36% 44% out of those were uniquely mapped. The total number of detected unique gene transcripts was 11187 of which 10096 of these were already present at 1 cell stage. The largest number of common transcripts was observed between 1 cell stage and 16 cell stage. An enrichment of gene transcripts with molecular functions of DNA binding protein folding and processing as well as metal ion binding was observed with progression of development. To confirm our RNA Seq results and to further investigate the developmental expression of specific genes the transcript levels of a subset of genes were analyzed using TaqMan® array micro fluidic card TLDA. Conclusion: Clustering analysis of the detected transcripts show a majority of gene transcripts being present at steady levels with a minority of the gene transcripts clustering as increasing or decreasing in expression during development. Developmental stages pre MBT were similar when comparing highly expressed genes whereas 50% epiboly stage differed from the earlier three stages in highly expressed genes number of uniquely expressed genes and enrichment of GO molecular functions.     RNA extracted from zebrafish embryo at 50% epiboly stage zebrafish embryo 50 epiboly SAMEA791629 Department of Biosciences and Nutrition, Karolinska Institutet, Sweden ENA first public:2011 06 09|ENA last update:2018 03 08|External Id:SAMEA791629|INSDC center alias:KI BN|INSDC center name:Department of Biosciences and Nutrition Karolinska Institutet Sweden|INSDC first public:2011 06 09T11:04:10Z|INSDC last update:2018 03 08T15:26:39Z|INSDC status:public|Submitter Id:KI BN JKE DRERIO RNASEQ 2011 50epiboly|common name:zebrafish|sample name:KI BN JKE DRERIO RNASEQ 2011 50epiboly|sex:mixed|strain:Tuebingen                 Transcriptome profiling of early zebrafish development KI BN JKE DRERIO RNASEQ 2011 50epiboly JKE Drerio rna seq Transcriptome profiling of 50% epiboly stages of zebrafish embryos. Total RNA was extracted from approximately 150 embryos per developmental stage using Trireagent Sigma Aldrich. The total RNA was then processed further according to the Small RNA Expression Kit Applied Biosystems.   RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ABI_SOLID AB SOLiD System 3.0 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP000635 AB SOLiD System 3.0 sequencing; Transcriptome profiling of early zebrafish development ENA FIRST PUBLIC:2011 06 09|ENA LAST UPDATE:2018 11 16 KI-BN-JKE-DRERIO-RNASEQ-2011-50epiboly.csfasta.gz KI-BN-JKE-DRERIO-RNASEQ-2011-50epiboly_QV.qual.gz SOLiD_native SOLiD_native 3929903550.0 78598071.0 KI BN JKE DRERIO RNASEQ 2011 50epiboly 0:50   50                 ERX012653 ERS032268 ERA029959 KI-BN|Department of Biosciences and Nutrition Department of Biosciences and Nutrition, Karolinska Institutet, Sweden 1 0.60757   0.09893   0.94899   0.77821   50   B   usable mapping rate legacy early unknown random_priming unknown bulk unknown unknown   Sweden 2011-06-09 Gastrula Embryo Embryo Imprecise All anatomical structures
8089 8089 ERR034126 ERX012652 ERS032267 ERP000635 PRJEB2512 The Zebrafish transcriptome during early development KI-BN-JKE-DRERIO-RNASEQ-2011 Transcriptome Analysis Background: Zebrafish Danio rerio is an important model for the study of early vertebrate development. The transition from fertilized egg to embryo is accompanied by a multitude of changes in gene expression and the transcriptional events that underlie these processes have not been fully characterized. In this study we use RNA Seq to characterize and compare the transcriptome of four early developmental stages in zebrafish on a global scale. Results: An average of 79M total reads were detected from the different stages. Out of the total number of reads 65% 73% reads were successfully mapped to the zebrafish genome and 36% 44% out of those were uniquely mapped. The total number of detected unique gene transcripts was 11187 of which 10096 of these were already present at 1 cell stage. The largest number of common transcripts was observed between 1 cell stage and 16 cell stage. An enrichment of gene transcripts with molecular functions of DNA binding protein folding and processing as well as metal ion binding was observed with progression of development. To confirm our RNA Seq results and to further investigate the developmental expression of specific genes the transcript levels of a subset of genes were analyzed using TaqMan® array micro fluidic card TLDA. Conclusion: Clustering analysis of the detected transcripts show a majority of gene transcripts being present at steady levels with a minority of the gene transcripts clustering as increasing or decreasing in expression during development. Developmental stages pre MBT were similar when comparing highly expressed genes whereas 50% epiboly stage differed from the earlier three stages in highly expressed genes number of uniquely expressed genes and enrichment of GO molecular functions.     RNA extracted from zebrafish embryo at 512 cell stage zebrafish embryo 512 cell SAMEA791632 Department of Biosciences and Nutrition, Karolinska Institutet, Sweden ENA first public:2011 06 09|ENA last update:2018 03 08|External Id:SAMEA791632|INSDC center alias:KI BN|INSDC center name:Department of Biosciences and Nutrition Karolinska Institutet Sweden|INSDC first public:2011 06 09T11:04:10Z|INSDC last update:2018 03 08T15:26:39Z|INSDC status:public|Submitter Id:KI BN JKE DRERIO RNASEQ 2011 512cell|common name:zebrafish|sample name:KI BN JKE DRERIO RNASEQ 2011 512cell|sex:mixed|strain:Tuebingen                 Transcriptome profiling of early zebrafish development KI BN JKE DRERIO RNASEQ 2011 512cell JKE Drerio rna seq Transcriptome profiling of 512 cell stage of zebrafish embryos. Total RNA was extracted from approximately 150 embryos per developmental stage using Trireagent Sigma Aldrich. The total RNA was then processed further according to the Small RNA Expression Kit Applied Biosystems.   RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ABI_SOLID AB SOLiD System 3.0 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP000635 AB SOLiD System 3.0 sequencing; Transcriptome profiling of early zebrafish development ENA FIRST PUBLIC:2011 06 09|ENA LAST UPDATE:2018 11 16 KI-BN-JKE-DRERIO-RNASEQ-2011-512cell.csfasta.gz KI-BN-JKE-DRERIO-RNASEQ-2011-512cell_QV.qual.gz SOLiD_native SOLiD_native 3918756250.0 78375125.0 KI BN JKE DRERIO RNASEQ 2011 512cell 0:50   50                 ERX012652 ERS032267 ERA029959 KI-BN|Department of Biosciences and Nutrition Department of Biosciences and Nutrition, Karolinska Institutet, Sweden 1 0.63824   0.09111   0.91969   0.73496   50   B   usable mapping rate legacy early unknown random_priming unknown bulk unknown unknown   Sweden 2011-06-09 Blastula Embryo Embryo Imprecise All anatomical structures
8090 8090 ERR034125 ERX012651 ERS032266 ERP000635 PRJEB2512 The Zebrafish transcriptome during early development KI-BN-JKE-DRERIO-RNASEQ-2011 Transcriptome Analysis Background: Zebrafish Danio rerio is an important model for the study of early vertebrate development. The transition from fertilized egg to embryo is accompanied by a multitude of changes in gene expression and the transcriptional events that underlie these processes have not been fully characterized. In this study we use RNA Seq to characterize and compare the transcriptome of four early developmental stages in zebrafish on a global scale. Results: An average of 79M total reads were detected from the different stages. Out of the total number of reads 65% 73% reads were successfully mapped to the zebrafish genome and 36% 44% out of those were uniquely mapped. The total number of detected unique gene transcripts was 11187 of which 10096 of these were already present at 1 cell stage. The largest number of common transcripts was observed between 1 cell stage and 16 cell stage. An enrichment of gene transcripts with molecular functions of DNA binding protein folding and processing as well as metal ion binding was observed with progression of development. To confirm our RNA Seq results and to further investigate the developmental expression of specific genes the transcript levels of a subset of genes were analyzed using TaqMan® array micro fluidic card TLDA. Conclusion: Clustering analysis of the detected transcripts show a majority of gene transcripts being present at steady levels with a minority of the gene transcripts clustering as increasing or decreasing in expression during development. Developmental stages pre MBT were similar when comparing highly expressed genes whereas 50% epiboly stage differed from the earlier three stages in highly expressed genes number of uniquely expressed genes and enrichment of GO molecular functions.     RNA extracted from zebrafish embryo at 16 cell stage zebrafish embryo 16 cell SAMEA791631 Department of Biosciences and Nutrition, Karolinska Institutet, Sweden ENA first public:2011 06 09|ENA last update:2018 03 08|External Id:SAMEA791631|INSDC center alias:KI BN|INSDC center name:Department of Biosciences and Nutrition Karolinska Institutet Sweden|INSDC first public:2011 06 09T11:04:10Z|INSDC last update:2018 03 08T15:26:39Z|INSDC status:public|Submitter Id:KI BN JKE DRERIO RNASEQ 2011 16cell|common name:zebrafish|sample name:KI BN JKE DRERIO RNASEQ 2011 16cell|sex:mixed|strain:Tuebingen                 Transcriptome profiling of early zebrafish development KI BN JKE DRERIO RNASEQ 2011 16cell JKE Drerio rna seq Transcriptome profiling of 16 cell stage of zebrafish embryos. Total RNA was extracted from approximately 150 embryos per developmental stage using Trireagent Sigma Aldrich. The total RNA was then processed further according to the Small RNA Expression Kit Applied Biosystems.   RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ABI_SOLID AB SOLiD System 3.0 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP000635 AB SOLiD System 3.0 sequencing; Transcriptome profiling of early zebrafish development ENA FIRST PUBLIC:2011 06 09|ENA LAST UPDATE:2018 11 16 KI-BN-JKE-DRERIO-RNASEQ-2011-16cell.csfasta.gz KI-BN-JKE-DRERIO-RNASEQ-2011-16cell_QV.qual.gz SOLiD_native SOLiD_native 4256756500.0 85135130.0 KI BN JKE DRERIO RNASEQ 2011 16cell 0:50   50                 ERX012651 ERS032266 ERA029959 KI-BN|Department of Biosciences and Nutrition Department of Biosciences and Nutrition, Karolinska Institutet, Sweden 1 0.57946   0.08115   0.91896   0.72164   50   B   usable mapping rate legacy early unknown random_priming unknown bulk unknown unknown   Sweden 2011-06-09 Cleavage Embryo Embryo Imprecise All anatomical structures
8091 8091 ERR034124 ERX012650 ERS032265 ERP000635 PRJEB2512 The Zebrafish transcriptome during early development KI-BN-JKE-DRERIO-RNASEQ-2011 Transcriptome Analysis Background: Zebrafish Danio rerio is an important model for the study of early vertebrate development. The transition from fertilized egg to embryo is accompanied by a multitude of changes in gene expression and the transcriptional events that underlie these processes have not been fully characterized. In this study we use RNA Seq to characterize and compare the transcriptome of four early developmental stages in zebrafish on a global scale. Results: An average of 79M total reads were detected from the different stages. Out of the total number of reads 65% 73% reads were successfully mapped to the zebrafish genome and 36% 44% out of those were uniquely mapped. The total number of detected unique gene transcripts was 11187 of which 10096 of these were already present at 1 cell stage. The largest number of common transcripts was observed between 1 cell stage and 16 cell stage. An enrichment of gene transcripts with molecular functions of DNA binding protein folding and processing as well as metal ion binding was observed with progression of development. To confirm our RNA Seq results and to further investigate the developmental expression of specific genes the transcript levels of a subset of genes were analyzed using TaqMan® array micro fluidic card TLDA. Conclusion: Clustering analysis of the detected transcripts show a majority of gene transcripts being present at steady levels with a minority of the gene transcripts clustering as increasing or decreasing in expression during development. Developmental stages pre MBT were similar when comparing highly expressed genes whereas 50% epiboly stage differed from the earlier three stages in highly expressed genes number of uniquely expressed genes and enrichment of GO molecular functions.     RNA extracted from zebrafish embryo at 1 cell stage zebrafish embryo 1 cell SAMEA791630 Department of Biosciences and Nutrition, Karolinska Institutet, Sweden ENA first public:2011 06 09|ENA last update:2018 03 08|External Id:SAMEA791630|INSDC center alias:KI BN|INSDC center name:Department of Biosciences and Nutrition Karolinska Institutet Sweden|INSDC first public:2011 06 09T11:04:10Z|INSDC last update:2018 03 08T15:26:39Z|INSDC status:public|Submitter Id:KI BN JKE DRERIO RNASEQ 2011 1cell|common name:zebrafish|sample name:KI BN JKE DRERIO RNASEQ 2011 1cell|sex:mixed|strain:Tuebingen                 Transcriptome profiling of early zebrafish development KI BN JKE DRERIO RNASEQ 2011 1cell JKE Drerio rna seq Transcriptome profiling of 1 cell stage of zebrafish embryos. Total RNA was extracted from approximately 150 embryos per developmental stage using Trireagent Sigma Aldrich. The total RNA was then processed further according to the Small RNA Expression Kit Applied Biosystems.   RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ABI_SOLID AB SOLiD System 3.0 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP000635 AB SOLiD System 3.0 sequencing; Transcriptome profiling of early zebrafish development ENA FIRST PUBLIC:2011 06 09|ENA LAST UPDATE:2018 11 16 KI-BN-JKE-DRERIO-RNASEQ-2011-1cell.csfasta.gz KI-BN-JKE-DRERIO-RNASEQ-2011-1cell_QV.qual.gz SOLiD_native SOLiD_native 3676380950.0 73527619.0 KI BN JKE DRERIO RNASEQ 2011 1cell 0:50   50                 ERX012650 ERS032265 ERA029959 KI-BN|Department of Biosciences and Nutrition Department of Biosciences and Nutrition, Karolinska Institutet, Sweden 1 0.64855   0.08432   0.9052   0.74223   50   B   usable mapping rate legacy early unknown random_priming unknown bulk unknown unknown   Sweden 2011-06-09 Zygote Embryo Embryo Imprecise All anatomical structures
9825 9825 ERR2102841 ERX2160152 ERS1883528 ERP040145 PRJEB37796 Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf E-MTAB-5992 Transcriptome Analysis We wanted to compare gene expression from control untreated zebrafish larvae and 2 mM NaBu treated larvae for 24 hours in order to assess the effect of inhibition of the HDAC pathway in these animals ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2017 08 23|ArrayExpress:E MTAB 5992   Protocols: zebrafish were isolated during pharyngula stage daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001 N3 nabu RNA SAMEA104224510 Fundacao Champalimaud ENA first public:2017 08 29|ENA last update:2017 08 23|External Id:SAMEA104224510|INSDC center alias:Fundacao Champalimaud|INSDC center name:Fundacao Champalimaud|INSDC first public:2017 08 29T17:02:02Z|INSDC last update:2017 08 23T09:55:35Z|INSDC status:public|Submitter Id:E MTAB 5992:N3 nabu RNA|age:8|broker name:ArrayExpress|common name:zebrafish|disease:normal|genotype:wild type genotype|sample name:E MTAB 5992:N3 nabu RNA|strain:AB                 Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf E MTAB 5992:N3 nabu RNA s N3 nabu RNA s Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf zebrafish were isolated during pharyngula stage daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001 Experimental Factor: compound:NaBu|Experimental Factor: dose:2 RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina Genome Analyzer IIx   ERP040145 Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2018 11 16 N3_R1_all.fastq.gz fastq 1410139550.0 18670564.0 E MTAB 5992:N3 nabu RNA 0:75.53 1:0 A:353294009;C:340727934;G:322476371;T:393200193;N:441043 75 0     353294009 340727934 322476371 393200193 441043 ERX2160152 ERS1883528 ERA1011308 Fundacao Champalimaud|European Nucleotide Archive Fundacao Champalimaud|European Nucleotide Archive 1 0.95434   0.08906   0.66935   0.47788   76   B   usable mapping rate illumina early_illumina unknown random_priming trueseq bulk unknown unknown   Portugal 2017-08-23 Multi-stage Multi-stage Whole Organism All anatomical structures
9826 9826 ERR2102840 ERX2160151 ERS1883527 ERP040145 PRJEB37796 Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf E-MTAB-5992 Transcriptome Analysis We wanted to compare gene expression from control untreated zebrafish larvae and 2 mM NaBu treated larvae for 24 hours in order to assess the effect of inhibition of the HDAC pathway in these animals ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2017 08 23|ArrayExpress:E MTAB 5992   Protocols: zebrafish were isolated during pharyngula stage daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001 N2 nabu RNA SAMEA104224509 Fundacao Champalimaud ENA first public:2017 08 29|ENA last update:2017 08 23|External Id:SAMEA104224509|INSDC center alias:Fundacao Champalimaud|INSDC center name:Fundacao Champalimaud|INSDC first public:2017 08 29T17:02:02Z|INSDC last update:2017 08 23T09:55:35Z|INSDC status:public|Submitter Id:E MTAB 5992:N2 nabu RNA|age:8|broker name:ArrayExpress|common name:zebrafish|disease:normal|genotype:wild type genotype|sample name:E MTAB 5992:N2 nabu RNA|strain:AB                 Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf E MTAB 5992:N2 nabu RNA s N2 nabu RNA s Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf zebrafish were isolated during pharyngula stage daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001 Experimental Factor: compound:NaBu|Experimental Factor: dose:2 RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina Genome Analyzer IIx   ERP040145 Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2018 11 16 N2_R1_all.fastq.gz fastq 1478621168.0 19576865.0 E MTAB 5992:N2 nabu RNA 0:75.53 1:0 A:369453299;C:359092235;G:341176884;T:408389810;N:508940 75 0     369453299 359092235 341176884 408389810 508940 ERX2160151 ERS1883527 ERA1011308 Fundacao Champalimaud|European Nucleotide Archive Fundacao Champalimaud|European Nucleotide Archive 1 0.95582   0.08202   0.67718   0.47812   76   B   usable mapping rate illumina early_illumina unknown random_priming trueseq bulk unknown unknown   Portugal 2017-08-23 Multi-stage Multi-stage Whole Organism All anatomical structures
9827 9827 ERR2102839 ERX2160150 ERS1883526 ERP040145 PRJEB37796 Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf E-MTAB-5992 Transcriptome Analysis We wanted to compare gene expression from control untreated zebrafish larvae and 2 mM NaBu treated larvae for 24 hours in order to assess the effect of inhibition of the HDAC pathway in these animals ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2017 08 23|ArrayExpress:E MTAB 5992   Protocols: zebrafish were isolated during pharyngula stage daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001 N1 nabu RNA SAMEA104224508 Fundacao Champalimaud ENA first public:2017 08 29|ENA last update:2017 08 23|External Id:SAMEA104224508|INSDC center alias:Fundacao Champalimaud|INSDC center name:Fundacao Champalimaud|INSDC first public:2017 08 29T17:02:02Z|INSDC last update:2017 08 23T09:55:35Z|INSDC status:public|Submitter Id:E MTAB 5992:N1 nabu RNA|age:8|broker name:ArrayExpress|common name:zebrafish|disease:normal|genotype:wild type genotype|sample name:E MTAB 5992:N1 nabu RNA|strain:AB                 Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf E MTAB 5992:N1 nabu RNA s N1 nabu RNA s Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf zebrafish were isolated during pharyngula stage daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001 Experimental Factor: compound:NaBu|Experimental Factor: dose:2 RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina Genome Analyzer IIx   ERP040145 Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2018 11 16 N1_R1_all.fastq.gz fastq 1531713181.0 20277882.0 E MTAB 5992:N1 nabu RNA 0:75.54 1:0 A:386600603;C:373317031;G:350339456;T:420938891;N:517200 75 0     386600603 373317031 350339456 420938891 517200 ERX2160150 ERS1883526 ERA1011308 Fundacao Champalimaud|European Nucleotide Archive Fundacao Champalimaud|European Nucleotide Archive 1 0.9552   0.08124   0.67685   0.47578   76   B   usable mapping rate illumina early_illumina unknown random_priming trueseq bulk unknown unknown   Portugal 2017-08-23 Multi-stage Multi-stage Whole Organism All anatomical structures
9828 9828 ERR2102838 ERX2160149 ERS1883525 ERP040145 PRJEB37796 Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf E-MTAB-5992 Transcriptome Analysis We wanted to compare gene expression from control untreated zebrafish larvae and 2 mM NaBu treated larvae for 24 hours in order to assess the effect of inhibition of the HDAC pathway in these animals ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2017 08 23|ArrayExpress:E MTAB 5992   Protocols: zebrafish were isolated during pharyngula stage daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001 C3 control RNA SAMEA104224507 Fundacao Champalimaud ENA first public:2017 08 29|ENA last update:2017 08 23|External Id:SAMEA104224507|INSDC center alias:Fundacao Champalimaud|INSDC center name:Fundacao Champalimaud|INSDC first public:2017 08 29T17:02:02Z|INSDC last update:2017 08 23T09:55:35Z|INSDC status:public|Submitter Id:E MTAB 5992:C3 control RNA|age:8|broker name:ArrayExpress|common name:zebrafish|disease:normal|genotype:wild type genotype|sample name:E MTAB 5992:C3 control RNA|strain:AB                 Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf E MTAB 5992:C3 control RNA s C3 control RNA s Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf zebrafish were isolated during pharyngula stage daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001 Experimental Factor: compound:PBS RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina Genome Analyzer IIx   ERP040145 Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2018 11 16 C3_R1_all.fastq.gz fastq 1380662008.0 18279108.0 E MTAB 5992:C3 control RNA 0:75.53 1:0 A:345997031;C:338444594;G:316575258;T:379195977;N:449148 75 0     345997031 338444594 316575258 379195977 449148 ERX2160149 ERS1883525 ERA1011308 Fundacao Champalimaud|European Nucleotide Archive Fundacao Champalimaud|European Nucleotide Archive 1 0.95615   0.08131   0.68694   0.45267   74   B   usable mapping rate illumina early_illumina unknown random_priming trueseq bulk unknown unknown   Portugal 2017-08-23 Multi-stage Multi-stage Whole Organism All anatomical structures
9829 9829 ERR2102837 ERX2160148 ERS1883524 ERP040145 PRJEB37796 Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf E-MTAB-5992 Transcriptome Analysis We wanted to compare gene expression from control untreated zebrafish larvae and 2 mM NaBu treated larvae for 24 hours in order to assess the effect of inhibition of the HDAC pathway in these animals ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2017 08 23|ArrayExpress:E MTAB 5992   Protocols: zebrafish were isolated during pharyngula stage daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001 C2 control RNA SAMEA104224506 Fundacao Champalimaud ENA first public:2017 08 29|ENA last update:2017 08 23|External Id:SAMEA104224506|INSDC center alias:Fundacao Champalimaud|INSDC center name:Fundacao Champalimaud|INSDC first public:2017 08 29T17:02:02Z|INSDC last update:2017 08 23T09:55:35Z|INSDC status:public|Submitter Id:E MTAB 5992:C2 control RNA|age:8|broker name:ArrayExpress|common name:zebrafish|disease:normal|genotype:wild type genotype|sample name:E MTAB 5992:C2 control RNA|strain:AB                 Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf E MTAB 5992:C2 control RNA s C2 control RNA s Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf zebrafish were isolated during pharyngula stage daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001 Experimental Factor: compound:PBS RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina Genome Analyzer IIx   ERP040145 Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2018 11 16 C2_R1_all.fastq.gz fastq 1336640735.0 17695627.0 E MTAB 5992:C2 control RNA 0:75.54 1:0 A:338213530;C:326808990;G:303983789;T:367147896;N:486530 75 0     338213530 326808990 303983789 367147896 486530 ERX2160148 ERS1883524 ERA1011308 Fundacao Champalimaud|European Nucleotide Archive Fundacao Champalimaud|European Nucleotide Archive 1 0.95427   0.08628   0.67706   0.47245   76   B   usable mapping rate illumina early_illumina unknown random_priming trueseq bulk unknown unknown   Portugal 2017-08-23 Multi-stage Multi-stage Whole Organism All anatomical structures
9830 9830 ERR2102836 ERX2160147 ERS1883523 ERP040145 PRJEB37796 Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf E-MTAB-5992 Transcriptome Analysis We wanted to compare gene expression from control untreated zebrafish larvae and 2 mM NaBu treated larvae for 24 hours in order to assess the effect of inhibition of the HDAC pathway in these animals ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2017 08 23|ArrayExpress:E MTAB 5992   Protocols: zebrafish were isolated during pharyngula stage daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001 C1 control RNA SAMEA104224505 Fundacao Champalimaud ENA first public:2017 08 29|ENA last update:2017 08 23|External Id:SAMEA104224505|INSDC center alias:Fundacao Champalimaud|INSDC center name:Fundacao Champalimaud|INSDC first public:2017 08 29T17:02:02Z|INSDC last update:2017 08 23T09:55:35Z|INSDC status:public|Submitter Id:E MTAB 5992:C1 control RNA|age:8|broker name:ArrayExpress|common name:zebrafish|disease:normal|genotype:wild type genotype|sample name:E MTAB 5992:C1 control RNA|strain:AB                 Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf E MTAB 5992:C1 control RNA s C1 control RNA s Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf zebrafish were isolated during pharyngula stage daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001 Experimental Factor: compound:PBS RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina Genome Analyzer IIx   ERP040145 Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2018 11 16 C1_R1_all.fastq.gz fastq 1297694845.0 17180544.0 E MTAB 5992:C1 control RNA 0:75.53 1:0 A:322048172;C:316542683;G:299227724;T:359449433;N:426833 75 0     322048172 316542683 299227724 359449433 426833 ERX2160147 ERS1883523 ERA1011308 Fundacao Champalimaud|European Nucleotide Archive Fundacao Champalimaud|European Nucleotide Archive 1 0.95505   0.08541   0.67659   0.48159   75   B   usable mapping rate illumina early_illumina unknown random_priming trueseq bulk unknown unknown   Portugal 2017-08-23 Multi-stage Multi-stage Whole Organism All anatomical structures
19087 19087 ERR13834862 ERX13237628 ERS21098715 ERP164534 PRJEB80557 RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed Other This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol. ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01   retinal neurons 48HC1 S20 R1 001.fastq.gz SAMEA116100635 GIMM ENA first public:2024 01 01|INSDC center name:GIMM|INSDC status:public|Submitter Id:48 HC1|collected by:Jaakko Lehtimaki|collection date:2021 11 24|common name:zebrafish|dev stage:48 hpf location country and/or sea:Portugal|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|sample name:48 HC1|scientific name:Danio rerio|tissue type:retina                 Raw reads: 48 HC1 webin reads 48 HC1         RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq X   ERP164534 Raw reads: 48 HC1 ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01 48HC1_S20_R1_001.fastq.gz fastq 3768442091.0 38065677.0 webin reads 48 HC1 0:99.00 A:1055463738;C:792073627;G:817607736;T:1103223790;N:73200 99       1055463738 792073627 817607736 1103223790 73200 ERX13237628 ERS21098715 ERA30883416 Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive Gulbenkian Institute for Molecular Medicine                       B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_plate smartseq   Belgium 2024-01-01 Hatching Embryo Eye Sensory System
19088 19088 ERR13834951 ERX13237717 ERS21098721 ERP164534 PRJEB80557 RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed Other This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol. ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01   retinal neurons 58PR3 S26 R1 001.fastq.gz 58 PR3   organism:Danio rerio|collection date:2021 12 02|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:58 hpf type:retina|geographic location country and/or sea:Portugal                 Raw reads: 58 PR3 webin reads 58 PR3         RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq X   ERP164534 Raw reads: 58 PR3 ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01 58PR3_S26_R1_001.fastq.gz fastq 3869469736.0 38850717.0 webin reads 58 PR3 0:99.60 A:1103909449;C:804146524;G:827344036;T:1134036010;N:33717 99       1103909449 804146524 827344036 1134036010 33717 ERX13237717 ERS21098721 ERA30883529 Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive Gulbenkian Institute for Molecular Medicine                       B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_plate smartseq   Belgium 2025-01-01 Hatching Embryo Eye Sensory System
19089 19089 ERR13835010 ERX13237776 ERS21098726 ERP164534 PRJEB80557 RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed Other This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol. ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01   retinal neurons 58AC4 S31 R1 001.fastq.gz SAMEA116100646 GIMM ENA first public:2024 01 01|INSDC center name:GIMM|INSDC status:public|Submitter Id:58 AC4|collected by:Jaakko Lehtimaki|collection date:2021 12 02|common name:zebrafish|dev stage:58 hpf location country and/or sea:Portugal|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|sample name:58 AC4|scientific name:Danio rerio|tissue type:retina                 Raw reads: 58 AC4 webin reads 58 AC4         RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq X   ERP164534 Raw reads: 58 AC4 ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01 58AC4_S31_R1_001.fastq.gz fastq 3607648651.0 36331933.0 webin reads 58 AC4 0:99.30 A:1038047870;C:736262498;G:759315202;T:1073962987;N:60094 99       1038047870 736262498 759315202 1073962987 60094 ERX13237776 ERS21098726 ERA30883721 Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive Gulbenkian Institute for Molecular Medicine                       B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_plate smartseq   Belgium 2024-01-01 Hatching Embryo Eye Sensory System
19090 19090 ERR13822794 ERX13225546 ERS21098708 ERP164534 PRJEB80557 RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed Other This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol. ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01   retinal neurons 48PR2 S13 R1 001.fastq.gz 48 PR2   organism:Danio rerio|collection date:2021 11 24|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:48 hpf type:retina|geographic location country and/or sea:Portugal                 Raw reads: 48 PR2 webin reads 48 PR2         RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq X   ERP164534 Raw reads: 48 PR2 ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01 48PR2_S13_R1_001.fastq.gz fastq 3809299607.0 38404185.0 webin reads 48 PR2 0:99.19 A:1067728192;C:802585802;G:828435932;T:1110435904;N:113777 99       1067728192 802585802 828435932 1110435904 113777 ERX13225546 ERS21098708 ERA30879682 Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive Gulbenkian Institute for Molecular Medicine                       B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_plate smartseq   Belgium 2025-01-01 Hatching Embryo Eye Sensory System
19091 19091 ERR13834854 ERX13237620 ERS21098714 ERP164534 PRJEB80557 RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed Other This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol. ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01   retinal neurons 48AC4 S19 R1 001.fastq.gz 48 AC4   organism:Danio rerio|collection date:2021 11 24|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:48 hpf type:retina|geographic location country and/or sea:Portugal                 Raw reads: 48 AC4 webin reads 48 AC4         RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq X   ERP164534 Raw reads: 48 AC4 ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01 48AC4_S19_R1_001.fastq.gz fastq 3410801894.0 34443068.0 webin reads 48 AC4 0:99.03 A:966160063;C:707754156;G:733039262;T:1003772756;N:75657 99       966160063 707754156 733039262 1003772756 75657 ERX13237620 ERS21098714 ERA30883390 Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive Gulbenkian Institute for Molecular Medicine                       B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_plate smartseq   Belgium 2025-01-01 Hatching Embryo Eye Sensory System
19092 19092 ERR13828824 ERX13231590 ERS21098710 ERP164534 PRJEB80557 RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed Other This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol. ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01   retinal neurons 48PR4 S15 R1 001.fastq.gz 48 PR4   organism:Danio rerio|collection date:2021 11 24|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:48 hpf type:retina|geographic location country and/or sea:Portugal                 Raw reads: 48 PR4 webin reads 48 PR4         RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq X   ERP164534 Raw reads: 48 PR4 ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01 48PR4_S15_R1_001.fastq.gz fastq 4365943927.0 44278278.0 webin reads 48 PR4 0:98.60 A:1214448497;C:927512154;G:957491418;T:1266385355;N:106503 98       1214448497 927512154 957491418 1266385355 106503 ERX13231590 ERS21098710 ERA30883309 Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive Gulbenkian Institute for Molecular Medicine                       B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_plate smartseq   Belgium 2025-01-01 Hatching Embryo Eye Sensory System
19093 19093 ERR13834993 ERX13237759 ERS21098723 ERP164534 PRJEB80557 RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed Other This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol. ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01   retinal neurons 58AC1 S28 R1 001.fastq.gz 58 AC1   organism:Danio rerio|collection date:2021 12 02|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:58 hpf type:retina|geographic location country and/or sea:Portugal                 Raw reads: 58 AC1 webin reads 58 AC1         RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq X   ERP164534 Raw reads: 58 AC1 ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01 58AC1_S28_R1_001.fastq.gz fastq 3710768269.0 37364763.0 webin reads 58 AC1 0:99.31 A:1060419097;C:761984557;G:786533722;T:1101603428;N:227465 99       1060419097 761984557 786533722 1101603428 227465 ERX13237759 ERS21098723 ERA30883659 Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive Gulbenkian Institute for Molecular Medicine                       B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_plate smartseq   Belgium 2025-01-01 Hatching Embryo Eye Sensory System
19094 19094 ERR13834875 ERX13237641 ERS21098717 ERP164534 PRJEB80557 RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed Other This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol. ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01   retinal neurons 48HC3 S22 R1 001.fastq.gz 48 HC3   organism:Danio rerio|collection date:2021 11 24|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:48 hpf type:retina|geographic location country and/or sea:Portugal                 Raw reads: 48 HC3 webin reads 48 HC3         RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq X   ERP164534 Raw reads: 48 HC3 ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01 48HC3_S22_R1_001.fastq.gz fastq 3083078586.0 31073491.0 webin reads 48 HC3 0:99.22 A:856250957;C:655140994;G:677078911;T:894558582;N:49142 99       856250957 655140994 677078911 894558582 49142 ERX13237641 ERS21098717 ERA30883447 Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive Gulbenkian Institute for Molecular Medicine                       B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_plate smartseq   Belgium 2025-01-01 Hatching Embryo Eye Sensory System
19095 19095 ERR13834899 ERX13237665 ERS21098720 ERP164534 PRJEB80557 RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed Other This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol. ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01   retinal neurons 58PR2 S25 R1 001.fastq.gz 58 PR2   organism:Danio rerio|collection date:2021 12 02|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:58 hpf type:retina|geographic location country and/or sea:Portugal                 Raw reads: 58 PR2 webin reads 58 PR2         RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq X   ERP164534 Raw reads: 58 PR2 ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01 58PR2_S25_R1_001.fastq.gz fastq 3849571818.0 38706841.0 webin reads 58 PR2 0:99.45 A:1089593011;C:803322469;G:827777017;T:1128836774;N:42547 99       1089593011 803322469 827777017 1128836774 42547 ERX13237665 ERS21098720 ERA30883518 Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive Gulbenkian Institute for Molecular Medicine                       B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_plate smartseq   Belgium 2025-01-01 Hatching Embryo Eye Sensory System
19096 19096 ERR13834889 ERX13237655 ERS21098719 ERP164534 PRJEB80557 RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed Other This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol. ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01   retinal neurons 58PR1 S24 R1 001.fastq.gz 58 PR1   organism:Danio rerio|collection date:2021 12 02|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:58 hpf type:retina|geographic location country and/or sea:Portugal                 Raw reads: 58 PR1 webin reads 58 PR1         RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq X   ERP164534 Raw reads: 58 PR1 ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01 58PR1_S24_R1_001.fastq.gz fastq 3945671240.0 39514922.0 webin reads 58 PR1 0:99.85 A:1135075173;C:807489123;G:827964380;T:1175109762;N:32802 99       1135075173 807489123 827964380 1175109762 32802 ERX13237655 ERS21098719 ERA30883497 Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive Gulbenkian Institute for Molecular Medicine                       B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_plate smartseq   Belgium 2025-01-01 Hatching Embryo Eye Sensory System
19097 19097 ERR13835019 ERX13237785 ERS21098728 ERP164534 PRJEB80557 RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed Other This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol. ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01   retinal neurons 58HC2 S33 R1 001.fastq.gz SAMEA116100648 GIMM ENA first public:2024 01 01|INSDC center name:GIMM|INSDC status:public|Submitter Id:58 HC2|collected by:Jaakko Lehtimaki|collection date:2021 12 02|common name:zebrafish|dev stage:58 hpf location country and/or sea:Portugal|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|sample name:58 HC2|scientific name:Danio rerio|tissue type:retina                 Raw reads: 58 HC2 webin reads 58 HC2         RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq X   ERP164534 Raw reads: 58 HC2 ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01 58HC2_S33_R1_001.fastq.gz fastq 3711237069.0 37217240.0 webin reads 58 HC2 0:99.72 A:1070592288;C:757099665;G:780689044;T:1102575310;N:280762 99       1070592288 757099665 780689044 1102575310 280762 ERX13237785 ERS21098728 ERA30883748 Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive Gulbenkian Institute for Molecular Medicine                       B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_plate smartseq   Belgium 2024-01-01 Hatching Embryo Eye Sensory System
19098 19098 ERR13822110 ERX13224862 ERS21098697 ERP164534 PRJEB80557 RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed Other This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol. ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01   retinal neurons 38PR2 S2 R1 001.fastq.gz 38 PR2   organism:Danio rerio|collection date:2021 11 30|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:38 hpf type:retina|geographic location country and/or sea:Portugal                 Raw reads: 38 PR2 webin reads 38 PR2         RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq X   ERP164534 Raw reads: 38 PR2 ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01 38PR2_S2_R1_001.fastq.gz fastq 3463281109.0 34821985.0 webin reads 38 PR2 0:99.46 A:969862466;C:733798241;G:755135957;T:1004440555;N:43890 99       969862466 733798241 755135957 1004440555 43890 ERX13224862 ERS21098697 ERA30879238 Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive Gulbenkian Institute for Molecular Medicine                       B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_plate smartseq   Belgium 2025-01-01 Pharyngula Embryo Eye Sensory System
19099 19099 ERR13822784 ERX13225536 ERS21098706 ERP164534 PRJEB80557 RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed Other This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol. ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01   retinal neurons 38HC3 S11 R1 001.fastq.gz 38 HC3   organism:Danio rerio|collection date:2021 12 07|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:38 hpf type:retina|geographic location country and/or sea:Portugal                 Raw reads: 38 HC3 webin reads 38 HC3         RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq X   ERP164534 Raw reads: 38 HC3 ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01 38HC3_S11_R1_001.fastq.gz fastq 4360921873.0 44107486.0 webin reads 38 HC3 0:98.87 A:1222778761;C:918257887;G:948838973;T:1270939370;N:106882 98       1222778761 918257887 948838973 1270939370 106882 ERX13225536 ERS21098706 ERA30879613 Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive Gulbenkian Institute for Molecular Medicine                       B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_plate smartseq   Belgium 2025-01-01 Pharyngula Embryo Eye Sensory System
19100 19100 ERR13828836 ERX13231602 ERS21098712 ERP164534 PRJEB80557 RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed Other This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol. ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01   retinal neurons 48AC2 S17 R1 001.fastq.gz 48 AC2   organism:Danio rerio|collection date:2021 11 24|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:48 hpf type:retina|geographic location country and/or sea:Portugal                 Raw reads: 48 AC2 webin reads 48 AC2         RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq X   ERP164534 Raw reads: 48 AC2 ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01 48AC2_S17_R1_001.fastq.gz fastq 3205206588.0 32424632.0 webin reads 48 AC2 0:98.85 A:902438127;C:672433401;G:694813369;T:935445436;N:76255 98       902438127 672433401 694813369 935445436 76255 ERX13231602 ERS21098712 ERA30883343 Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive Gulbenkian Institute for Molecular Medicine                       B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_plate smartseq   Belgium 2025-01-01 Hatching Embryo Eye Sensory System
19101 19101 ERR13835004 ERX13237770 ERS21098725 ERP164534 PRJEB80557 RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed Other This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol. ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01   retinal neurons 58AC3 S30 R1 001.fastq.gz 58 AC3   organism:Danio rerio|collection date:2021 12 02|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:58 hpf type:retina|geographic location country and/or sea:Portugal                 Raw reads: 58 AC3 webin reads 58 AC3         RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq X   ERP164534 Raw reads: 58 AC3 ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01 58AC3_S30_R1_001.fastq.gz fastq 3782993133.0 38295959.0 webin reads 58 AC3 0:98.78 A:1080745150;C:779903026;G:803258485;T:1118994941;N:91531 98       1080745150 779903026 803258485 1118994941 91531 ERX13237770 ERS21098725 ERA30883697 Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive Gulbenkian Institute for Molecular Medicine                       B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_plate smartseq   Belgium 2025-01-01 Hatching Embryo Eye Sensory System
19102 19102 ERR13834868 ERX13237634 ERS21098716 ERP164534 PRJEB80557 RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed Other This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol. ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01   retinal neurons 48HC2 S21 R1 001.fastq.gz SAMEA116100636 GIMM ENA first public:2024 01 01|INSDC center name:GIMM|INSDC status:public|Submitter Id:48 HC2|collected by:Jaakko Lehtimaki|collection date:2021 11 24|common name:zebrafish|dev stage:48 hpf location country and/or sea:Portugal|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|sample name:48 HC2|scientific name:Danio rerio|tissue type:retina                 Raw reads: 48 HC2 webin reads 48 HC2         RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq X   ERP164534 Raw reads: 48 HC2 ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01 48HC2_S21_R1_001.fastq.gz fastq 3424347865.0 34510204.0 webin reads 48 HC2 0:99.23 A:959488173;C:721171249;G:745705870;T:997922014;N:60559 99       959488173 721171249 745705870 997922014 60559 ERX13237634 ERS21098716 ERA30883434 Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive Gulbenkian Institute for Molecular Medicine                       B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_plate smartseq   Belgium 2024-01-01 Hatching Embryo Eye Sensory System
19103 19103 ERR13822197 ERX13224949 ERS21098704 ERP164534 PRJEB80557 RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed Other This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol. ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01   retinal neurons 38HC1 S9 R1 001.fastq.gz SAMEA116100624 GIMM ENA first public:2024 01 01|INSDC center name:GIMM|INSDC status:public|Submitter Id:38 HC1|collected by:Jaakko Lehtimaki|collection date:2021 11 30|common name:zebrafish|dev stage:38 hpf location country and/or sea:Portugal|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|sample name:38 HC1|scientific name:Danio rerio|tissue type:retina                 Raw reads: 38 HC1 webin reads 38 HC1         RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq X   ERP164534 Raw reads: 38 HC1 ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01 38HC1_S9_R1_001.fastq.gz fastq 3784641498.0 38331162.0 webin reads 38 HC1 0:98.74 A:1064199311;C:791310791;G:818910597;T:1110118632;N:102167 98       1064199311 791310791 818910597 1110118632 102167 ERX13224949 ERS21098704 ERA30879548 Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive Gulbenkian Institute for Molecular Medicine                       B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_plate smartseq   Belgium 2024-01-01 Pharyngula Embryo Eye Sensory System
19104 19104 ERR13834880 ERX13237646 ERS21098718 ERP164534 PRJEB80557 RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed Other This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol. ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01   retinal neurons 48HC4 S23 R1 001.fastq.gz 48 HC4   organism:Danio rerio|collection date:2021 11 24|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:48 hpf type:retina|geographic location country and/or sea:Portugal                 Raw reads: 48 HC4 webin reads 48 HC4         RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq X   ERP164534 Raw reads: 48 HC4 ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01 48HC4_S23_R1_001.fastq.gz fastq 3660674315.0 36821474.0 webin reads 48 HC4 0:99.42 A:1035049987;C:763030378;G:788062167;T:1074303516;N:228267 99       1035049987 763030378 788062167 1074303516 228267 ERX13237646 ERS21098718 ERA30883470 Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive Gulbenkian Institute for Molecular Medicine                       B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_plate smartseq   Belgium 2025-01-01 Hatching Embryo Eye Sensory System
19105 19105 ERR13822867 ERX13225633 ERS21098709 ERP164534 PRJEB80557 RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed Other This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol. ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01   retinal neurons 48PR3 S14 R1 001.fastq.gz 48 PR3   organism:Danio rerio|collection date:2021 11 24|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:48 hpf type:retina|geographic location country and/or sea:Portugal                 Raw reads: 48 PR3 webin reads 48 PR3         RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq X   ERP164534 Raw reads: 48 PR3 ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01 48PR3_S14_R1_001.fastq.gz fastq 4232170464.0 42534853.0 webin reads 48 PR3 0:99.50 A:1195251409;C:889346003;G:917240118;T:1230272855;N:60079 99       1195251409 889346003 917240118 1230272855 60079 ERX13225633 ERS21098709 ERA30879704 Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive Gulbenkian Institute for Molecular Medicine                       B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_plate smartseq   Belgium 2025-01-01 Hatching Embryo Eye Sensory System
19106 19106 ERR13822131 ERX13224883 ERS21098700 ERP164534 PRJEB80557 RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed Other This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol. ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01   retinal neurons 38AC1 S5 R1 001.fastq.gz SAMEA116100620 GIMM ENA first public:2024 01 01|INSDC center name:GIMM|INSDC status:public|Submitter Id:38 AC1|collected by:Jaakko Lehtimaki|collection date:2021 11 30|common name:zebrafish|dev stage:38 hpf location country and/or sea:Portugal|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|sample name:38 AC1|scientific name:Danio rerio|tissue type:retina                 Raw reads: 38 AC1 webin reads 38 AC1         RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq X   ERP164534 Raw reads: 38 AC1 ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01 38AC1_S5_R1_001.fastq.gz fastq 3836921113.0 38702139.0 webin reads 38 AC1 0:99.14 A:1066720805;C:818958589;G:843762182;T:1107403844;N:75693 99       1066720805 818958589 843762182 1107403844 75693 ERX13224883 ERS21098700 ERA30879356 Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive Gulbenkian Institute for Molecular Medicine                       B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_plate smartseq   Belgium 2024-01-01 Pharyngula Embryo Eye Sensory System
19107 19107 ERR13822143 ERX13224895 ERS21098702 ERP164534 PRJEB80557 RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed Other This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol. ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01   retinal neurons 38AC3 S7 R1 001.fastq.gz 38 AC3   organism:Danio rerio|collection date:2021 12 07|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:38 hpf type:retina|geographic location country and/or sea:Portugal                 Raw reads: 38 AC3 webin reads 38 AC3         RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq X   ERP164534 Raw reads: 38 AC3 ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01 38AC3_S7_R1_001.fastq.gz fastq 3452707377.0 34902410.0 webin reads 38 AC3 0:98.92 A:970868997;C:726795179;G:750560378;T:1004408693;N:74130 98       970868997 726795179 750560378 1004408693 74130 ERX13224895 ERS21098702 ERA30879451 Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive Gulbenkian Institute for Molecular Medicine                       B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_plate smartseq   Belgium 2025-01-01 Pharyngula Embryo Eye Sensory System
19108 19108 ERR13828843 ERX13234350 ERS21098713 ERP164534 PRJEB80557 RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed Other This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol. ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01   retinal neurons 48AC3 S18 R1 001.fastq.gz 48 AC3   organism:Danio rerio|collection date:2021 11 24|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:48 hpf type:retina|geographic location country and/or sea:Portugal                 Raw reads: 48 AC3 webin reads 48 AC3         RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq X   ERP164534 Raw reads: 48 AC3 ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01 48AC3_S18_R1_001.fastq.gz fastq 3733628911.0 37779462.0 webin reads 48 AC3 0:98.83 A:1047204450;C:786943605;G:812327274;T:1086893109;N:260473 98       1047204450 786943605 812327274 1086893109 260473 ERX13234350 ERS21098713 ERA30883366 Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive Gulbenkian Institute for Molecular Medicine                       B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_plate smartseq   Belgium 2025-01-01 Hatching Embryo Eye Sensory System
19109 19109 ERR13822153 ERX13224905 ERS21098703 ERP164534 PRJEB80557 RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed Other This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol. ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01   retinal neurons 38AC4 S8 R1 001.fastq.gz 38 AC4   organism:Danio rerio|collection date:2021 12 07|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:38 hpf type:retina|geographic location country and/or sea:Portugal                 Raw reads: 38 AC4 webin reads 38 AC4         RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq X   ERP164534 Raw reads: 38 AC4 ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01 38AC4_S8_R1_001.fastq.gz fastq 4130629624.0 41794865.0 webin reads 38 AC4 0:98.83 A:1156746387;C:877063962;G:905379690;T:1191264308;N:175277 98       1156746387 877063962 905379690 1191264308 175277 ERX13224905 ERS21098703 ERA30879532 Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive Gulbenkian Institute for Molecular Medicine                       B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_plate smartseq   Belgium 2025-01-01 Pharyngula Embryo Eye Sensory System
19110 19110 ERR13822201 ERX13224953 ERS21098705 ERP164534 PRJEB80557 RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed Other This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol. ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01   retinal neurons 38HC2 S10 R1 001.fastq.gz 38 HC2   organism:Danio rerio|collection date:2021 11 30|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:38 hpf type:retina|geographic location country and/or sea:Portugal                 Raw reads: 38 HC2 webin reads 38 HC2         RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq X   ERP164534 Raw reads: 38 HC2 ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01 38HC2_S10_R1_001.fastq.gz fastq 4221340137.0 42584743.0 webin reads 38 HC2 0:99.13 A:1195817135;C:879958039;G:908085464;T:1237394738;N:84761 99       1195817135 879958039 908085464 1237394738 84761 ERX13224953 ERS21098705 ERA30879582 Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive Gulbenkian Institute for Molecular Medicine                       B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_plate smartseq   Belgium 2025-01-01 Pharyngula Embryo Eye Sensory System
19111 19111 ERR13822114 ERX13224866 ERS21098698 ERP164534 PRJEB80557 RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed Other This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol. ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01   retinal neurons 38PR3 S3 R1 001.fastq.gz SAMEA116100618 GIMM ENA first public:2024 01 01|INSDC center name:GIMM|INSDC status:public|Submitter Id:38 PR3|collected by:Jaakko Lehtimaki|collection date:2021 12 07|common name:zebrafish|dev stage:38 hpf location country and/or sea:Portugal|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|sample name:38 PR3|scientific name:Danio rerio|tissue type:retina                 Raw reads: 38 PR3 webin reads 38 PR3         RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq X   ERP164534 Raw reads: 38 PR3 ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01 38PR3_S3_R1_001.fastq.gz fastq 3894010106.0 39196855.0 webin reads 38 PR3 0:99.34 A:1093221995;C:818047738;G:843661747;T:1138957138;N:121488 99       1093221995 818047738 843661747 1138957138 121488 ERX13224866 ERS21098698 ERA30879273 Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive Gulbenkian Institute for Molecular Medicine                       B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_plate smartseq   Belgium 2024-01-01 Pharyngula Embryo Eye Sensory System
19112 19112 ERR13822135 ERX13224887 ERS21098701 ERP164534 PRJEB80557 RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed Other This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol. ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01   retinal neurons 38AC2 S6 R1 001.fastq.gz 38 AC2   organism:Danio rerio|collection date:2021 11 30|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:38 hpf type:retina|geographic location country and/or sea:Portugal                 Raw reads: 38 AC2 webin reads 38 AC2         RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq X   ERP164534 Raw reads: 38 AC2 ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01 38AC2_S6_R1_001.fastq.gz fastq 3913343007.0 39682834.0 webin reads 38 AC2 0:98.62 A:1089960083;C:827936673;G:855955684;T:1139372607;N:117960 98       1089960083 827936673 855955684 1139372607 117960 ERX13224887 ERS21098701 ERA30879382 Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive Gulbenkian Institute for Molecular Medicine                       B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_plate smartseq   Belgium 2025-01-01 Pharyngula Embryo Eye Sensory System
19113 19113 ERR13835032 ERX13237798 ERS21098730 ERP164534 PRJEB80557 RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed Other This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol. ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01   retinal neurons 58HC4 S35 R1 001.fastq.gz 58 HC4   organism:Danio rerio|collection date:2021 12 02|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:58 hpf type:retina|geographic location country and/or sea:Portugal                 Raw reads: 58 HC4 webin reads 58 HC4         RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq X   ERP164534 Raw reads: 58 HC4 ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01 58HC4_S35_R1_001.fastq.gz fastq 4418556015.0 44331835.0 webin reads 58 HC4 0:99.67 A:1255080581;C:916490847;G:946212615;T:1300735054;N:36918 99       1255080581 916490847 946212615 1300735054 36918 ERX13237798 ERS21098730 ERA30883773 Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive Gulbenkian Institute for Molecular Medicine                       B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_plate smartseq   Belgium 2025-01-01 Hatching Embryo Eye Sensory System
19114 19114 ERR13828829 ERX13231595 ERS21098711 ERP164534 PRJEB80557 RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed Other This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol. ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01   retinal neurons 48AC1 S16 R1 001.fastq.gz 48 AC1   organism:Danio rerio|collection date:2021 11 24|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:48 hpf type:retina|geographic location country and/or sea:Portugal                 Raw reads: 48 AC1 webin reads 48 AC1         RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq X   ERP164534 Raw reads: 48 AC1 ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01 48AC1_S16_R1_001.fastq.gz fastq 3933669121.0 39695406.0 webin reads 48 AC1 0:99.10 A:1105258159;C:824538054;G:854253688;T:1149538152;N:81068 99       1105258159 824538054 854253688 1149538152 81068 ERX13231595 ERS21098711 ERA30883326 Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive Gulbenkian Institute for Molecular Medicine                       B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_plate smartseq   Belgium 2025-01-01 Hatching Embryo Eye Sensory System
19115 19115 ERR13822099 ERX13224851 ERS21098696 ERP164534 PRJEB80557 RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed Other This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol. ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01   retinal neurons 38PR1 S1 R1 001.fastq.gz 38 PR1   organism:Danio rerio|collection date:2021 11 30|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:38 hpf type:retina|geographic location country and/or sea:Portugal                 Raw reads: 38 PR1 webin reads 38 PR1         RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq X   ERP164534 Raw reads: 38 PR1 ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01 38PR1_S1_R1_001.fastq.gz fastq 4256158288.0 42658127.0 webin reads 38 PR1 0:99.77 A:1193880575;C:899261652;G:926114030;T:1236860186;N:41845 99       1193880575 899261652 926114030 1236860186 41845 ERX13224851 ERS21098696 ERA30879152 Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive Gulbenkian Institute for Molecular Medicine                       B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_plate smartseq   Belgium 2025-01-01 Pharyngula Embryo Eye Sensory System
19116 19116 ERR13822119 ERX13224871 ERS21098699 ERP164534 PRJEB80557 RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed Other This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol. ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01   retinal neurons 38PR4 S4 R1 001.fastq.gz 38 PR4   organism:Danio rerio|collection date:2021 12 07|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:38 hpf type:retina|geographic location country and/or sea:Portugal                 Raw reads: 38 PR4 webin reads 38 PR4         RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq X   ERP164534 Raw reads: 38 PR4 ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01 38PR4_S4_R1_001.fastq.gz fastq 3726308046.0 37591038.0 webin reads 38 PR4 0:99.13 A:1043231302;C:789255840;G:812957881;T:1080801843;N:61180 99       1043231302 789255840 812957881 1080801843 61180 ERX13224871 ERS21098699 ERA30879302 Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive Gulbenkian Institute for Molecular Medicine                       B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_plate smartseq   Belgium 2025-01-01 Pharyngula Embryo Eye Sensory System
19117 19117 ERR13835025 ERX13237791 ERS21098729 ERP164534 PRJEB80557 RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed Other This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol. ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01   retinal neurons 58HC3 S34 R1 001.fastq.gz 58 HC3   organism:Danio rerio|collection date:2021 12 02|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:58 hpf type:retina|geographic location country and/or sea:Portugal                 Raw reads: 58 HC3 webin reads 58 HC3         RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq X   ERP164534 Raw reads: 58 HC3 ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01 58HC3_S34_R1_001.fastq.gz fastq 3523899212.0 35292613.0 webin reads 58 HC3 0:99.85 A:1012516999;C:723225071;G:745152410;T:1042976092;N:28640 99       1012516999 723225071 745152410 1042976092 28640 ERX13237791 ERS21098729 ERA30883757 Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive Gulbenkian Institute for Molecular Medicine                       B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_plate smartseq   Belgium 2025-01-01 Hatching Embryo Eye Sensory System
19118 19118 ERR13835014 ERX13237780 ERS21098727 ERP164534 PRJEB80557 RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed Other This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol. ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01   retinal neurons 58HC1 S32 R1 001.fastq.gz 58 HC1   organism:Danio rerio|collection date:2021 12 02|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:58 hpf type:retina|geographic location country and/or sea:Portugal                 Raw reads: 58 HC1 webin reads 58 HC1         RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq X   ERP164534 Raw reads: 58 HC1 ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01 58HC1_S32_R1_001.fastq.gz fastq 3436493821.0 34597887.0 webin reads 58 HC1 0:99.33 A:980894291;C:707196785;G:729948858;T:1018400124;N:53763 99       980894291 707196785 729948858 1018400124 53763 ERX13237780 ERS21098727 ERA30883731 Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive Gulbenkian Institute for Molecular Medicine                       B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_plate smartseq   Belgium 2025-01-01 Hatching Embryo Eye Sensory System
19119 19119 ERR13834987 ERX13237753 ERS21098722 ERP164534 PRJEB80557 RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed Other This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol. ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01   retinal neurons 58PR4 S27 R1 001.fastq.gz 58 PR4   organism:Danio rerio|collection date:2021 12 02|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:58 hpf type:retina|geographic location country and/or sea:Portugal                 Raw reads: 58 PR4 webin reads 58 PR4         RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq X   ERP164534 Raw reads: 58 PR4 ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01 58PR4_S27_R1_001.fastq.gz fastq 3069040814.0 30923422.0 webin reads 58 PR4 0:99.25 A:875776938;C:633951750;G:653308475;T:905949639;N:54012 99       875776938 633951750 653308475 905949639 54012 ERX13237753 ERS21098722 ERA30883641 Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive Gulbenkian Institute for Molecular Medicine                       B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_plate smartseq   Belgium 2025-01-01 Hatching Embryo Eye Sensory System
19120 19120 ERR13822788 ERX13225540 ERS21098707 ERP164534 PRJEB80557 RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed Other This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol. ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01   retinal neurons 38HC4 S12 R1 001.fastq.gz 38 HC4   organism:Danio rerio|collection date:2021 12 07|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:38 hpf type:retina|geographic location country and/or sea:Portugal                 Raw reads: 38 HC4 webin reads 38 HC4         RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq X   ERP164534 Raw reads: 38 HC4 ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01 38HC4_S12_R1_001.fastq.gz fastq 3353994440.0 33744828.0 webin reads 38 HC4 0:99.39 A:939537209;C:709367668;G:731849729;T:973193819;N:46015 99       939537209 709367668 731849729 973193819 46015 ERX13225540 ERS21098707 ERA30879650 Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive Gulbenkian Institute for Molecular Medicine                       B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_plate smartseq   Belgium 2025-01-01 Pharyngula Embryo Eye Sensory System
19121 19121 ERR13834997 ERX13237763 ERS21098724 ERP164534 PRJEB80557 RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed Other This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol. ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01   retinal neurons 58AC2 S29 R1 001.fastq.gz 58 AC2   organism:Danio rerio|collection date:2021 12 02|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:58 hpf type:retina|geographic location country and/or sea:Portugal                 Raw reads: 58 AC2 webin reads 58 AC2         RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq X   ERP164534 Raw reads: 58 AC2 ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01 58AC2_S29_R1_001.fastq.gz fastq 3872162091.0 38898173.0 webin reads 58 AC2 0:99.55 A:1111663794;C:793747086;G:817730996;T:1148980297;N:39918 99       1111663794 793747086 817730996 1148980297 39918 ERX13237763 ERS21098724 ERA30883678 Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive Gulbenkian Institute for Molecular Medicine                       B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_plate smartseq   Belgium 2025-01-01 Hatching Embryo Eye Sensory System
32370 32370 SRR29180530 SRX24700714 SRS21428245 SRP509851 PRJNA1116337 Ioxynil and diethylstilbestrol disrupt vascular and heart development in zebrafish PRJNA1116337 Other Endocrine disruption is one of the consequences of industrialization and chemicals released into theenvironment have a profound impact on organisms. Waterborne micromolar concentrations of ioxynil IOX and diethylstilbestrol DES in fish affect the development of the heart vasculature and thyroid gland.         DES   isolate:exposure to DES|age:48 hpf|dev stage:embryos|collection date:2018 06|geo loc name:Portugal|sex:pooled male and female|tissue:embryos|treatment:exposure to DES|BioSampleModel:Model organism or animal                 RNA seq of DES treated DES DES Sequencing the transcriptomes of zebrafish embryos of DES treated     RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 4000   SRP509851     DES_TAAGGC_L001_R1_001.fastq.gz DES_TAAGGC_L001_R2_001.fastq.gz fastq fastq 9169560000.0 30565200.0 DES TAAGGC L001 R1 001.fastq.gz 0:150 1:150 A:2545096687;C:2037322055;G:2024787099;T:2562124529;N:229630 150 150     2545096687 2037322055 2024787099 2562124529 229630 SRX24700714 SRS21428245 SRA1878028 Shanghai Ocean University|College of Fisheries and Life Science Shanghai Ocean University                       B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2024-05-25 Hatching Embryo Embryo Imprecise All anatomical structures
34282 34282 SRR31640757 SRX27004210 SRS23468967 SRP550004 PRJNA1195374 Cortex Dictamni induces retinitis pigmentosa in zebrafish by inhibiting pde6a post transcriptional activity via mmu mir 6240 p3 2 PRJNA1195374 Other Ethnopharmacological relevance: Cortex Dictamni CD is the dried root skin of Dictamnus dasycarpus Turcz widely used in the field of traditional Chinese medicine. mainly for the treatment of skin diseases. Recent adverse reactions to CD limited the clinical application in combination with other traditional Chinese medicines.Aim of the study: To investigate the retinitis pigmentosa RP effects of CD using the zebrafish model and elucidate the underlying molecular mechanism of CD induced RP in zebrafish.Materials and methods: The 3 dpf zebrafish larvae were divided into control and CD group. RNA sequencing followed with qRT PCR validating miRNAs and mRNAs. Dual luciferase reporter assay confirmed mmu mir 6240 p3 2's interaction with pde6a. HT22 cells were transfected treated with CD and evaluated for migration invasion malondialdehyde level superoxide dismutase and acetylcholine activities.Results: The results showed 6228 differentially expressed genes and 66 miRNAs differentially expressed in zebrafish exposed to CD. The personal correlation coefficient results showed that mmu mir 6240 p3 2 had the highest correlation coefficient with pde6a and had a negative regulatory relationship. The results of dual luciferase reporter gene further showed that pde6a gene was the direct target of mmu mir 6240 p3 2. Cell experiment results showed that inhibiting mir 6240 p3 2 can upregulate pde6a expression alleviate HT22 cell injury and reverse the inhibition of cell migration and invasion induced by CD.Conclusions: CD induces RP in zebrafish by inhibiting pde6a post transcriptional activity via mmu mir 6240 p3 2. These findings have important implications for understanding the potential side effects of CD and for developing safer therapeutic strategies involving traditional Chinese medicines.         CD1   strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|collection date:not applicable|geo loc name:not applicable|sex:not applicable|tissue:not applicable|treatment:Experiment group replicate1|BioSampleModel:Model organism or animal                 microRNA seq of Danio rerio: Experiment group BXP 1 BXP 1       miRNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina NovaSeq 6000   SRP550004     BXP_1.fq.gz fastq 816499035.0 16009785.0 BXP 1.fq.gz 0:51 A:191280900;C:189440771;G:247005615;T:188686493;N:85256 51       191280900 189440771 247005615 188686493 85256 SRX27004210 SRS23468967 SRA2029520 Heilongjiang University of Chinese Medicine|College of Traditional Chinese Medicine Heilongjiang University of Chinese Medicine                       T   under 1.2% mapping rate illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2024-12-07 Undetermined Larval Undetermined Undetermined
34283 34283 SRR31640758 SRX27004209 SRS23468966 SRP550004 PRJNA1195374 Cortex Dictamni induces retinitis pigmentosa in zebrafish by inhibiting pde6a post transcriptional activity via mmu mir 6240 p3 2 PRJNA1195374 Other Ethnopharmacological relevance: Cortex Dictamni CD is the dried root skin of Dictamnus dasycarpus Turcz widely used in the field of traditional Chinese medicine. mainly for the treatment of skin diseases. Recent adverse reactions to CD limited the clinical application in combination with other traditional Chinese medicines.Aim of the study: To investigate the retinitis pigmentosa RP effects of CD using the zebrafish model and elucidate the underlying molecular mechanism of CD induced RP in zebrafish.Materials and methods: The 3 dpf zebrafish larvae were divided into control and CD group. RNA sequencing followed with qRT PCR validating miRNAs and mRNAs. Dual luciferase reporter assay confirmed mmu mir 6240 p3 2's interaction with pde6a. HT22 cells were transfected treated with CD and evaluated for migration invasion malondialdehyde level superoxide dismutase and acetylcholine activities.Results: The results showed 6228 differentially expressed genes and 66 miRNAs differentially expressed in zebrafish exposed to CD. The personal correlation coefficient results showed that mmu mir 6240 p3 2 had the highest correlation coefficient with pde6a and had a negative regulatory relationship. The results of dual luciferase reporter gene further showed that pde6a gene was the direct target of mmu mir 6240 p3 2. Cell experiment results showed that inhibiting mir 6240 p3 2 can upregulate pde6a expression alleviate HT22 cell injury and reverse the inhibition of cell migration and invasion induced by CD.Conclusions: CD induces RP in zebrafish by inhibiting pde6a post transcriptional activity via mmu mir 6240 p3 2. These findings have important implications for understanding the potential side effects of CD and for developing safer therapeutic strategies involving traditional Chinese medicines.         Control3   strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|collection date:not applicable|geo loc name:not applicable|sex:not applicable|tissue:not applicable|treatment:Control group replicate3|BioSampleModel:Model organism or animal                 microRNA seq of Danio rerio: Control group Control 3 Control 3       miRNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina NovaSeq 6000   SRP550004     Control_3.fq.gz fastq 662560023.0 12991373.0 Control 3.fq.gz 0:51 A:151053320;C:152811933;G:203340354;T:155283230;N:71186 51       151053320 152811933 203340354 155283230 71186 SRX27004209 SRS23468966 SRA2029520 Heilongjiang University of Chinese Medicine|College of Traditional Chinese Medicine Heilongjiang University of Chinese Medicine                       T   under 1.2% mapping rate illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2024-12-07 Undetermined Larval Undetermined Undetermined
34284 34284 SRR31640759 SRX27004208 SRS23468963 SRP550004 PRJNA1195374 Cortex Dictamni induces retinitis pigmentosa in zebrafish by inhibiting pde6a post transcriptional activity via mmu mir 6240 p3 2 PRJNA1195374 Other Ethnopharmacological relevance: Cortex Dictamni CD is the dried root skin of Dictamnus dasycarpus Turcz widely used in the field of traditional Chinese medicine. mainly for the treatment of skin diseases. Recent adverse reactions to CD limited the clinical application in combination with other traditional Chinese medicines.Aim of the study: To investigate the retinitis pigmentosa RP effects of CD using the zebrafish model and elucidate the underlying molecular mechanism of CD induced RP in zebrafish.Materials and methods: The 3 dpf zebrafish larvae were divided into control and CD group. RNA sequencing followed with qRT PCR validating miRNAs and mRNAs. Dual luciferase reporter assay confirmed mmu mir 6240 p3 2's interaction with pde6a. HT22 cells were transfected treated with CD and evaluated for migration invasion malondialdehyde level superoxide dismutase and acetylcholine activities.Results: The results showed 6228 differentially expressed genes and 66 miRNAs differentially expressed in zebrafish exposed to CD. The personal correlation coefficient results showed that mmu mir 6240 p3 2 had the highest correlation coefficient with pde6a and had a negative regulatory relationship. The results of dual luciferase reporter gene further showed that pde6a gene was the direct target of mmu mir 6240 p3 2. Cell experiment results showed that inhibiting mir 6240 p3 2 can upregulate pde6a expression alleviate HT22 cell injury and reverse the inhibition of cell migration and invasion induced by CD.Conclusions: CD induces RP in zebrafish by inhibiting pde6a post transcriptional activity via mmu mir 6240 p3 2. These findings have important implications for understanding the potential side effects of CD and for developing safer therapeutic strategies involving traditional Chinese medicines.         Control2   strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|collection date:not applicable|geo loc name:not applicable|sex:not applicable|tissue:not applicable|treatment:Control group replicate2|BioSampleModel:Model organism or animal                 microRNA seq of Danio rerio: Control group Control 2 Control 2       miRNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina NovaSeq 6000   SRP550004     Control_2.fq.gz fastq 648856119.0 12722669.0 Control 2.fq.gz 0:51 A:149869576;C:151844056;G:195830503;T:151241215;N:70769 51       149869576 151844056 195830503 151241215 70769 SRX27004208 SRS23468963 SRA2029520 Heilongjiang University of Chinese Medicine|College of Traditional Chinese Medicine Heilongjiang University of Chinese Medicine                       T   under 1.2% mapping rate illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2024-12-07 Undetermined Larval Undetermined Undetermined
34285 34285 SRR31640760 SRX27004207 SRS23468962 SRP550004 PRJNA1195374 Cortex Dictamni induces retinitis pigmentosa in zebrafish by inhibiting pde6a post transcriptional activity via mmu mir 6240 p3 2 PRJNA1195374 Other Ethnopharmacological relevance: Cortex Dictamni CD is the dried root skin of Dictamnus dasycarpus Turcz widely used in the field of traditional Chinese medicine. mainly for the treatment of skin diseases. Recent adverse reactions to CD limited the clinical application in combination with other traditional Chinese medicines.Aim of the study: To investigate the retinitis pigmentosa RP effects of CD using the zebrafish model and elucidate the underlying molecular mechanism of CD induced RP in zebrafish.Materials and methods: The 3 dpf zebrafish larvae were divided into control and CD group. RNA sequencing followed with qRT PCR validating miRNAs and mRNAs. Dual luciferase reporter assay confirmed mmu mir 6240 p3 2's interaction with pde6a. HT22 cells were transfected treated with CD and evaluated for migration invasion malondialdehyde level superoxide dismutase and acetylcholine activities.Results: The results showed 6228 differentially expressed genes and 66 miRNAs differentially expressed in zebrafish exposed to CD. The personal correlation coefficient results showed that mmu mir 6240 p3 2 had the highest correlation coefficient with pde6a and had a negative regulatory relationship. The results of dual luciferase reporter gene further showed that pde6a gene was the direct target of mmu mir 6240 p3 2. Cell experiment results showed that inhibiting mir 6240 p3 2 can upregulate pde6a expression alleviate HT22 cell injury and reverse the inhibition of cell migration and invasion induced by CD.Conclusions: CD induces RP in zebrafish by inhibiting pde6a post transcriptional activity via mmu mir 6240 p3 2. These findings have important implications for understanding the potential side effects of CD and for developing safer therapeutic strategies involving traditional Chinese medicines.         Control1   strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|collection date:not applicable|geo loc name:not applicable|sex:not applicable|tissue:not applicable|treatment:Control group replicate1|BioSampleModel:Model organism or animal                 microRNA seq of Danio rerio: Control group Control 1 Control 1       miRNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina NovaSeq 6000   SRP550004     Control_1.fq.gz fastq 835887501.0 16389951.0 Control 1.fq.gz 0:51 A:193253330;C:196900031;G:252690178;T:192797500;N:246462 51       193253330 196900031 252690178 192797500 246462 SRX27004207 SRS23468962 SRA2029520 Heilongjiang University of Chinese Medicine|College of Traditional Chinese Medicine Heilongjiang University of Chinese Medicine                       T   under 1.2% mapping rate illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2024-12-07 Undetermined Larval Undetermined Undetermined
34290 34290 SRR31640765 SRX27004202 SRS23468965 SRP550004 PRJNA1195374 Cortex Dictamni induces retinitis pigmentosa in zebrafish by inhibiting pde6a post transcriptional activity via mmu mir 6240 p3 2 PRJNA1195374 Other Ethnopharmacological relevance: Cortex Dictamni CD is the dried root skin of Dictamnus dasycarpus Turcz widely used in the field of traditional Chinese medicine. mainly for the treatment of skin diseases. Recent adverse reactions to CD limited the clinical application in combination with other traditional Chinese medicines.Aim of the study: To investigate the retinitis pigmentosa RP effects of CD using the zebrafish model and elucidate the underlying molecular mechanism of CD induced RP in zebrafish.Materials and methods: The 3 dpf zebrafish larvae were divided into control and CD group. RNA sequencing followed with qRT PCR validating miRNAs and mRNAs. Dual luciferase reporter assay confirmed mmu mir 6240 p3 2's interaction with pde6a. HT22 cells were transfected treated with CD and evaluated for migration invasion malondialdehyde level superoxide dismutase and acetylcholine activities.Results: The results showed 6228 differentially expressed genes and 66 miRNAs differentially expressed in zebrafish exposed to CD. The personal correlation coefficient results showed that mmu mir 6240 p3 2 had the highest correlation coefficient with pde6a and had a negative regulatory relationship. The results of dual luciferase reporter gene further showed that pde6a gene was the direct target of mmu mir 6240 p3 2. Cell experiment results showed that inhibiting mir 6240 p3 2 can upregulate pde6a expression alleviate HT22 cell injury and reverse the inhibition of cell migration and invasion induced by CD.Conclusions: CD induces RP in zebrafish by inhibiting pde6a post transcriptional activity via mmu mir 6240 p3 2. These findings have important implications for understanding the potential side effects of CD and for developing safer therapeutic strategies involving traditional Chinese medicines.         CD3   strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|collection date:not applicable|geo loc name:not applicable|sex:not applicable|tissue:not applicable|treatment:Experiment group replicate3|BioSampleModel:Model organism or animal                 microRNA seq of Danio rerio: Experiment group BXP 3 BXP 3       miRNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina NovaSeq 6000   SRP550004     BXP_3.fq.gz fastq 656139327.0 12865477.0 BXP 3.fq.gz 0:51 A:152349522;C:156353407;G:196379918;T:150985088;N:71392 51       152349522 156353407 196379918 150985088 71392 SRX27004202 SRS23468965 SRA2029520 Heilongjiang University of Chinese Medicine|College of Traditional Chinese Medicine Heilongjiang University of Chinese Medicine                       T   under 1.2% mapping rate illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2024-12-07 Undetermined Larval Undetermined Undetermined
34291 34291 SRR31640766 SRX27004201 SRS23468964 SRP550004 PRJNA1195374 Cortex Dictamni induces retinitis pigmentosa in zebrafish by inhibiting pde6a post transcriptional activity via mmu mir 6240 p3 2 PRJNA1195374 Other Ethnopharmacological relevance: Cortex Dictamni CD is the dried root skin of Dictamnus dasycarpus Turcz widely used in the field of traditional Chinese medicine. mainly for the treatment of skin diseases. Recent adverse reactions to CD limited the clinical application in combination with other traditional Chinese medicines.Aim of the study: To investigate the retinitis pigmentosa RP effects of CD using the zebrafish model and elucidate the underlying molecular mechanism of CD induced RP in zebrafish.Materials and methods: The 3 dpf zebrafish larvae were divided into control and CD group. RNA sequencing followed with qRT PCR validating miRNAs and mRNAs. Dual luciferase reporter assay confirmed mmu mir 6240 p3 2's interaction with pde6a. HT22 cells were transfected treated with CD and evaluated for migration invasion malondialdehyde level superoxide dismutase and acetylcholine activities.Results: The results showed 6228 differentially expressed genes and 66 miRNAs differentially expressed in zebrafish exposed to CD. The personal correlation coefficient results showed that mmu mir 6240 p3 2 had the highest correlation coefficient with pde6a and had a negative regulatory relationship. The results of dual luciferase reporter gene further showed that pde6a gene was the direct target of mmu mir 6240 p3 2. Cell experiment results showed that inhibiting mir 6240 p3 2 can upregulate pde6a expression alleviate HT22 cell injury and reverse the inhibition of cell migration and invasion induced by CD.Conclusions: CD induces RP in zebrafish by inhibiting pde6a post transcriptional activity via mmu mir 6240 p3 2. These findings have important implications for understanding the potential side effects of CD and for developing safer therapeutic strategies involving traditional Chinese medicines.         CD2   strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|collection date:not applicable|geo loc name:not applicable|sex:not applicable|tissue:not applicable|treatment:Experiment group replicate2|BioSampleModel:Model organism or animal                 microRNA seq of Danio rerio: Experiment group BXP 2 BXP 2       miRNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina NovaSeq 6000   SRP550004     BXP_2.fq.gz fastq 644434827.0 12635977.0 BXP 2.fq.gz 0:51 A:151820167;C:153674905;G:190467723;T:148402934;N:69098 51       151820167 153674905 190467723 148402934 69098 SRX27004201 SRS23468964 SRA2029520 Heilongjiang University of Chinese Medicine|College of Traditional Chinese Medicine Heilongjiang University of Chinese Medicine                       T   under 1.2% mapping rate illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2024-12-07 Undetermined Larval Undetermined Undetermined
39827 39827 SRR2441454 SRX1321833 SRS1109642 SRP062493 PRJNA293106 Danio rerio Raw sequence reads PRJNA293106 Metagenomics Zebrafish Hypoxia RNAseq     RNAseq at 24hpf following hypoxia   24hpf hypoxia   strain:TU|age:24hpf|sex:not determined|tissue:brain|treatment:hypoxia|BioSampleModel:Model organism or animal                 Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample 24hpf hypoxia 24hpf.hypoxia.3.10329X21 24hpf.hypoxia.3.10329X21 We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition. For hypoxia we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected. We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages. At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation. RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer. The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides single end stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.     RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP062493     10329X21_130822_SN141_0719_AD2CK5ACXX_7.txt.gz fastq 1205447950.0 24108959.0 24hpf.hypoxia.3.10329X21 0:50 A:299680333;C:267717935;G:264833481;T:357936794;N:15279407 50       299680333 267717935 264833481 357936794 15279407 SRX1321833 SRS1109642 SRA289450 University of Utah|Bonkowsky University of Utah 1 0.87455   0.24266   0.74121   0.57777   50   B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   United States 2015-10-10 Pharyngula Embryo Brain Nervous System
39828 39828 SRR2437828 SRX1321832 SRS1109643 SRP062493 PRJNA293106 Danio rerio Raw sequence reads PRJNA293106 Metagenomics Zebrafish Hypoxia RNAseq     RNAseq at 48hpf following normoxia   48hpf normoxia   strain:TU|age:48hpf|sex:not determined|tissue:brain|treatment:normoxia|BioSampleModel:Model organism or animal                 Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample 48hpf normoxia 48hpf.normoxia.3.10329X16 48hpf.normoxia.3.10329X16 We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition. For hypoxia we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected. We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages. At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation. RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer. The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides single end stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.     RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP062493     10329X16_130822_SN141_0719_AD2CK5ACXX_6.txt.gz fastq 985942500.0 19718850.0 48hpf.normoxia.3.10329X16 0:50 A:251856100;C:223081125;G:216430606;T:294554748;N:19921 50       251856100 223081125 216430606 294554748 19921 SRX1321832 SRS1109643 SRA289450 University of Utah|Bonkowsky University of Utah 1 0.94791   0.26704   0.68708   0.54445   50   B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   United States 2015-10-10 Hatching Embryo Brain Nervous System
39829 39829 SRR2434699 SRX1321831 SRS1109642 SRP062493 PRJNA293106 Danio rerio Raw sequence reads PRJNA293106 Metagenomics Zebrafish Hypoxia RNAseq     RNAseq at 24hpf following hypoxia   24hpf hypoxia   strain:TU|age:24hpf|sex:not determined|tissue:brain|treatment:hypoxia|BioSampleModel:Model organism or animal                 Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample 24hpf hypoxia 24hpf.hypoxia.2.10329X11 24hpf.hypoxia.2.10329X11 We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition. For hypoxia we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected. We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages. At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation. RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer. The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides single end stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.     RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP062493     10329X11_130822_SN141_0719_AD2CK5ACXX_5.txt.gz fastq 1227682750.0 24553655.0 24hpf.hypoxia.2.10329X11 0:50 A:299759613;C:292757497;G:281904026;T:353193075;N:68539 50       299759613 292757497 281904026 353193075 68539 SRX1321831 SRS1109642 SRA289450 University of Utah|Bonkowsky University of Utah 1 0.94855   0.27579   0.73298   0.58307   50   B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   United States 2015-10-07 Pharyngula Embryo Brain Nervous System
39830 39830 SRR2433795 SRX1321830 SRS1109644 SRP062493 PRJNA293106 Danio rerio Raw sequence reads PRJNA293106 Metagenomics Zebrafish Hypoxia RNAseq     RNAseq at 60hpf following normoxia   60hpf Normoxia   strain:TU|age:60hpf|sex:not determined|tissue:brain|treatment:normoxia|BioSampleModel:Model organism or animal                 Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample 60hpf Normoxia 60hpf.normoxia.3. 60hpf.normoxia.3. We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition. For hypoxia we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected. We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages. At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation. RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer. The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides single end stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.     RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP062493     10329X8_130822_SN141_0719_AD2CK5ACXX_5.txt.gz fastq 1112799950.0 22255999.0 60hpf.normoxia.3. 0:50 A:294304558;C:248234752;G:238088577;T:332109252;N:62811 50       294304558 248234752 238088577 332109252 62811 SRX1321830 SRS1109644 SRA289450 University of Utah|Bonkowsky University of Utah 1 0.94922   0.34314   0.67838   0.51455   50   B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   United States 2015-10-10 Hatching Embryo Brain Nervous System
39831 39831 SRR2426760 SRX1321829 SRS1109645 SRP062493 PRJNA293106 Danio rerio Raw sequence reads PRJNA293106 Metagenomics Zebrafish Hypoxia RNAseq     RNAseq at 36hpf following hypoxia   36hpf hypoxia   strain:TU|age:36hpf|sex:not determined|tissue:brain|treatment:hypoxia|BioSampleModel:Model organism or animal                 Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample 36hpf hypoxia 36hpf.hypoxia.1.10329X4 36hpf.hypoxia.1.10329X4 We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition. For hypoxia we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected. We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages. At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation. RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer. The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides single end stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.     RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP062493     10329X4_130822_SN141_0719_AD2CK5ACXX_4.txt.gz fastq 1604107450.0 32082149.0 36hpf.hypoxia.1.10329X4 0:50 A:395786409;C:358263833;G:358391489;T:491601452;N:64267 50       395786409 358263833 358391489 491601452 64267 SRX1321829 SRS1109645 SRA289450 University of Utah|Bonkowsky University of Utah 1 0.95408   0.28965   0.69593   0.54826   50   B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   United States 2015-10-10 Pharyngula Embryo Brain Nervous System
39832 39832 SRR2417497 SRX1321828 SRS1109646 SRP062493 PRJNA293106 Danio rerio Raw sequence reads PRJNA293106 Metagenomics Zebrafish Hypoxia RNAseq     RNAseq at 48hpf following hypoxia   48hpf hypoxia   strain:TU|age:48hpf|sex:not determined|tissue:brain|treatment:hypoxia|BioSampleModel:Model organism or animal                 Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample 48hpf hypoxia 48hpf.hypoxia.3.10329X25 48hpf.hypoxia.3.10329X25 We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition. For hypoxia we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected. We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages. At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation. RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer. The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides single end stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.     RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP062493     10329X25_130822_SN141_0719_AD2CK5ACXX_8.txt.gz fastq 1234710500.0 24694210.0 48hpf.hypoxia.3.10329X25 0:50 A:309392529;C:284311489;G:275471070;T:365515358;N:20054 50       309392529 284311489 275471070 365515358 20054 SRX1321828 SRS1109646 SRA289450 University of Utah|Bonkowsky University of Utah 1 0.94675   0.25877   0.71453   0.5239   50   B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   United States 2015-09-16 Hatching Embryo Brain Nervous System
39833 39833 SRR2417496 SRX1321827 SRS1109644 SRP062493 PRJNA293106 Danio rerio Raw sequence reads PRJNA293106 Metagenomics Zebrafish Hypoxia RNAseq     RNAseq at 60hpf following normoxia   60hpf Normoxia   strain:TU|age:60hpf|sex:not determined|tissue:brain|treatment:normoxia|BioSampleModel:Model organism or animal                 Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample 60hpf Normoxia 60hpf.normoxia.2.10329X28 60hpf.normoxia.2.10329X28 We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition. For hypoxia we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected. We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages. At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation. RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer. The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides single end stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.     RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP062493     10329X28_130822_SN141_0719_AD2CK5ACXX_8.txt.gz fastq 1015786750.0 20315735.0 60hpf.normoxia.2.10329X28 0:50 A:259102784;C:230364456;G:226008843;T:300294199;N:16468 50       259102784 230364456 226008843 300294199 16468 SRX1321827 SRS1109644 SRA289450 University of Utah|Bonkowsky University of Utah 1 0.95197   0.30503   0.68333   0.52243   50   B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   United States 2015-09-16 Hatching Embryo Brain Nervous System
39834 39834 SRR2400601 SRX1321826 SRS1109642 SRP062493 PRJNA293106 Danio rerio Raw sequence reads PRJNA293106 Metagenomics Zebrafish Hypoxia RNAseq     RNAseq at 24hpf following hypoxia   24hpf hypoxia   strain:TU|age:24hpf|sex:not determined|tissue:brain|treatment:hypoxia|BioSampleModel:Model organism or animal                 Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample 24hpf hypoxia 24hpf.hypoxia.1.10329X2 24hpf.hypoxia.1.10329X2 We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition. For hypoxia we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected. We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages. At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation. RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer. The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides single end stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.     RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP062493     10329X2_130822_SN141_0719_AD2CK5ACXX_4.txt.gz fastq 1249046350.0 24980927.0 24hpf.hypoxia.1.10329X2 0:50 A:309098695;C:281875016;G:278706888;T:379315616;N:50135 50       309098695 281875016 278706888 379315616 50135 SRX1321826 SRS1109642 SRA289450 University of Utah|Bonkowsky University of Utah 1 0.95443   0.27405   0.69747   0.40987   50   B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   United States 2015-10-10 Pharyngula Embryo Brain Nervous System
39835 39835 SRR2382596 SRX1321825 SRS1109647 SRP062493 PRJNA293106 Danio rerio Raw sequence reads PRJNA293106 Metagenomics Zebrafish Hypoxia RNAseq     RNAseq at 72hpf following normoxia   72hpf normoxia   strain:TU|age:72hpf|sex:not determined|tissue:brain|treatment:normoxia|BioSampleModel:Model organism or animal                 Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample 72hpf normoxia 72hpf.normoxia.3.10329X30 72hpf.normoxia.3.10329X30 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     10329X30_130822_SN141_0719_AD2CK5ACXX_8.txt.gz fastq 1202543000.0 24050860.0 72hpf.normoxia.3.10329X30 0:50 A:317814132;C:265339479;G:263354488;T:356015292;N:19609 50       317814132 265339479 263354488 356015292 19609 SRX1321825 SRS1109647 SRA289450 University of Utah|Bonkowsky University of Utah 1 0.94396   0.39792   0.68592   0.51696   50   B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   United States 2015-10-10 Larval Larval Brain Nervous System
39836 39836 SRR2346975 SRX1321824 SRS1109649 SRP062493 PRJNA293106 Danio rerio Raw sequence reads PRJNA293106 Metagenomics Zebrafish Hypoxia RNAseq     RNAseq at 72hpf following hypoxia   72hpf hypoxia   strain:TU|age:72hpf|sex:not determined|tissue:brain|treatment:hypoxia|BioSampleModel:Model organism or animal                 Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample 72hpf hypoxia 72hpf.hypoxia.3.10329X29 72hpf.hypoxia.3.10329X29 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     10329X29_130822_SN141_0719_AD2CK5ACXX_8.txt.gz fastq 977694000.0 19553880.0 72hpf.hypoxia.3.10329X29 0:50 A:252845467;C:218082615;G:213237499;T:293512810;N:15609 50       252845467 218082615 213237499 293512810 15609 SRX1321824 SRS1109649 SRA289450 University of Utah|Bonkowsky University of Utah 1 0.94858   0.35206   0.68889   0.53177   50   B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   United States 2015-09-10 Larval Larval Brain Nervous System
39837 39837 SRR2342161 SRX1321823 SRS1109648 SRP062493 PRJNA293106 Danio rerio Raw sequence reads PRJNA293106 Metagenomics Zebrafish Hypoxia RNAseq     RNAseq at 60hpf following hypoxia   60hpf hypoxia   strain:TU|age:60hpf|sex:not determined|tissue:brain|treatment:hypoxia|BioSampleModel:Model organism or animal                 Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample 60hpf hypoxia 60hpf.hypoxia.3.10329X27 60hpf.hypoxia.3.10329X27 We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition. For hypoxia we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected. We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages. At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation. RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer. The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides single end stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.     RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP062493     10329X27_130822_SN141_0719_AD2CK5ACXX_8.txt.gz fastq 1073269500.0 21465390.0 60hpf.hypoxia.3.10329X27 0:50 A:280500644;C:237758835;G:234061287;T:320931292;N:17442 50       280500644 237758835 234061287 320931292 17442 SRX1321823 SRS1109648 SRA289450 University of Utah|Bonkowsky University of Utah 1 0.94774   0.36354   0.70065   0.51075   50   B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   United States 2015-10-10 Hatching Embryo Brain Nervous System
39838 39838 SRR2341509 SRX1321822 SRS1109643 SRP062493 PRJNA293106 Danio rerio Raw sequence reads PRJNA293106 Metagenomics Zebrafish Hypoxia RNAseq     RNAseq at 48hpf following normoxia   48hpf normoxia   strain:TU|age:48hpf|sex:not determined|tissue:brain|treatment:normoxia|BioSampleModel:Model organism or animal                 Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample 48hpf normoxia 48hpf.normoxia.210329X26 48hpf.normoxia.210329X26 We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition. For hypoxia we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected. We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages. At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation. RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer. The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides single end stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.     RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP062493     10329X26_130822_SN141_0719_AD2CK5ACXX_8.txt.gz fastq 1075868850.0 21517377.0 48hpf.normoxia.210329X26 0:50 A:271795722;C:246789566;G:240496674;T:316769688;N:17200 50       271795722 246789566 240496674 316769688 17200 SRX1321822 SRS1109643 SRA289450 University of Utah|Bonkowsky University of Utah 1 0.94644   0.26805   0.68745   0.53833   50   B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   United States 2015-10-10 Hatching Embryo Brain Nervous System
39839 39839 SRR2340149 SRX1321821 SRS1109650 SRP062493 PRJNA293106 Danio rerio Raw sequence reads PRJNA293106 Metagenomics Zebrafish Hypoxia RNAseq     RNAseq at 36hpf following normoxia   36hpf normoxia   strain:TU|age:36hpf|sex:not determined|tissue:brain|treatment:normoxia|BioSampleModel:Model organism or animal                 Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample 36hpf normoxia 36hpf.normoxia.3.10329X24 36hpf.normoxia.3.10329X24 We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition. For hypoxia we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected. We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages. At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation. RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer. The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides single end stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.     RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP062493     10329X24_130822_SN141_0719_AD2CK5ACXX_7.txt.gz fastq 1588630750.0 31772615.0 36hpf.normoxia.3.10329X24 0:50 A:404319446;C:349459823;G:346545846;T:468209953;N:20095682 50       404319446 349459823 346545846 468209953 20095682 SRX1321821 SRS1109650 SRA289450 University of Utah|Bonkowsky University of Utah 1 0.8739   0.32489   0.71701   0.51646   50   B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   United States 2015-10-10 Pharyngula Embryo Brain Nervous System
39840 39840 SRR2245887 SRX1321820 SRS1109645 SRP062493 PRJNA293106 Danio rerio Raw sequence reads PRJNA293106 Metagenomics Zebrafish Hypoxia RNAseq     RNAseq at 36hpf following hypoxia   36hpf hypoxia   strain:TU|age:36hpf|sex:not determined|tissue:brain|treatment:hypoxia|BioSampleModel:Model organism or animal                 Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample 36hpf hypoxia 36hpf.hypoxia.3.10329X23 36hpf.hypoxia.3.10329X23 We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition. For hypoxia we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected. We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages. At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation. RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer. The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides single end stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.     RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP062493     10329X23_130822_SN141_0719_AD2CK5ACXX_7.txt.gz fastq 1207331350.0 24146627.0 36hpf.hypoxia.3.10329X23 0:50 A:305628501;C:266059461;G:259888045;T:360487730;N:15267613 50       305628501 266059461 259888045 360487730 15267613 SRX1321820 SRS1109645 SRA289450 University of Utah|Bonkowsky University of Utah 1 0.87814   0.27249   0.72853   0.53527   50   B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   United States 2015-10-10 Pharyngula Embryo Brain Nervous System
39841 39841 SRR2245257 SRX1321819 SRS1109651 SRP062493 PRJNA293106 Danio rerio Raw sequence reads PRJNA293106 Metagenomics Zebrafish Hypoxia RNAseq     RNAseq at 24hpf following normoxia   24hpf normoxia   strain:TU|age:24hpf|sex:not determined|tissue:brain|treatment:normoxia|BioSampleModel:Model organism or animal                 Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample 24hpf normoxia 24hpf.normoxia.3.10329X22 24hpf.normoxia.3.10329X22 We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition. For hypoxia we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected. We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages. At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation. RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer. The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides single end stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.     RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP062493     10329X22_130822_SN141_0719_AD2CK5ACXX_7.txt.gz fastq 1257159050.0 25143181.0 24hpf.normoxia.3.10329X22 0:50 A:320558638;C:275312235;G:271710647;T:373637690;N:15939840 50       320558638 275312235 271710647 373637690 15939840 SRX1321819 SRS1109651 SRA289450 University of Utah|Bonkowsky University of Utah 1 0.87634   0.30298   0.71356   0.54673   50   B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   United States 2015-10-10 Pharyngula Embryo Brain Nervous System
39842 39842 SRR2243358 SRX1321818 SRS1109647 SRP062493 PRJNA293106 Danio rerio Raw sequence reads PRJNA293106 Metagenomics Zebrafish Hypoxia RNAseq     RNAseq at 72hpf following normoxia   72hpf normoxia   strain:TU|age:72hpf|sex:not determined|tissue:brain|treatment:normoxia|BioSampleModel:Model organism or animal                 Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample 72hpf normoxia 72hpf.normoxia.2.10329X20 72hpf.normoxia.2.10329X20 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     10329X20_130822_SN141_0719_AD2CK5ACXX_7.txt.gz fastq 1530276050.0 30605521.0 72hpf.normoxia.2.10329X20 0:50 A:387360143;C:340062704;G:324515181;T:458965961;N:19372061 50       387360143 340062704 324515181 458965961 19372061 SRX1321818 SRS1109647 SRA289450 University of Utah|Bonkowsky University of Utah 1 0.8774   0.25469   0.68799   0.52777   50   B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   United States 2015-10-10 Larval Larval Brain Nervous System
39843 39843 SRR2243161 SRX1321817 SRS1109649 SRP062493 PRJNA293106 Danio rerio Raw sequence reads PRJNA293106 Metagenomics Zebrafish Hypoxia RNAseq     RNAseq at 72hpf following hypoxia   72hpf hypoxia   strain:TU|age:72hpf|sex:not determined|tissue:brain|treatment:hypoxia|BioSampleModel:Model organism or animal                 Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample 72hpf hypoxia 72hpf.hypoxia.2.10329X19 72hpf.hypoxia.2.10329X19 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     10329X19_130822_SN141_0719_AD2CK5ACXX_7.txt.gz fastq 1866619850.0 37332397.0 72hpf.hypoxia.2.10329X19 0:50 A:465524152;C:423400277;G:418937882;T:535202326;N:23555213 50       465524152 423400277 418937882 535202326 23555213 SRX1321817 SRS1109649 SRA289450 University of Utah|Bonkowsky University of Utah 1 0.85514   0.26828   0.7041   0.54006   50   B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   United States 2015-10-10 Larval Larval Brain Nervous System
39844 39844 SRR2241311 SRX1321816 SRS1109644 SRP062493 PRJNA293106 Danio rerio Raw sequence reads PRJNA293106 Metagenomics Zebrafish Hypoxia RNAseq     RNAseq at 60hpf following normoxia   60hpf Normoxia   strain:TU|age:60hpf|sex:not determined|tissue:brain|treatment:normoxia|BioSampleModel:Model organism or animal                 Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample 60hpf Normoxia 60hpf.normoxia.1.10329X18 60hpf.normoxia.1.10329X18 We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition. For hypoxia we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected. We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages. At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation. RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer. The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides single end stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.     RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP062493     10329X18_130822_SN141_0719_AD2CK5ACXX_6.txt.gz fastq 1118115050.0 22362301.0 60hpf.normoxia.1.10329X18 0:50 A:287072563;C:255244675;G:248573701;T:327203388;N:20723 50       287072563 255244675 248573701 327203388 20723 SRX1321816 SRS1109644 SRA289450 University of Utah|Bonkowsky University of Utah 1 0.93238   0.30064   0.68574   0.51934   50   B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   United States 2015-10-10 Hatching Embryo Brain Nervous System
39845 39845 SRR2240748 SRX1321815 SRS1109648 SRP062493 PRJNA293106 Danio rerio Raw sequence reads PRJNA293106 Metagenomics Zebrafish Hypoxia RNAseq     RNAseq at 60hpf following hypoxia   60hpf hypoxia   strain:TU|age:60hpf|sex:not determined|tissue:brain|treatment:hypoxia|BioSampleModel:Model organism or animal                 Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample 60hpf hypoxia 60hpf.hypoxia.2.10329X17 60hpf.hypoxia.2.10329X17 We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition. For hypoxia we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected. We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages. At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation. RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer. The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides single end stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.     RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP062493     10329X17_130822_SN141_0719_AD2CK5ACXX_6.txt.gz fastq 1074686900.0 21493738.0 60hpf.hypoxia.2.10329X17 0:50 A:276432361;C:244039609;G:234638386;T:319556004;N:20540 50       276432361 244039609 234638386 319556004 20540 SRX1321815 SRS1109648 SRA289450 University of Utah|Bonkowsky University of Utah 1 0.9502   0.3077   0.6899   0.50645   50   B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   United States 2015-09-03 Hatching Embryo Brain Nervous System
39846 39846 SRR2239869 SRX1321814 SRS1109646 SRP062493 PRJNA293106 Danio rerio Raw sequence reads PRJNA293106 Metagenomics Zebrafish Hypoxia RNAseq     RNAseq at 48hpf following hypoxia   48hpf hypoxia   strain:TU|age:48hpf|sex:not determined|tissue:brain|treatment:hypoxia|BioSampleModel:Model organism or animal                 Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample 48hpf hypoxia 48hpf.hypoxia.2.10329X15 48hpf.hypoxia.2.10329X15 We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition. For hypoxia we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected. We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages. At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation. RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer. The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides single end stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.     RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP062493     10329X15_130822_SN141_0719_AD2CK5ACXX_6.txt.gz fastq 1111913550.0 22238271.0 48hpf.hypoxia.2.10329X15 0:50 A:288023952;C:248947169;G:243195362;T:331723738;N:23329 50       288023952 248947169 243195362 331723738 23329 SRX1321814 SRS1109646 SRA289450 University of Utah|Bonkowsky University of Utah 1 0.93753   0.34521   0.70246   0.51535   50   B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   United States 2015-10-10 Hatching Embryo Brain Nervous System
39847 39847 SRR2239772 SRX1321813 SRS1109650 SRP062493 PRJNA293106 Danio rerio Raw sequence reads PRJNA293106 Metagenomics Zebrafish Hypoxia RNAseq     RNAseq at 36hpf following normoxia   36hpf normoxia   strain:TU|age:36hpf|sex:not determined|tissue:brain|treatment:normoxia|BioSampleModel:Model organism or animal                 Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample 36hpf normoxia 36hpf.normoxia.2.10329X14 36hpf.normoxia.2.10329X14 We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition. For hypoxia we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected. We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages. At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation. RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer. The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides single end stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.     RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP062493     10329X14_130822_SN141_0719_AD2CK5ACXX_6.txt.gz fastq 1533885200.0 30677704.0 36hpf.normoxia.2.10329X14 0:50 A:392813056;C:354469675;G:348871622;T:437692730;N:38117 50       392813056 354469675 348871622 437692730 38117 SRX1321813 SRS1109650 SRA289450 University of Utah|Bonkowsky University of Utah 1 0.91439   0.31812   0.70863   0.51667   50   B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   United States 2015-10-10 Pharyngula Embryo Brain Nervous System
39848 39848 SRR2232685 SRX1321812 SRS1109645 SRP062493 PRJNA293106 Danio rerio Raw sequence reads PRJNA293106 Metagenomics Zebrafish Hypoxia RNAseq     RNAseq at 36hpf following hypoxia   36hpf hypoxia   strain:TU|age:36hpf|sex:not determined|tissue:brain|treatment:hypoxia|BioSampleModel:Model organism or animal                 Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample 36hpf hypoxia 36hpf.hypoxia.2.10329X13 36hpf.hypoxia.2.10329X13 We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition. For hypoxia we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected. We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages. At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation. RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer. The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides single end stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.     RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP062493     10329X13_130822_SN141_0719_AD2CK5ACXX_6.txt.gz fastq 1112846200.0 22256924.0 36hpf.hypoxia.2.10329X13 0:50 A:279147206;C:259582122;G:249642505;T:324452965;N:21402 50       279147206 259582122 249642505 324452965 21402 SRX1321812 SRS1109645 SRA289450 University of Utah|Bonkowsky University of Utah 1 0.94469   0.25952   0.72243   0.52701   50   B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   United States 2015-10-10 Pharyngula Embryo Brain Nervous System
39849 39849 SRR2227658 SRX1321811 SRS1109651 SRP062493 PRJNA293106 Danio rerio Raw sequence reads PRJNA293106 Metagenomics Zebrafish Hypoxia RNAseq     RNAseq at 24hpf following normoxia   24hpf normoxia   strain:TU|age:24hpf|sex:not determined|tissue:brain|treatment:normoxia|BioSampleModel:Model organism or animal                 Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample 24hpf normoxia 24hpf.normoxia.2.10329X12 24hpf.normoxia.2.10329X12 We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition. For hypoxia we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected. We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages. At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation. RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer. The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides single end stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.     RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP062493     10329X12_130822_SN141_0719_AD2CK5ACXX_5.txt.gz fastq 1243623750.0 24872475.0 24hpf.normoxia.2.10329X12 0:50 A:317179221;C:285081899;G:274648790;T:366643275;N:70565 50       317179221 285081899 274648790 366643275 70565 SRX1321811 SRS1109651 SRA289450 University of Utah|Bonkowsky University of Utah 1 0.95045   0.27525   0.69688   0.53555   50   B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   United States 2015-09-01 Pharyngula Embryo Brain Nervous System
39850 39850 SRR2227378 SRX1321810 SRS1109647 SRP062493 PRJNA293106 Danio rerio Raw sequence reads PRJNA293106 Metagenomics Zebrafish Hypoxia RNAseq     RNAseq at 72hpf following normoxia   72hpf normoxia   strain:TU|age:72hpf|sex:not determined|tissue:brain|treatment:normoxia|BioSampleModel:Model organism or animal                 Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample 72hpf normoxia 72hpf.normoxia.1.10329X10 72hpf.normoxia.1.10329X10 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     10329X10_130822_SN141_0719_AD2CK5ACXX_5.txt.gz fastq 1268552500.0 25371050.0 72hpf.normoxia.1.10329X10 0:50 A:334230065;C:286785060;G:271795849;T:375668734;N:72792 50       334230065 286785060 271795849 375668734 72792 SRX1321810 SRS1109647 SRA289450 University of Utah|Bonkowsky University of Utah 1 0.94017   0.34471   0.67109   0.5244   50   B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   United States 2015-09-18 Larval Larval Brain Nervous System
39851 39851 SRR2226742 SRX1321809 SRS1109649 SRP062493 PRJNA293106 Danio rerio Raw sequence reads PRJNA293106 Metagenomics Zebrafish Hypoxia RNAseq     RNAseq at 72hpf following hypoxia   72hpf hypoxia   strain:TU|age:72hpf|sex:not determined|tissue:brain|treatment:hypoxia|BioSampleModel:Model organism or animal                 Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample 72hpf hypoxia 72hpf.hypoxia.1.10329X9 72hpf.hypoxia.1.10329X9 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     10329X9_130822_SN141_0719_AD2CK5ACXX_5.txt.gz fastq 1625518100.0 32510362.0 72hpf.hypoxia.1.10329X9 0:50 A:428393257;C:366720934;G:349089971;T:481221434;N:92504 50       428393257 366720934 349089971 481221434 92504 SRX1321809 SRS1109649 SRA289450 University of Utah|Bonkowsky University of Utah 1 0.9444   0.36232   0.67503   0.53278   50   B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   United States 2015-10-10 Larval Larval Brain Nervous System
39852 39852 SRR2225888 SRX1321808 SRS1109648 SRP062493 PRJNA293106 Danio rerio Raw sequence reads PRJNA293106 Metagenomics Zebrafish Hypoxia RNAseq     RNAseq at 60hpf following hypoxia   60hpf hypoxia   strain:TU|age:60hpf|sex:not determined|tissue:brain|treatment:hypoxia|BioSampleModel:Model organism or animal                 Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample 60hpf hypoxia 60hpf.hypoxia.1.10329X7 60hpf.hypoxia.1.10329X7 We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition. For hypoxia we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected. We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages. At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation. RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer. The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides single end stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.     RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP062493     10329X7_130822_SN141_0719_AD2CK5ACXX_5.txt.gz fastq 1102232350.0 22044647.0 60hpf.hypoxia.1.10329X7 0:50 A:288570352;C:247978180;G:238128703;T:327492563;N:62552 50       288570352 247978180 238128703 327492563 62552 SRX1321808 SRS1109648 SRA289450 University of Utah|Bonkowsky University of Utah 1 0.94824   0.31808   0.69244   0.51505   50   B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   United States 2015-10-10 Hatching Embryo Brain Nervous System
39853 39853 SRR2225789 SRX1321807 SRS1109646 SRP062493 PRJNA293106 Danio rerio Raw sequence reads PRJNA293106 Metagenomics Zebrafish Hypoxia RNAseq     RNAseq at 48hpf following hypoxia   48hpf hypoxia   strain:TU|age:48hpf|sex:not determined|tissue:brain|treatment:hypoxia|BioSampleModel:Model organism or animal                 Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample 48hpf hypoxia 48hpf.hypoxia.1.10329X6 48hpf.hypoxia.1.10329X6 We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition. For hypoxia we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected. We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages. At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation. RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer. The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides single end stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.     RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP062493     10329X6_130822_SN141_0719_AD2CK5ACXX_4.txt.gz fastq 1250042950.0 25000859.0 48hpf.hypoxia.1.10329X6 0:50 A:312511165;C:283310381;G:277279378;T:376891744;N:50282 50       312511165 283310381 277279378 376891744 50282 SRX1321807 SRS1109646 SRA289450 University of Utah|Bonkowsky University of Utah 1 0.94959   0.28331   0.68757   0.53976   50   B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   United States 2015-09-01 Hatching Embryo Brain Nervous System
39854 39854 SRR2225675 SRX1321806 SRS1109650 SRP062493 PRJNA293106 Danio rerio Raw sequence reads PRJNA293106 Metagenomics Zebrafish Hypoxia RNAseq     RNAseq at 36hpf following normoxia   36hpf normoxia   strain:TU|age:36hpf|sex:not determined|tissue:brain|treatment:normoxia|BioSampleModel:Model organism or animal                 Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample 36hpf normoxia 36hpf.normoxia.1.10329X5 36hpf.normoxia.1.10329X5 We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition. For hypoxia we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected. We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages. At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation. RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer. The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides single end stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.     RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP062493     10329X5_130822_SN141_0719_AD2CK5ACXX_4.txt.gz fastq 1244744700.0 24894894.0 36hpf.normoxia.1.10329X5 0:50 A:301597123;C:287750990;G:281194881;T:374152417;N:49289 50       301597123 287750990 281194881 374152417 49289 SRX1321806 SRS1109650 SRA289450 University of Utah|Bonkowsky University of Utah 1 0.95571   0.22791   0.71177   0.53801   50   B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   United States 2015-10-10 Pharyngula Embryo Brain Nervous System
39855 39855 SRR2225572 SRX1321805 SRS1109651 SRP062493 PRJNA293106 Danio rerio Raw sequence reads PRJNA293106 Metagenomics Zebrafish Hypoxia RNAseq     RNAseq at 24hpf following normoxia   24hpf normoxia   strain:TU|age:24hpf|sex:not determined|tissue:brain|treatment:normoxia|BioSampleModel:Model organism or animal                 Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample 24hpf normoxia 24hpf.normoxia.1.10329X3 24hpf.normoxia.1.10329X3 We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition. For hypoxia we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected. We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages. At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation. RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer. The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides single end stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.     RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP062493     10329X3_130822_SN141_0719_AD2CK5ACXX_4.txt.gz fastq 1293605500.0 25872110.0 24hpf.normoxia.1.10329X3 0:50 A:310265067;C:296406990;G:295054246;T:391826687;N:52510 50       310265067 296406990 295054246 391826687 52510 SRX1321805 SRS1109651 SRA289450 University of Utah|Bonkowsky University of Utah 1 0.95596   0.21907   0.71512   0.39029   50   B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   United States 2015-09-01 Pharyngula Embryo Brain Nervous System
39856 39856 SRR2222835 SRX1321804 SRS1109643 SRP062493 PRJNA293106 Danio rerio Raw sequence reads PRJNA293106 Metagenomics Zebrafish Hypoxia RNAseq     RNAseq at 48hpf following normoxia   48hpf normoxia   strain:TU|age:48hpf|sex:not determined|tissue:brain|treatment:normoxia|BioSampleModel:Model organism or animal                 Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample 48hpf normoxia 48hpf.1.10329X1 48hpf.1.10329X1 We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition. For hypoxia we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected. We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages. At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation. RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer. The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides single end stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.     RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP062493     10329X1_130822_SN141_0719_AD2CK5ACXX_4.txt.gz fastq 1215136450.0 24302729.0 48hpf.1.10329X1 0:50 A:291802893;C:276442849;G:277217342;T:369624915;N:48451 50       291802893 276442849 277217342 369624915 48451 SRX1321804 SRS1109643 SRA289450 University of Utah|Bonkowsky University of Utah 1 0.95575   0.23021   0.72679   0.60296   50   B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   United States 2015-09-01 Hatching Embryo Brain Nervous System

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