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687 rows where devstage_curation = "Pharyngula" and tissue_curation = "Brain"

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technology 4

experiment.platform 2

experiment.library_source 2

experiment.library_selection 2

experiment.library_layout 2

tissue_curation_coarse 1

tissue_curation 1

  • Brain · 687 ✖

experiment.library_strategy 1

devstage_curation_coarse 1

devstage_curation 1

  • Pharyngula · 687 ✖
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
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
35387 35387 SRR32649450 SRX27953869 SRS24319773 SRP569567 PRJNA1234533 Delta family protocadhins contribute to protoglomerular targeting of olfactory sensory neuron axons in the olfactory bulb GSE291626 Transcriptome Analysis To understand how neural circuits are assembled it is essential to identify and characterize the axonal guidance cues and receptors that determine the axonal trajectories and connections between neurons. We performed single cell RNA sequencing of olfactory sensory neurons from zebrafish to identify candidate axonal guidance related genes that are differentially expressed according to sensory axon target location in the olfactory bulb. Among the candidates we identified were several members of the non clustered delta protocadherin family of adhesion molecules. We found that two members of the delta1 protocadherin family pcdh7b and pcdh11 are most highly expressed in sensory neurons that project to the DZ protoglomerulus. Knocking down either one impairs the ability of sensory axons to terminate within the DZ protoglomerulus but does not affect the ability of other sensory axons from terminating normally in the CZ protoglomerulus. In contrast two members of the delta2 protocadherin family pcdh10b and pcdh17 are most highly expressed in sensory neurons that project to the CZ protoglomerulus. Knocking down pcdh10b induces ectopic terminations of CZ projecting sensory axons. Knocking down pcdh17 induces substantial ectopic axonal trajectories and impairs CZ projecting sensory axons from finding and terminating in the CZ protoglomerulus. Knockdowns of either pcdh10b or pcdh17 do not affect DZ projecting sensory axons. These findings suggest that delta1 protocadherins help DZ projecting sensory axons enter and remain within the DZ protoglomerulus while delta2 protocadherins help CZ projecting sensory axons navigate to the CZ protoglomerulus. Overall design: Roughly 2000 zebrafish embryos we sacraficed at 36 48 hpf and 72 hpf. Olfactory tissue was dissociated in FACSmax dissosciation medium and then FACsorted to isolate OMP:RFP positive neurons.       OMP positive Olfactory Sensory Neurons from 36hpf Zebrafish GSM8838716   source name:Olfactory Sensory Tissue|tissue:Olfactory Sensory Tissue|cell line:Olactory Sensory Neurons|cell type:Neurons|sample age:36 hpf|genotype:Tgomp:lyn RFP|geo loc name:missing|collection date:missing OMP positive Olfactory Sensory Neurons from 36hpf Zebrafish Cell Ranger V3.0.1 Assembly: GRCz11 Supplementary files format and content: Demultiplexed 10x Genomics Files. Olfactory Sensory Tissue   10X Genomics V3.3   tissue:Olfactory Sensory Tissue|cell line:Olactory Sensory Neurons|cell type:Neurons|sample age:36 hpf|genotype:Tgomp:lyn RFP GSM8838716 GSM8838716: OMP positive Olfactory Sensory Neurons from 36hpf Zebrafish; Danio rerio; RNA Seq GSM8838716 r1 GSM8838716 1 10X Genomics V3.3   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP569567   loader:fastq load.py 97366_S7_L001_I1_001.fastq.gz 97366_S7_L001_R1_001.fastq.gz 97366_S7_L001_R2_001.fastq.gz fastq fastq fastq 5962313630.0 45863951.0 GSM8838716 r1 0:8 1:28 2:94 A:1285269727;C:856096209;G:931439088;T:1238303640;N:102730 8 28 94   1285269727 856096209 931439088 1238303640 102730 SRX27953869 SRS24319773 SRA2091725 Department of Neuroscience, University of Pennsylvania Department of Neuroscience, University of Pennsylvania                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2025-03-11 Pharyngula Embryo Brain Nervous System
35388 35388 SRR32649451 SRX27953869 SRS24319773 SRP569567 PRJNA1234533 Delta family protocadhins contribute to protoglomerular targeting of olfactory sensory neuron axons in the olfactory bulb GSE291626 Transcriptome Analysis To understand how neural circuits are assembled it is essential to identify and characterize the axonal guidance cues and receptors that determine the axonal trajectories and connections between neurons. We performed single cell RNA sequencing of olfactory sensory neurons from zebrafish to identify candidate axonal guidance related genes that are differentially expressed according to sensory axon target location in the olfactory bulb. Among the candidates we identified were several members of the non clustered delta protocadherin family of adhesion molecules. We found that two members of the delta1 protocadherin family pcdh7b and pcdh11 are most highly expressed in sensory neurons that project to the DZ protoglomerulus. Knocking down either one impairs the ability of sensory axons to terminate within the DZ protoglomerulus but does not affect the ability of other sensory axons from terminating normally in the CZ protoglomerulus. In contrast two members of the delta2 protocadherin family pcdh10b and pcdh17 are most highly expressed in sensory neurons that project to the CZ protoglomerulus. Knocking down pcdh10b induces ectopic terminations of CZ projecting sensory axons. Knocking down pcdh17 induces substantial ectopic axonal trajectories and impairs CZ projecting sensory axons from finding and terminating in the CZ protoglomerulus. Knockdowns of either pcdh10b or pcdh17 do not affect DZ projecting sensory axons. These findings suggest that delta1 protocadherins help DZ projecting sensory axons enter and remain within the DZ protoglomerulus while delta2 protocadherins help CZ projecting sensory axons navigate to the CZ protoglomerulus. Overall design: Roughly 2000 zebrafish embryos we sacraficed at 36 48 hpf and 72 hpf. Olfactory tissue was dissociated in FACSmax dissosciation medium and then FACsorted to isolate OMP:RFP positive neurons.       OMP positive Olfactory Sensory Neurons from 36hpf Zebrafish GSM8838716   source name:Olfactory Sensory Tissue|tissue:Olfactory Sensory Tissue|cell line:Olactory Sensory Neurons|cell type:Neurons|sample age:36 hpf|genotype:Tgomp:lyn RFP|geo loc name:missing|collection date:missing OMP positive Olfactory Sensory Neurons from 36hpf Zebrafish Cell Ranger V3.0.1 Assembly: GRCz11 Supplementary files format and content: Demultiplexed 10x Genomics Files. Olfactory Sensory Tissue   10X Genomics V3.3   tissue:Olfactory Sensory Tissue|cell line:Olactory Sensory Neurons|cell type:Neurons|sample age:36 hpf|genotype:Tgomp:lyn RFP GSM8838716 GSM8838716: OMP positive Olfactory Sensory Neurons from 36hpf Zebrafish; Danio rerio; RNA Seq GSM8838716 r1 GSM8838716 1 10X Genomics V3.3   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP569567   loader:fastq load.py 97366_S7_L002_I1_001.fastq.gz 97366_S7_L002_R1_001.fastq.gz 97366_S7_L002_R2_001.fastq.gz fastq fastq fastq 5980615420.0 46004734.0 GSM8838716 r2 0:8 1:28 2:94 A:1289600464;C:857667521;G:934976316;T:1242064603;N:136092 8 28 94   1289600464 857667521 934976316 1242064603 136092 SRX27953869 SRS24319773 SRA2091725 Department of Neuroscience, University of Pennsylvania Department of Neuroscience, University of Pennsylvania                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2025-03-11 Pharyngula Embryo Brain Nervous System
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
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
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
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
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
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
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
41534 41534 SRR5006037 SRX2337865 SRS1791084 SRP092952 PRJNA352869 The Biotagging toolkit for analysis of specific cell populations in zebrafish reveals gene regulatory logic encoded in the nuclear transcriptome GSE89670 Other Interrogation of gene regulatory circuits in complex organisms requires precise tools for the selection of individual cell types as well as robust methods for tissue specific labeling and biochemical profiling of target proteins. By exploiting multiple transgenesis strategies we have developed a tissue specific binary in vivo biotinylation system in zebrafish termed "biotagging" a versatile methodology that uses genetically encoded components to biotinylate target proteins enabling in depth genome wide analyses of their molecular interactions. Using tissue specific transgenic drivers and individual cell compartment effector lines from our "biotagging" toolkit we demonstrate the specificity of our approach at the biochemical cellular and transcriptional levels. By characterizing the in vivo transcriptional landscape of migratory neural crest and myocardial cells in two different cellular compartments ribosomes and nucleus we identify a comprehensive network of protein coding and non coding RNAs and uncover cis regulatory modules and regulatory logic conferring cell specific identity embedded in the complexity of the non coding nuclear transcriptomes. Our study demonstrates that "biotagging" eliminates background inherent to complex embryonic environments and allows analyses of molecular interactions in any cellular context at highest resolution. Overall design: Examination of RNA seq and ATAC seq using in vivo biotinylated nuclei and polysomes.   pubmed:28402863   Sox10 RNASeq Nuclear PolyA 2 GSM2386500   source name:Sox10 RNASeq Nuclear PolyA|strain/background:AB/TU|tissue:neural crest and otic|developmental stage:26hpf|assay:RNA seq|cellular comp1nt:nuclear|ribodepleted:polyA|isolation method:InVivoBiotinylatedNuclei|strand:unstranded Sox10 RNASeq Nuclear PolyA 2 ATAC seq reads were trimmed for quality using sickle v 1.33 and mapped using bowtie v.1.0.0. Smoothened bigWig files were generated using an enhanced Perl script courtesy of Jim Hughes. RNA seq reads were mapped using STAR v.2.4.2a. BAM files incorporating reads belonging to either DNA strand were generated using custom python script. Genome build: danRer7 Zv9 Supplementary files format and content: bigWig files Sox10 RNASeq Nuclear PolyA   Nuclei isolation using biotin tagged outer nuclear envelope adapted from INTACT procedure. Polyribosome isolation using biotin tagged Rpl10 protein adapted from TRAP procedure. FACS procedure using cell specific fluorescent marker following gentle dissociation of embryonic tissue. ATAC procedure adapted from Buenostro et al. 2013 adapted for FACS sorted embryonic cells. RNA pools extracted using RNAqueous Micro Scale Total RNA Isolation Kit. Non directional sequencing libraries post polyA selection of RNA transcripts NEBNext® PolyA mRNA Magnetic Isolation Module NEB were built using NEBnext Ultra RNA library kit for Illumina NEB. Following ribodepletion using Ribo ZeroTM Magnetic Kit Epicentre directional RNA seq libraries were constructed using Stranded RNA Seq Library Preparation Kit KAPABiosystems.   strain/background:AB/TU|tissue:neural crest and otic|developmental stage:26hpf|assay:RNA seq|cellular comp1nt:nuclear|ribodepleted:polyA|isolation method:InVivoBiotinylatedNuclei|strand:unstranded GSM2386500 GSM2386500: Sox10 RNASeq Nuclear PolyA 2; Danio rerio; RNA Seq GSM2386500   1 Nuclei isolation using biotin tagged outer nuclear envelope adapted from INTACT procedure. Polyribosome isolation using biotin tagged Rpl10 protein adapted from TRAP procedure. FACS procedure using cell specific fluorescent marker following gentle dissociation of embryonic tissue. ATAC procedure adapted from Buenostro et al. 2013 adapted for FACS sorted embryonic cells. RNA pools extracted using RNAqueous Micro Scale Total RNA Isolation Kit. Non directional sequencing libraries post polyA selection of RNA transcripts NEBNext® PolyA mRNA Magnetic Isolation Module NEB were built using NEBnext Ultra RNA library kit for Illumina NEB. Following ribodepletion using Ribo ZeroTM Magnetic Kit Epicentre directional RNA seq libraries were constructed using Stranded RNA Seq Library Preparation Kit KAPABiosystems. GEO Accession:GSM2386500 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP092952     Sox10_RNASeq_Nuclear_PolyA_2.fastq.gz fastq 1790084450.0 35801689.0 GSM2386500 r1 0:50 A:459421587;C:440246036;G:440346791;T:450052845;N:17191 50       459421587 440246036 440346791 450052845 17191 SRX2337865 SRS1791084 SRA491940 GEO Sauka-Spengler lab, University of Oxford, MRC Weatherall Institute of Molecular Medicine 1 0.40624   0.06355   0.79859   0.47871   50   B   usable mapping rate illumina hiseq_era unknown poly_a nebnext bulk unknown unknown   United Kingdom 2016-11-08 Pharyngula Embryo Brain Nervous System
41535 41535 SRR5006036 SRX2337864 SRS1791082 SRP092952 PRJNA352869 The Biotagging toolkit for analysis of specific cell populations in zebrafish reveals gene regulatory logic encoded in the nuclear transcriptome GSE89670 Other Interrogation of gene regulatory circuits in complex organisms requires precise tools for the selection of individual cell types as well as robust methods for tissue specific labeling and biochemical profiling of target proteins. By exploiting multiple transgenesis strategies we have developed a tissue specific binary in vivo biotinylation system in zebrafish termed "biotagging" a versatile methodology that uses genetically encoded components to biotinylate target proteins enabling in depth genome wide analyses of their molecular interactions. Using tissue specific transgenic drivers and individual cell compartment effector lines from our "biotagging" toolkit we demonstrate the specificity of our approach at the biochemical cellular and transcriptional levels. By characterizing the in vivo transcriptional landscape of migratory neural crest and myocardial cells in two different cellular compartments ribosomes and nucleus we identify a comprehensive network of protein coding and non coding RNAs and uncover cis regulatory modules and regulatory logic conferring cell specific identity embedded in the complexity of the non coding nuclear transcriptomes. Our study demonstrates that "biotagging" eliminates background inherent to complex embryonic environments and allows analyses of molecular interactions in any cellular context at highest resolution. Overall design: Examination of RNA seq and ATAC seq using in vivo biotinylated nuclei and polysomes.   pubmed:28402863   Sox10 RNASeq Nuclear PolyA 1 GSM2386499   source name:Sox10 RNASeq Nuclear PolyA|strain/background:AB/TU|tissue:neural crest|developmental stage:24hpf|assay:RNA seq|cellular comp1nt:nuclear|ribodepleted:polyA|isolation method:InVivoBiotinylatedNuclei|strand:unstranded Sox10 RNASeq Nuclear PolyA 1 ATAC seq reads were trimmed for quality using sickle v 1.33 and mapped using bowtie v.1.0.0. Smoothened bigWig files were generated using an enhanced Perl script courtesy of Jim Hughes. RNA seq reads were mapped using STAR v.2.4.2a. BAM files incorporating reads belonging to either DNA strand were generated using custom python script. Genome build: danRer7 Zv9 Supplementary files format and content: bigWig files Sox10 RNASeq Nuclear PolyA   Nuclei isolation using biotin tagged outer nuclear envelope adapted from INTACT procedure. Polyribosome isolation using biotin tagged Rpl10 protein adapted from TRAP procedure. FACS procedure using cell specific fluorescent marker following gentle dissociation of embryonic tissue. ATAC procedure adapted from Buenostro et al. 2013 adapted for FACS sorted embryonic cells. RNA pools extracted using RNAqueous Micro Scale Total RNA Isolation Kit. Non directional sequencing libraries post polyA selection of RNA transcripts NEBNext® PolyA mRNA Magnetic Isolation Module NEB were built using NEBnext Ultra RNA library kit for Illumina NEB. Following ribodepletion using Ribo ZeroTM Magnetic Kit Epicentre directional RNA seq libraries were constructed using Stranded RNA Seq Library Preparation Kit KAPABiosystems.   strain/background:AB/TU|tissue:neural crest|developmental stage:24hpf|assay:RNA seq|cellular comp1nt:nuclear|ribodepleted:polyA|isolation method:InVivoBiotinylatedNuclei|strand:unstranded GSM2386499 GSM2386499: Sox10 RNASeq Nuclear PolyA 1; Danio rerio; RNA Seq GSM2386499   1 Nuclei isolation using biotin tagged outer nuclear envelope adapted from INTACT procedure. Polyribosome isolation using biotin tagged Rpl10 protein adapted from TRAP procedure. FACS procedure using cell specific fluorescent marker following gentle dissociation of embryonic tissue. ATAC procedure adapted from Buenostro et al. 2013 adapted for FACS sorted embryonic cells. RNA pools extracted using RNAqueous Micro Scale Total RNA Isolation Kit. Non directional sequencing libraries post polyA selection of RNA transcripts NEBNext® PolyA mRNA Magnetic Isolation Module NEB were built using NEBnext Ultra RNA library kit for Illumina NEB. Following ribodepletion using Ribo ZeroTM Magnetic Kit Epicentre directional RNA seq libraries were constructed using Stranded RNA Seq Library Preparation Kit KAPABiosystems. GEO Accession:GSM2386499 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP092952     Sox10_RNASeq_Nuclear_PolyA_1.fastq.gz fastq 1579629350.0 31592587.0 GSM2386499 r1 0:50 A:432689406;C:359111028;G:365435408;T:422298396;N:95112 50       432689406 359111028 365435408 422298396 95112 SRX2337864 SRS1791082 SRA491940 GEO Sauka-Spengler lab, University of Oxford, MRC Weatherall Institute of Molecular Medicine 1 0.81632   0.13449   0.69956   0.45825   50   B   usable mapping rate illumina hiseq_era unknown poly_a nebnext bulk unknown unknown   United Kingdom 2016-11-08 Pharyngula Embryo Brain Nervous System
53003 53003 SRR9662036 SRX6422912 SRS5079701 SRP213938 PRJNA553572 A map of cis regulatory elements and 3D genome structures in zebrafish GSE134055 Other The zebrafish has been widely used for the study of human disease and development as 70% of the protein coding genes are conserved between the two species. Annotation of functional control elements of the zebrafish genome however has lagged behind that of other model systems such as mouse and Drosophila. Based on multi omics approaches taken in the ENCODE and Roadmap Epigenomics projects we performed RNA seq ATAC seq ChIP seq and Hi C experiments in ten adult and two embryonic tissues to generate a comprehensive map of transcriptomes and regulatory elements in the zebrafish Tuebingen reference strain. Overall we have identified 235 596 cis regulatory elements which potentially shape the tissue specific and developmental stage specific gene expression in zebrafish. A comparison of zebrafish human and mouse regulatory elements allowed us to identify both evolutionarily conserved and species specific regulatory sequences. Furthermore through the analysis of Hi C data in zebrafish brain and muscle we observed different levels of 3D genome organization including compartment topological associating domains TADs and chromatin loops in zebrafish. A subset of TADs are deeply conserved between zebrafish and human. This work provides an additional epigenomic anchor for the functional annotation of vertebrate genomes and the study of evolutionally conserved elements of 3D genome organization. Overall design: 13 tissues from adult and embryonic stage were examined using ChIP Seq H3K27ac and H3K4me3 RNA Seq 11 of them were examined using ATAC seq WGBS and ChIP seq H3K9me3 and H3K9me2 and one scATAC seq in brain. Additionally we performed HiC experiments in adult muscle and brain. Please note that for the samples GSM4661977 GSM4662088 [1] each processed data generated from both replicates is linked to the corresponding *rep1 sample records [2] the input sample used for each ChIP sample is indicated in the description field in the corresponding input sample records.   pubmed:33239788;pubmed:35649578   YueLab RNA Seq embryonic Brain rep2 GSM3934904   source name:Tissue|strain:Tuebingen|tissue:embryonic Brain YueLab RNA Seq embryonic Brain rep2 RNA seq reads were aligned to zv10 genome assembly using STAR; ChIP seq and ATAC seq reads were aligned to zv10 genome assembly using BWA HiC reads were aligned to zv10 genome assembly using Bowtie2 The TPM value of gene expression was caculated using RSEM ChIP seq and ATAC seq peaks were called using MACS2 with the following setting: ChIP seq q value <10e 2 p value<10e 5 Change>1 FC>2. ATAC seq: q value<10e 2 and p value<10e 5 HiC matrix was generated using HiC Pro Genome build: zv10 Supplementary files format and content: tab delimited text files include TPM values for each Sample; the narrowPeak files included the peaks for each Sample; The .hic file were the matrix of Hi C for each Sample.**All replicates were merged Tissue   For each RNA seq experiment the same tissues combined from at least two Tuebingen fish were used as one replicate. For embryonic trunk ten 1 dpf fish were dechorionated with pronase and trunk were cut off for RNA seq. For embryonic neuron green cells from TgHuc:Kaede cells were sorted by FACS and approxinately 20 000 cells were used for one replicate. The tissue RNA was extracted from Trizol® according to the protocol Invitrogen. The cDNA libraries were performed using SureSelect Strand Specific RNA Library Preparation Kit Agilent according to the manufacturer’s protocol. Briefly polyA RNA was purified from 1000 ng of total RNA using oligo dT beads Invitrogen. Extracted RNA was first fragmented then followed by reverse transcription end repair adenylation adaptor ligation and subsequent PCR amplification. The final product was checked by size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit Agilent and Kapa Library Quantification Kit Kapa Biosystems and then followed by pair end 2X 50 bp high throughput sequencing using HiSeq 2500 Illumina. Embryonic and ault Tuebingen zebrafish were raised under standard laboratory conditions strain:Tuebingen|tissue:embryonic Brain GSM3934904 GSM3934904: YueLab RNA Seq embryonic Brain rep2; Danio rerio; RNA Seq GSM3934904   1 For each RNA seq experiment the same tissues combined from at least two Tuebingen fish were used as one replicate. For embryonic trunk ten 1 dpf fish were dechorionated with pronase and trunk were cut off for RNA seq. For embryonic neuron green cells from TgHuc:Kaede cells were sorted by FACS and approxinately 20 000 cells were used for one replicate. The tissue RNA was extracted from Trizol® according to the protocol Invitrogen. The cDNA libraries were performed using SureSelect Strand Specific RNA Library Preparation Kit Agilent according to the manufacturer's protocol. Briefly polyA RNA was purified from 1000 ng of total RNA using oligo dT beads Invitrogen. Extracted RNA was first fragmented then followed by reverse transcription end repair adenylation adaptor ligation and subsequent PCR amplification. The final product was checked by size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit Agilent and Kapa Library Quantification Kit Kapa Biosystems and then followed by pair end 2X 50 bp high throughput sequencing using HiSeq 2500 Illumina. GEO Accession:GSM3934904 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina Genome Analyzer   SRP213938     YueLab-RNA-Seq-embryonic-Brain-rep2_1.fastq.gz YueLab-RNA-Seq-embryonic-Brain-rep2_2.fastq.gz fastq fastq 4356185472.0 21807597.0 GSM3934904 r1 0:99.63 1:100.13 A:1230794981;C:931477391;G:940054394;T:1251750673;N:2108033 99 100     1230794981 931477391 940054394 1251750673 2108033 SRX6422912 SRS5079701 SRA919194 GEO Feng Yue, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine 2 0.88944 0.89191 0.2053 0.20664 0.71242 0.71394 0.47557 0.47724 101 101 B B biological fallback assumption illumina early_illumina unknown poly_a unknown bulk unknown unknown   United States 2019-07-09 Pharyngula Embryo Brain Nervous System
53004 53004 SRR9662035 SRX6422911 SRS5079702 SRP213938 PRJNA553572 A map of cis regulatory elements and 3D genome structures in zebrafish GSE134055 Other The zebrafish has been widely used for the study of human disease and development as 70% of the protein coding genes are conserved between the two species. Annotation of functional control elements of the zebrafish genome however has lagged behind that of other model systems such as mouse and Drosophila. Based on multi omics approaches taken in the ENCODE and Roadmap Epigenomics projects we performed RNA seq ATAC seq ChIP seq and Hi C experiments in ten adult and two embryonic tissues to generate a comprehensive map of transcriptomes and regulatory elements in the zebrafish Tuebingen reference strain. Overall we have identified 235 596 cis regulatory elements which potentially shape the tissue specific and developmental stage specific gene expression in zebrafish. A comparison of zebrafish human and mouse regulatory elements allowed us to identify both evolutionarily conserved and species specific regulatory sequences. Furthermore through the analysis of Hi C data in zebrafish brain and muscle we observed different levels of 3D genome organization including compartment topological associating domains TADs and chromatin loops in zebrafish. A subset of TADs are deeply conserved between zebrafish and human. This work provides an additional epigenomic anchor for the functional annotation of vertebrate genomes and the study of evolutionally conserved elements of 3D genome organization. Overall design: 13 tissues from adult and embryonic stage were examined using ChIP Seq H3K27ac and H3K4me3 RNA Seq 11 of them were examined using ATAC seq WGBS and ChIP seq H3K9me3 and H3K9me2 and one scATAC seq in brain. Additionally we performed HiC experiments in adult muscle and brain. Please note that for the samples GSM4661977 GSM4662088 [1] each processed data generated from both replicates is linked to the corresponding *rep1 sample records [2] the input sample used for each ChIP sample is indicated in the description field in the corresponding input sample records.   pubmed:33239788;pubmed:35649578   YueLab RNA Seq embryonic Brain rep1 GSM3934903   source name:Tissue|strain:Tuebingen|tissue:embryonic Brain YueLab RNA Seq embryonic Brain rep1 RNA seq reads were aligned to zv10 genome assembly using STAR; ChIP seq and ATAC seq reads were aligned to zv10 genome assembly using BWA HiC reads were aligned to zv10 genome assembly using Bowtie2 The TPM value of gene expression was caculated using RSEM ChIP seq and ATAC seq peaks were called using MACS2 with the following setting: ChIP seq q value <10e 2 p value<10e 5 Change>1 FC>2. ATAC seq: q value<10e 2 and p value<10e 5 HiC matrix was generated using HiC Pro Genome build: zv10 Supplementary files format and content: tab delimited text files include TPM values for each Sample; the narrowPeak files included the peaks for each Sample; The .hic file were the matrix of Hi C for each Sample.**All replicates were merged Tissue   For each RNA seq experiment the same tissues combined from at least two Tuebingen fish were used as one replicate. For embryonic trunk ten 1 dpf fish were dechorionated with pronase and trunk were cut off for RNA seq. For embryonic neuron green cells from TgHuc:Kaede cells were sorted by FACS and approxinately 20 000 cells were used for one replicate. The tissue RNA was extracted from Trizol® according to the protocol Invitrogen. The cDNA libraries were performed using SureSelect Strand Specific RNA Library Preparation Kit Agilent according to the manufacturer’s protocol. Briefly polyA RNA was purified from 1000 ng of total RNA using oligo dT beads Invitrogen. Extracted RNA was first fragmented then followed by reverse transcription end repair adenylation adaptor ligation and subsequent PCR amplification. The final product was checked by size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit Agilent and Kapa Library Quantification Kit Kapa Biosystems and then followed by pair end 2X 50 bp high throughput sequencing using HiSeq 2500 Illumina. Embryonic and ault Tuebingen zebrafish were raised under standard laboratory conditions strain:Tuebingen|tissue:embryonic Brain GSM3934903 GSM3934903: YueLab RNA Seq embryonic Brain rep1; Danio rerio; RNA Seq GSM3934903   1 For each RNA seq experiment the same tissues combined from at least two Tuebingen fish were used as one replicate. For embryonic trunk ten 1 dpf fish were dechorionated with pronase and trunk were cut off for RNA seq. For embryonic neuron green cells from TgHuc:Kaede cells were sorted by FACS and approxinately 20 000 cells were used for one replicate. The tissue RNA was extracted from Trizol® according to the protocol Invitrogen. The cDNA libraries were performed using SureSelect Strand Specific RNA Library Preparation Kit Agilent according to the manufacturer's protocol. Briefly polyA RNA was purified from 1000 ng of total RNA using oligo dT beads Invitrogen. Extracted RNA was first fragmented then followed by reverse transcription end repair adenylation adaptor ligation and subsequent PCR amplification. The final product was checked by size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit Agilent and Kapa Library Quantification Kit Kapa Biosystems and then followed by pair end 2X 50 bp high throughput sequencing using HiSeq 2500 Illumina. GEO Accession:GSM3934903 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina Genome Analyzer   SRP213938     YueLab-RNA-Seq-embryonic-Brain-rep1_1.fastq.gz YueLab-RNA-Seq-embryonic-Brain-rep1_2.fastq.gz fastq fastq 4952296956.0 40592598.0 GSM3934903 r1 0:61 1:61 A:1372792073;C:1100482364;G:1106380994;T:1368907195;N:3734330 61 61     1372792073 1100482364 1106380994 1368907195 3734330 SRX6422911 SRS5079702 SRA919194 GEO Feng Yue, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine 2 0.8905 0.89281 0.09948 0.10148 0.7041 0.7097 0.46036 0.45663 61 61 B B biological fallback assumption illumina early_illumina unknown poly_a unknown bulk unknown unknown   United States 2019-07-09 Pharyngula Embryo Brain Nervous System
53025 53025 SRR9662014 SRX6422890 SRS5079680 SRP213938 PRJNA553572 A map of cis regulatory elements and 3D genome structures in zebrafish GSE134055 Other The zebrafish has been widely used for the study of human disease and development as 70% of the protein coding genes are conserved between the two species. Annotation of functional control elements of the zebrafish genome however has lagged behind that of other model systems such as mouse and Drosophila. Based on multi omics approaches taken in the ENCODE and Roadmap Epigenomics projects we performed RNA seq ATAC seq ChIP seq and Hi C experiments in ten adult and two embryonic tissues to generate a comprehensive map of transcriptomes and regulatory elements in the zebrafish Tuebingen reference strain. Overall we have identified 235 596 cis regulatory elements which potentially shape the tissue specific and developmental stage specific gene expression in zebrafish. A comparison of zebrafish human and mouse regulatory elements allowed us to identify both evolutionarily conserved and species specific regulatory sequences. Furthermore through the analysis of Hi C data in zebrafish brain and muscle we observed different levels of 3D genome organization including compartment topological associating domains TADs and chromatin loops in zebrafish. A subset of TADs are deeply conserved between zebrafish and human. This work provides an additional epigenomic anchor for the functional annotation of vertebrate genomes and the study of evolutionally conserved elements of 3D genome organization. Overall design: 13 tissues from adult and embryonic stage were examined using ChIP Seq H3K27ac and H3K4me3 RNA Seq 11 of them were examined using ATAC seq WGBS and ChIP seq H3K9me3 and H3K9me2 and one scATAC seq in brain. Additionally we performed HiC experiments in adult muscle and brain. Please note that for the samples GSM4661977 GSM4662088 [1] each processed data generated from both replicates is linked to the corresponding *rep1 sample records [2] the input sample used for each ChIP sample is indicated in the description field in the corresponding input sample records.   pubmed:33239788;pubmed:35649578   YueLab RNA Seq Brain rep2 GSM3934882   source name:Tissue|strain:Tuebingen|tissue:Brain YueLab RNA Seq Brain rep2 RNA seq reads were aligned to zv10 genome assembly using STAR; ChIP seq and ATAC seq reads were aligned to zv10 genome assembly using BWA HiC reads were aligned to zv10 genome assembly using Bowtie2 The TPM value of gene expression was caculated using RSEM ChIP seq and ATAC seq peaks were called using MACS2 with the following setting: ChIP seq q value <10e 2 p value<10e 5 Change>1 FC>2. ATAC seq: q value<10e 2 and p value<10e 5 HiC matrix was generated using HiC Pro Genome build: zv10 Supplementary files format and content: tab delimited text files include TPM values for each Sample; the narrowPeak files included the peaks for each Sample; The .hic file were the matrix of Hi C for each Sample.**All replicates were merged Tissue   For each RNA seq experiment the same tissues combined from at least two Tuebingen fish were used as one replicate. For embryonic trunk ten 1 dpf fish were dechorionated with pronase and trunk were cut off for RNA seq. For embryonic neuron green cells from TgHuc:Kaede cells were sorted by FACS and approxinately 20 000 cells were used for one replicate. The tissue RNA was extracted from Trizol® according to the protocol Invitrogen. The cDNA libraries were performed using SureSelect Strand Specific RNA Library Preparation Kit Agilent according to the manufacturer’s protocol. Briefly polyA RNA was purified from 1000 ng of total RNA using oligo dT beads Invitrogen. Extracted RNA was first fragmented then followed by reverse transcription end repair adenylation adaptor ligation and subsequent PCR amplification. The final product was checked by size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit Agilent and Kapa Library Quantification Kit Kapa Biosystems and then followed by pair end 2X 50 bp high throughput sequencing using HiSeq 2500 Illumina. Embryonic and ault Tuebingen zebrafish were raised under standard laboratory conditions strain:Tuebingen|tissue:Brain GSM3934882 GSM3934882: YueLab RNA Seq Brain rep2; Danio rerio; RNA Seq GSM3934882   1 For each RNA seq experiment the same tissues combined from at least two Tuebingen fish were used as one replicate. For embryonic trunk ten 1 dpf fish were dechorionated with pronase and trunk were cut off for RNA seq. For embryonic neuron green cells from TgHuc:Kaede cells were sorted by FACS and approxinately 20 000 cells were used for one replicate. The tissue RNA was extracted from Trizol® according to the protocol Invitrogen. The cDNA libraries were performed using SureSelect Strand Specific RNA Library Preparation Kit Agilent according to the manufacturer's protocol. Briefly polyA RNA was purified from 1000 ng of total RNA using oligo dT beads Invitrogen. Extracted RNA was first fragmented then followed by reverse transcription end repair adenylation adaptor ligation and subsequent PCR amplification. The final product was checked by size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit Agilent and Kapa Library Quantification Kit Kapa Biosystems and then followed by pair end 2X 50 bp high throughput sequencing using HiSeq 2500 Illumina. GEO Accession:GSM3934882 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina Genome Analyzer   SRP213938     YueLab-RNA-Seq-Brain-rep2_1.fastq.gz YueLab-RNA-Seq-Brain-rep2_2.fastq.gz fastq fastq 1334067600.0 13340676.0 GSM3934882 r1 0:50 1:50 A:359101169;C:310368468;G:310014940;T:353082339;N:1500684 50 50     359101169 310368468 310014940 353082339 1500684 SRX6422890 SRS5079680 SRA919194 GEO Feng Yue, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine 2 0.82713 0.80037 0.30115 0.2826 0.75463 0.75931 0.60033 0.57893 50 50 B B biological fallback assumption illumina early_illumina unknown poly_a unknown bulk unknown unknown   United States 2019-07-09 Pharyngula Embryo Brain Nervous System
53026 53026 SRR9662013 SRX6422889 SRS5079679 SRP213938 PRJNA553572 A map of cis regulatory elements and 3D genome structures in zebrafish GSE134055 Other The zebrafish has been widely used for the study of human disease and development as 70% of the protein coding genes are conserved between the two species. Annotation of functional control elements of the zebrafish genome however has lagged behind that of other model systems such as mouse and Drosophila. Based on multi omics approaches taken in the ENCODE and Roadmap Epigenomics projects we performed RNA seq ATAC seq ChIP seq and Hi C experiments in ten adult and two embryonic tissues to generate a comprehensive map of transcriptomes and regulatory elements in the zebrafish Tuebingen reference strain. Overall we have identified 235 596 cis regulatory elements which potentially shape the tissue specific and developmental stage specific gene expression in zebrafish. A comparison of zebrafish human and mouse regulatory elements allowed us to identify both evolutionarily conserved and species specific regulatory sequences. Furthermore through the analysis of Hi C data in zebrafish brain and muscle we observed different levels of 3D genome organization including compartment topological associating domains TADs and chromatin loops in zebrafish. A subset of TADs are deeply conserved between zebrafish and human. This work provides an additional epigenomic anchor for the functional annotation of vertebrate genomes and the study of evolutionally conserved elements of 3D genome organization. Overall design: 13 tissues from adult and embryonic stage were examined using ChIP Seq H3K27ac and H3K4me3 RNA Seq 11 of them were examined using ATAC seq WGBS and ChIP seq H3K9me3 and H3K9me2 and one scATAC seq in brain. Additionally we performed HiC experiments in adult muscle and brain. Please note that for the samples GSM4661977 GSM4662088 [1] each processed data generated from both replicates is linked to the corresponding *rep1 sample records [2] the input sample used for each ChIP sample is indicated in the description field in the corresponding input sample records.   pubmed:33239788;pubmed:35649578   YueLab RNA Seq Brain rep1 GSM3934881   source name:Tissue|strain:Tuebingen|tissue:Brain YueLab RNA Seq Brain rep1 RNA seq reads were aligned to zv10 genome assembly using STAR; ChIP seq and ATAC seq reads were aligned to zv10 genome assembly using BWA HiC reads were aligned to zv10 genome assembly using Bowtie2 The TPM value of gene expression was caculated using RSEM ChIP seq and ATAC seq peaks were called using MACS2 with the following setting: ChIP seq q value <10e 2 p value<10e 5 Change>1 FC>2. ATAC seq: q value<10e 2 and p value<10e 5 HiC matrix was generated using HiC Pro Genome build: zv10 Supplementary files format and content: tab delimited text files include TPM values for each Sample; the narrowPeak files included the peaks for each Sample; The .hic file were the matrix of Hi C for each Sample.**All replicates were merged Tissue   For each RNA seq experiment the same tissues combined from at least two Tuebingen fish were used as one replicate. For embryonic trunk ten 1 dpf fish were dechorionated with pronase and trunk were cut off for RNA seq. For embryonic neuron green cells from TgHuc:Kaede cells were sorted by FACS and approxinately 20 000 cells were used for one replicate. The tissue RNA was extracted from Trizol® according to the protocol Invitrogen. The cDNA libraries were performed using SureSelect Strand Specific RNA Library Preparation Kit Agilent according to the manufacturer’s protocol. Briefly polyA RNA was purified from 1000 ng of total RNA using oligo dT beads Invitrogen. Extracted RNA was first fragmented then followed by reverse transcription end repair adenylation adaptor ligation and subsequent PCR amplification. The final product was checked by size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit Agilent and Kapa Library Quantification Kit Kapa Biosystems and then followed by pair end 2X 50 bp high throughput sequencing using HiSeq 2500 Illumina. Embryonic and ault Tuebingen zebrafish were raised under standard laboratory conditions strain:Tuebingen|tissue:Brain GSM3934881 GSM3934881: YueLab RNA Seq Brain rep1; Danio rerio; RNA Seq GSM3934881   1 For each RNA seq experiment the same tissues combined from at least two Tuebingen fish were used as one replicate. For embryonic trunk ten 1 dpf fish were dechorionated with pronase and trunk were cut off for RNA seq. For embryonic neuron green cells from TgHuc:Kaede cells were sorted by FACS and approxinately 20 000 cells were used for one replicate. The tissue RNA was extracted from Trizol® according to the protocol Invitrogen. The cDNA libraries were performed using SureSelect Strand Specific RNA Library Preparation Kit Agilent according to the manufacturer's protocol. Briefly polyA RNA was purified from 1000 ng of total RNA using oligo dT beads Invitrogen. Extracted RNA was first fragmented then followed by reverse transcription end repair adenylation adaptor ligation and subsequent PCR amplification. The final product was checked by size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit Agilent and Kapa Library Quantification Kit Kapa Biosystems and then followed by pair end 2X 50 bp high throughput sequencing using HiSeq 2500 Illumina. GEO Accession:GSM3934881 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina Genome Analyzer   SRP213938     YueLab-RNA-Seq-Brain-rep1_1.fastq.gz YueLab-RNA-Seq-Brain-rep1_2.fastq.gz fastq fastq 3574226083.0 29586066.0 GSM3934881 r1 0:60.47 1:60.34 A:971773155;C:783073665;G:792147787;T:1027177082;N:54394 60 60     971773155 783073665 792147787 1027177082 54394 SRX6422889 SRS5079679 SRA919194 GEO Feng Yue, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine 2 0.96451 0.9695 0.20771 0.20662 0.69585 0.69781 0.48655 0.48646 60 61 B B biological fallback assumption illumina early_illumina unknown poly_a unknown bulk unknown unknown   United States 2019-07-09 Pharyngula Embryo Brain Nervous System
53598 53598 SRR9961216 SRX6708749 SRS5262464 SRP218232 PRJNA560046 Anterior Posterior gene expression differences in zebrafish Vagus motor neurons GSE135780 Transcriptome Analysis We profiled the transcriptome of anterior and posterior zebrafish Vagus motor neurons at 28 hpf 30 hpf to identify genes that are differentially expressed between these two cell populations. Overall design: We obtained cells by photoconverting the anterior or posterior 1/4 of Kaede expressing Vagus motor neurons dissecting the posterior hindbrain dissociating to single cell suspension and manually picking photoconverted cells. We sequenced 3 replicates of 100 cells per population.   pubmed:32302545   PR GSM4029959   tissue:Posterior Vagus motor neurons|cell type:Vagus motor neurons|developmental stage:28 hpf 30 hpf|genotype:Tgisl1:Kaede PR Image analysis and base calling were performed using Illumina's Real Time Analysis v1.18 software followed by 'demultiplexing' of indexed reads and generation of FASTQ files using Illumina's bcl2fastq v1.8.4 Reads of low quality were filtered out prior to alignment to GRCz10 using TopHat v2.1.0. Counts were generated from Tophat alignments at the gene level employing the "intersection strict" overlap mode in HTSeq v0.6.1. Genome build: GRCz10 Supplementary files format and content: tab delimited text files include counts genreated at the gene level by HTSeq count. Posterior Vagus motor neurons   The posterior hindbrain was manually dissected in calcium free Ringer’s solution with MESAB and dissected tissue was dissociated to single cell suspension by pipetting in 0.25%Trypsin EDTA for 5 minutes. Dissociated cells transferred into cold DPBS + 5% FBS + 1% BSA. The cell suspension was then transferred onto a glass coverslip covered with mineral oil and photoconverted cells were manually picked up using a 10m diameter transplant pipette and transferred into lysis buffer from the RNA isolation kit. RNA was isolated using the RNAqueous Micro Total RNA Isolation Kit cDNA was amplified using the SMART Seq v4 Ultra Low Input RNA Kit for Sequencing and libraries were prepared using the Nextera XT DNA library prep kit and sequenced on an Illumina HiSeq 2500 sequencer.   cell type:Vagus motor neurons|developmental stage:28 hpf 30 hpf|genotype:Tgisl1:Kaede GSM4029959 GSM4029959: PR; Danio rerio; RNA Seq GSM4029959   1 The posterior hindbrain was manually dissected in calcium free Ringer's solution with MESAB and dissected tissue was dissociated to single cell suspension by pipetting in 0.25%Trypsin EDTA for 5 minutes. Dissociated cells transferred into cold DPBS + 5% FBS + 1% BSA. The cell suspension was then transferred onto a glass coverslip covered with mineral oil and photoconverted cells were manually picked up using a 10m diameter transplant pipette and transferred into lysis buffer from the RNA isolation kit. RNA was isolated using the RNAqueous Micro Total RNA Isolation Kit cDNA was amplified using the SMART Seq v4 Ultra Low Input RNA Kit for Sequencing and libraries were prepared using the Nextera XT DNA library prep kit and sequenced on an Illumina HiSeq 2500 sequencer. GEO Accession:GSM4029959 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP218232     PR.R1.fastq.gz PR.R2.fastq.gz fastq fastq 2401786200.0 24017862.0 GSM4029959 r1 0:50 1:50 A:659290962;C:538233618;G:544650227;T:659578923;N:32470 50 50     659290962 538233618 544650227 659578923 32470 SRX6708749 SRS5262464 SRA938975 GEO Fred Hutchinson Cancer Research Center 2 0.89159 0.90132 0.08505 0.08525 0.79916 0.79997 0.4553 0.4539 50 50 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2019-08-13 Pharyngula Embryo Brain Nervous System
53599 53599 SRR9961215 SRX6708748 SRS5262463 SRP218232 PRJNA560046 Anterior Posterior gene expression differences in zebrafish Vagus motor neurons GSE135780 Transcriptome Analysis We profiled the transcriptome of anterior and posterior zebrafish Vagus motor neurons at 28 hpf 30 hpf to identify genes that are differentially expressed between these two cell populations. Overall design: We obtained cells by photoconverting the anterior or posterior 1/4 of Kaede expressing Vagus motor neurons dissecting the posterior hindbrain dissociating to single cell suspension and manually picking photoconverted cells. We sequenced 3 replicates of 100 cells per population.   pubmed:32302545   PG GSM4029958   tissue:Posterior Vagus motor neurons|cell type:Vagus motor neurons|developmental stage:28 hpf 30 hpf|genotype:Tgisl1:Kaede PG Image analysis and base calling were performed using Illumina's Real Time Analysis v1.18 software followed by 'demultiplexing' of indexed reads and generation of FASTQ files using Illumina's bcl2fastq v1.8.4 Reads of low quality were filtered out prior to alignment to GRCz10 using TopHat v2.1.0. Counts were generated from Tophat alignments at the gene level employing the "intersection strict" overlap mode in HTSeq v0.6.1. Genome build: GRCz10 Supplementary files format and content: tab delimited text files include counts genreated at the gene level by HTSeq count. Posterior Vagus motor neurons   The posterior hindbrain was manually dissected in calcium free Ringer’s solution with MESAB and dissected tissue was dissociated to single cell suspension by pipetting in 0.25%Trypsin EDTA for 5 minutes. Dissociated cells transferred into cold DPBS + 5% FBS + 1% BSA. The cell suspension was then transferred onto a glass coverslip covered with mineral oil and photoconverted cells were manually picked up using a 10m diameter transplant pipette and transferred into lysis buffer from the RNA isolation kit. RNA was isolated using the RNAqueous Micro Total RNA Isolation Kit cDNA was amplified using the SMART Seq v4 Ultra Low Input RNA Kit for Sequencing and libraries were prepared using the Nextera XT DNA library prep kit and sequenced on an Illumina HiSeq 2500 sequencer.   cell type:Vagus motor neurons|developmental stage:28 hpf 30 hpf|genotype:Tgisl1:Kaede GSM4029958 GSM4029958: PG; Danio rerio; RNA Seq GSM4029958   1 The posterior hindbrain was manually dissected in calcium free Ringer's solution with MESAB and dissected tissue was dissociated to single cell suspension by pipetting in 0.25%Trypsin EDTA for 5 minutes. Dissociated cells transferred into cold DPBS + 5% FBS + 1% BSA. The cell suspension was then transferred onto a glass coverslip covered with mineral oil and photoconverted cells were manually picked up using a 10m diameter transplant pipette and transferred into lysis buffer from the RNA isolation kit. RNA was isolated using the RNAqueous Micro Total RNA Isolation Kit cDNA was amplified using the SMART Seq v4 Ultra Low Input RNA Kit for Sequencing and libraries were prepared using the Nextera XT DNA library prep kit and sequenced on an Illumina HiSeq 2500 sequencer. GEO Accession:GSM4029958 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP218232     PG.R1.fastq.gz PG.R2.fastq.gz fastq fastq 2088408300.0 20884083.0 GSM4029958 r1 0:50 1:50 A:575165459;C:466900649;G:473144365;T:573170304;N:27523 50 50     575165459 466900649 473144365 573170304 27523 SRX6708748 SRS5262463 SRA938975 GEO Fred Hutchinson Cancer Research Center 2 0.87591 0.88321 0.08999 0.0895 0.8099 0.80973 0.4632 0.46188 50 50 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2019-08-13 Pharyngula Embryo Brain Nervous System
53600 53600 SRR9961214 SRX6708747 SRS5262462 SRP218232 PRJNA560046 Anterior Posterior gene expression differences in zebrafish Vagus motor neurons GSE135780 Transcriptome Analysis We profiled the transcriptome of anterior and posterior zebrafish Vagus motor neurons at 28 hpf 30 hpf to identify genes that are differentially expressed between these two cell populations. Overall design: We obtained cells by photoconverting the anterior or posterior 1/4 of Kaede expressing Vagus motor neurons dissecting the posterior hindbrain dissociating to single cell suspension and manually picking photoconverted cells. We sequenced 3 replicates of 100 cells per population.   pubmed:32302545   PB GSM4029957   tissue:Posterior Vagus motor neurons|cell type:Vagus motor neurons|developmental stage:28 hpf 30 hpf|genotype:Tgisl1:Kaede PB Image analysis and base calling were performed using Illumina's Real Time Analysis v1.18 software followed by 'demultiplexing' of indexed reads and generation of FASTQ files using Illumina's bcl2fastq v1.8.4 Reads of low quality were filtered out prior to alignment to GRCz10 using TopHat v2.1.0. Counts were generated from Tophat alignments at the gene level employing the "intersection strict" overlap mode in HTSeq v0.6.1. Genome build: GRCz10 Supplementary files format and content: tab delimited text files include counts genreated at the gene level by HTSeq count. Posterior Vagus motor neurons   The posterior hindbrain was manually dissected in calcium free Ringer’s solution with MESAB and dissected tissue was dissociated to single cell suspension by pipetting in 0.25%Trypsin EDTA for 5 minutes. Dissociated cells transferred into cold DPBS + 5% FBS + 1% BSA. The cell suspension was then transferred onto a glass coverslip covered with mineral oil and photoconverted cells were manually picked up using a 10m diameter transplant pipette and transferred into lysis buffer from the RNA isolation kit. RNA was isolated using the RNAqueous Micro Total RNA Isolation Kit cDNA was amplified using the SMART Seq v4 Ultra Low Input RNA Kit for Sequencing and libraries were prepared using the Nextera XT DNA library prep kit and sequenced on an Illumina HiSeq 2500 sequencer.   cell type:Vagus motor neurons|developmental stage:28 hpf 30 hpf|genotype:Tgisl1:Kaede GSM4029957 GSM4029957: PB; Danio rerio; RNA Seq GSM4029957   1 The posterior hindbrain was manually dissected in calcium free Ringer's solution with MESAB and dissected tissue was dissociated to single cell suspension by pipetting in 0.25%Trypsin EDTA for 5 minutes. Dissociated cells transferred into cold DPBS + 5% FBS + 1% BSA. The cell suspension was then transferred onto a glass coverslip covered with mineral oil and photoconverted cells were manually picked up using a 10m diameter transplant pipette and transferred into lysis buffer from the RNA isolation kit. RNA was isolated using the RNAqueous Micro Total RNA Isolation Kit cDNA was amplified using the SMART Seq v4 Ultra Low Input RNA Kit for Sequencing and libraries were prepared using the Nextera XT DNA library prep kit and sequenced on an Illumina HiSeq 2500 sequencer. GEO Accession:GSM4029957 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP218232     PB.R1.fastq.gz PB.R2.fastq.gz fastq fastq 1947375800.0 19473758.0 GSM4029957 r1 0:50 1:50 A:540064062;C:431763279;G:436932637;T:538589534;N:26288 50 50     540064062 431763279 436932637 538589534 26288 SRX6708747 SRS5262462 SRA938975 GEO Fred Hutchinson Cancer Research Center 2 0.87385 0.88639 0.10632 0.10717 0.84025 0.84011 0.46398 0.46592 50 50 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2019-08-13 Pharyngula Embryo Brain Nervous System
53601 53601 SRR9961213 SRX6708746 SRS5262461 SRP218232 PRJNA560046 Anterior Posterior gene expression differences in zebrafish Vagus motor neurons GSE135780 Transcriptome Analysis We profiled the transcriptome of anterior and posterior zebrafish Vagus motor neurons at 28 hpf 30 hpf to identify genes that are differentially expressed between these two cell populations. Overall design: We obtained cells by photoconverting the anterior or posterior 1/4 of Kaede expressing Vagus motor neurons dissecting the posterior hindbrain dissociating to single cell suspension and manually picking photoconverted cells. We sequenced 3 replicates of 100 cells per population.   pubmed:32302545   AR GSM4029956   tissue:Anterior Vagus motor neurons|cell type:Vagus motor neurons|developmental stage:28 hpf 30 hpf|genotype:Tgisl1:Kaede AR Image analysis and base calling were performed using Illumina's Real Time Analysis v1.18 software followed by 'demultiplexing' of indexed reads and generation of FASTQ files using Illumina's bcl2fastq v1.8.4 Reads of low quality were filtered out prior to alignment to GRCz10 using TopHat v2.1.0. Counts were generated from Tophat alignments at the gene level employing the "intersection strict" overlap mode in HTSeq v0.6.1. Genome build: GRCz10 Supplementary files format and content: tab delimited text files include counts genreated at the gene level by HTSeq count. Anterior Vagus motor neurons   The posterior hindbrain was manually dissected in calcium free Ringer’s solution with MESAB and dissected tissue was dissociated to single cell suspension by pipetting in 0.25%Trypsin EDTA for 5 minutes. Dissociated cells transferred into cold DPBS + 5% FBS + 1% BSA. The cell suspension was then transferred onto a glass coverslip covered with mineral oil and photoconverted cells were manually picked up using a 10m diameter transplant pipette and transferred into lysis buffer from the RNA isolation kit. RNA was isolated using the RNAqueous Micro Total RNA Isolation Kit cDNA was amplified using the SMART Seq v4 Ultra Low Input RNA Kit for Sequencing and libraries were prepared using the Nextera XT DNA library prep kit and sequenced on an Illumina HiSeq 2500 sequencer.   cell type:Vagus motor neurons|developmental stage:28 hpf 30 hpf|genotype:Tgisl1:Kaede GSM4029956 GSM4029956: AR; Danio rerio; RNA Seq GSM4029956   1 The posterior hindbrain was manually dissected in calcium free Ringer's solution with MESAB and dissected tissue was dissociated to single cell suspension by pipetting in 0.25%Trypsin EDTA for 5 minutes. Dissociated cells transferred into cold DPBS + 5% FBS + 1% BSA. The cell suspension was then transferred onto a glass coverslip covered with mineral oil and photoconverted cells were manually picked up using a 10m diameter transplant pipette and transferred into lysis buffer from the RNA isolation kit. RNA was isolated using the RNAqueous Micro Total RNA Isolation Kit cDNA was amplified using the SMART Seq v4 Ultra Low Input RNA Kit for Sequencing and libraries were prepared using the Nextera XT DNA library prep kit and sequenced on an Illumina HiSeq 2500 sequencer. GEO Accession:GSM4029956 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP218232     AR.R1.fastq.gz AR.R2.fastq.gz fastq fastq 2384691900.0 23846919.0 GSM4029956 r1 0:50 1:50 A:653468293;C:532843393;G:540027782;T:658320541;N:31891 50 50     653468293 532843393 540027782 658320541 31891 SRX6708746 SRS5262461 SRA938975 GEO Fred Hutchinson Cancer Research Center 2 0.87197 0.87963 0.14589 0.14667 0.78348 0.78539 0.45808 0.46291 50 50 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2019-08-13 Pharyngula Embryo Brain Nervous System
53602 53602 SRR9961212 SRX6708745 SRS5262460 SRP218232 PRJNA560046 Anterior Posterior gene expression differences in zebrafish Vagus motor neurons GSE135780 Transcriptome Analysis We profiled the transcriptome of anterior and posterior zebrafish Vagus motor neurons at 28 hpf 30 hpf to identify genes that are differentially expressed between these two cell populations. Overall design: We obtained cells by photoconverting the anterior or posterior 1/4 of Kaede expressing Vagus motor neurons dissecting the posterior hindbrain dissociating to single cell suspension and manually picking photoconverted cells. We sequenced 3 replicates of 100 cells per population.   pubmed:32302545   AG GSM4029955   tissue:Anterior Vagus motor neurons|cell type:Vagus motor neurons|developmental stage:28 hpf 30 hpf|genotype:Tgisl1:Kaede AG Image analysis and base calling were performed using Illumina's Real Time Analysis v1.18 software followed by 'demultiplexing' of indexed reads and generation of FASTQ files using Illumina's bcl2fastq v1.8.4 Reads of low quality were filtered out prior to alignment to GRCz10 using TopHat v2.1.0. Counts were generated from Tophat alignments at the gene level employing the "intersection strict" overlap mode in HTSeq v0.6.1. Genome build: GRCz10 Supplementary files format and content: tab delimited text files include counts genreated at the gene level by HTSeq count. Anterior Vagus motor neurons   The posterior hindbrain was manually dissected in calcium free Ringer’s solution with MESAB and dissected tissue was dissociated to single cell suspension by pipetting in 0.25%Trypsin EDTA for 5 minutes. Dissociated cells transferred into cold DPBS + 5% FBS + 1% BSA. The cell suspension was then transferred onto a glass coverslip covered with mineral oil and photoconverted cells were manually picked up using a 10m diameter transplant pipette and transferred into lysis buffer from the RNA isolation kit. RNA was isolated using the RNAqueous Micro Total RNA Isolation Kit cDNA was amplified using the SMART Seq v4 Ultra Low Input RNA Kit for Sequencing and libraries were prepared using the Nextera XT DNA library prep kit and sequenced on an Illumina HiSeq 2500 sequencer.   cell type:Vagus motor neurons|developmental stage:28 hpf 30 hpf|genotype:Tgisl1:Kaede GSM4029955 GSM4029955: AG; Danio rerio; RNA Seq GSM4029955   1 The posterior hindbrain was manually dissected in calcium free Ringer's solution with MESAB and dissected tissue was dissociated to single cell suspension by pipetting in 0.25%Trypsin EDTA for 5 minutes. Dissociated cells transferred into cold DPBS + 5% FBS + 1% BSA. The cell suspension was then transferred onto a glass coverslip covered with mineral oil and photoconverted cells were manually picked up using a 10m diameter transplant pipette and transferred into lysis buffer from the RNA isolation kit. RNA was isolated using the RNAqueous Micro Total RNA Isolation Kit cDNA was amplified using the SMART Seq v4 Ultra Low Input RNA Kit for Sequencing and libraries were prepared using the Nextera XT DNA library prep kit and sequenced on an Illumina HiSeq 2500 sequencer. GEO Accession:GSM4029955 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP218232     AG.R1.fastq.gz AG.R2.fastq.gz fastq fastq 2638571200.0 26385712.0 GSM4029955 r1 0:50 1:50 A:718841383;C:596495936;G:604225667;T:718972746;N:35468 50 50     718841383 596495936 604225667 718972746 35468 SRX6708745 SRS5262460 SRA938975 GEO Fred Hutchinson Cancer Research Center 2 0.85778 0.86626 0.09168 0.09248 0.80079 0.80135 0.47265 0.47114 50 50 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2019-08-13 Pharyngula Embryo Brain Nervous System
53603 53603 SRR9961211 SRX6708744 SRS5262459 SRP218232 PRJNA560046 Anterior Posterior gene expression differences in zebrafish Vagus motor neurons GSE135780 Transcriptome Analysis We profiled the transcriptome of anterior and posterior zebrafish Vagus motor neurons at 28 hpf 30 hpf to identify genes that are differentially expressed between these two cell populations. Overall design: We obtained cells by photoconverting the anterior or posterior 1/4 of Kaede expressing Vagus motor neurons dissecting the posterior hindbrain dissociating to single cell suspension and manually picking photoconverted cells. We sequenced 3 replicates of 100 cells per population.   pubmed:32302545   AB GSM4029954   tissue:Anterior Vagus motor neurons|cell type:Vagus motor neurons|developmental stage:28 hpf 30 hpf|genotype:Tgisl1:Kaede AB Image analysis and base calling were performed using Illumina's Real Time Analysis v1.18 software followed by 'demultiplexing' of indexed reads and generation of FASTQ files using Illumina's bcl2fastq v1.8.4 Reads of low quality were filtered out prior to alignment to GRCz10 using TopHat v2.1.0. Counts were generated from Tophat alignments at the gene level employing the "intersection strict" overlap mode in HTSeq v0.6.1. Genome build: GRCz10 Supplementary files format and content: tab delimited text files include counts genreated at the gene level by HTSeq count. Anterior Vagus motor neurons   The posterior hindbrain was manually dissected in calcium free Ringer’s solution with MESAB and dissected tissue was dissociated to single cell suspension by pipetting in 0.25%Trypsin EDTA for 5 minutes. Dissociated cells transferred into cold DPBS + 5% FBS + 1% BSA. The cell suspension was then transferred onto a glass coverslip covered with mineral oil and photoconverted cells were manually picked up using a 10m diameter transplant pipette and transferred into lysis buffer from the RNA isolation kit. RNA was isolated using the RNAqueous Micro Total RNA Isolation Kit cDNA was amplified using the SMART Seq v4 Ultra Low Input RNA Kit for Sequencing and libraries were prepared using the Nextera XT DNA library prep kit and sequenced on an Illumina HiSeq 2500 sequencer.   cell type:Vagus motor neurons|developmental stage:28 hpf 30 hpf|genotype:Tgisl1:Kaede GSM4029954 GSM4029954: AB; Danio rerio; RNA Seq GSM4029954   1 The posterior hindbrain was manually dissected in calcium free Ringer's solution with MESAB and dissected tissue was dissociated to single cell suspension by pipetting in 0.25%Trypsin EDTA for 5 minutes. Dissociated cells transferred into cold DPBS + 5% FBS + 1% BSA. The cell suspension was then transferred onto a glass coverslip covered with mineral oil and photoconverted cells were manually picked up using a 10m diameter transplant pipette and transferred into lysis buffer from the RNA isolation kit. RNA was isolated using the RNAqueous Micro Total RNA Isolation Kit cDNA was amplified using the SMART Seq v4 Ultra Low Input RNA Kit for Sequencing and libraries were prepared using the Nextera XT DNA library prep kit and sequenced on an Illumina HiSeq 2500 sequencer. GEO Accession:GSM4029954 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP218232     AB.R1.fastq.gz AB.R2.fastq.gz fastq fastq 2240766800.0 22407668.0 GSM4029954 r1 0:50 1:50 A:613677740;C:504126555;G:512178339;T:610754298;N:29868 50 50     613677740 504126555 512178339 610754298 29868 SRX6708744 SRS5262459 SRA938975 GEO Fred Hutchinson Cancer Research Center 2 0.87484 0.88129 0.09542 0.0961 0.82008 0.82209 0.46606 0.46753 50 50 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2019-08-13 Pharyngula Embryo Brain Nervous System
53604 53604 SRR9961222 SRX6708755 SRS5262470 SRP218233 PRJNA560048 Gene expression changes in Retinoic Acid treated zebrafish Vagus motor neurons GSE135781 Transcriptome Analysis Weprofiled the transcriptomes of DMSO treated control and Retinoic Acid treated zebrafish Vagus motor neurons at 38 hpf to identifiy genes that are differentially expressed between these two treatments. Overall design: We obtained cells by dissecting the hindbrains of Tgisl1:Kaede expressing embryos dissociating to single cell suspension and sorting for Kaede positive cells by flow cytometry. We sequenced 3 replicates of 4500 10000 cells per condition.   pubmed:32302545   12 RA GSM4029965   tissue:Vagus motor neurons|cell type:Vagus motor neurons|developmental stage:38 hpf|genotype:Tgisl1:Kaede 12 RA Image analysis and base calling were performed using Illumina's Real Time Analysis v1.18 software followed by 'demultiplexing' of indexed reads and generation of FASTQ files using Illumina's bcl2fastq v1.8.4 Reads of low quality were filtered out prior to alignment to GRCz11 using STAR 2.5.2a in 2 pass mode. Counts were generated from STAR alignments at the gene level using featureCounts from the Subread package v1.5.0. Genome build: GRCz11 Supplementary files format and content: tab delimited text files include counts generated at the gene level by featureCounts Vagus motor neurons Embryos were treated 0.2mM PTU as well as with 50nM Retinoic Acid in DMSO or the equivalent volumen of DMSO as a control beginning at 24hpf. The posterior hindbrain was manually dissected in calcium free Ringer’s solution with MESAB and dissected tissue was dissociated to single cell suspension by pipetting in 0.25%Trypsin EDTA for 5 minutes. dissociated cells were transferred into cold DPBS + 1%BSA + 2g/mL DAPI. Cells were then sorted on an BD FACS ARIA II flow cytometer. Kaede+ DAPI cells were collected in lysis buffer from the RNA isolation kit and immediately processed. RNA was isolated using the RNAqueous Micro Total RNA Isolation Kit cDNA was amplified using the SMART Seq v4 Ultra Low Input RNA Kit for Sequencing and libraries were prepared using the Nextera XT DNA library prep kit and sequenced on an Illumina HiSeq 2500 sequencer.   cell type:Vagus motor neurons|developmental stage:38 hpf|genotype:Tgisl1:Kaede GSM4029965 GSM4029965: 12 RA; Danio rerio; RNA Seq GSM4029965   1 The posterior hindbrain was manually dissected in calcium free Ringer's solution with MESAB and dissected tissue was dissociated to single cell suspension by pipetting in 0.25%Trypsin EDTA for 5 minutes. dissociated cells were transferred into cold DPBS + 1%BSA + 2g/mL DAPI. Cells were then sorted on an BD FACS ARIA II flow cytometer. Kaede+ DAPI cells were collected in lysis buffer from the RNA isolation kit and immediately processed. RNA was isolated using the RNAqueous Micro Total RNA Isolation Kit cDNA was amplified using the SMART Seq v4 Ultra Low Input RNA Kit for Sequencing and libraries were prepared using the Nextera XT DNA library prep kit and sequenced on an Illumina HiSeq 2500 sequencer. GEO Accession:GSM4029965 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP218233     12_RA.R1.fastq.gz 12_RA.R2.fastq.gz fastq fastq 2411994500.0 24119945.0 GSM4029965 r1 0:50 1:50 A:651875311;C:553371750;G:560482904;T:645562467;N:702068 50 50     651875311 553371750 560482904 645562467 702068 SRX6708755 SRS5262470 SRA938976 GEO Fred Hutchinson Cancer Research Center 2 0.91 0.912 0.0868 0.09489 0.73531 0.74257 0.48209 0.48433 50 50 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2019-08-13 Pharyngula Embryo Brain Nervous System
53605 53605 SRR9961221 SRX6708754 SRS5262469 SRP218233 PRJNA560048 Gene expression changes in Retinoic Acid treated zebrafish Vagus motor neurons GSE135781 Transcriptome Analysis Weprofiled the transcriptomes of DMSO treated control and Retinoic Acid treated zebrafish Vagus motor neurons at 38 hpf to identifiy genes that are differentially expressed between these two treatments. Overall design: We obtained cells by dissecting the hindbrains of Tgisl1:Kaede expressing embryos dissociating to single cell suspension and sorting for Kaede positive cells by flow cytometry. We sequenced 3 replicates of 4500 10000 cells per condition.   pubmed:32302545   9 RA GSM4029964   tissue:Vagus motor neurons|cell type:Vagus motor neurons|developmental stage:38 hpf|genotype:Tgisl1:Kaede 9 RA Image analysis and base calling were performed using Illumina's Real Time Analysis v1.18 software followed by 'demultiplexing' of indexed reads and generation of FASTQ files using Illumina's bcl2fastq v1.8.4 Reads of low quality were filtered out prior to alignment to GRCz11 using STAR 2.5.2a in 2 pass mode. Counts were generated from STAR alignments at the gene level using featureCounts from the Subread package v1.5.0. Genome build: GRCz11 Supplementary files format and content: tab delimited text files include counts generated at the gene level by featureCounts Vagus motor neurons Embryos were treated 0.2mM PTU as well as with 50nM Retinoic Acid in DMSO or the equivalent volumen of DMSO as a control beginning at 24hpf. The posterior hindbrain was manually dissected in calcium free Ringer’s solution with MESAB and dissected tissue was dissociated to single cell suspension by pipetting in 0.25%Trypsin EDTA for 5 minutes. dissociated cells were transferred into cold DPBS + 1%BSA + 2g/mL DAPI. Cells were then sorted on an BD FACS ARIA II flow cytometer. Kaede+ DAPI cells were collected in lysis buffer from the RNA isolation kit and immediately processed. RNA was isolated using the RNAqueous Micro Total RNA Isolation Kit cDNA was amplified using the SMART Seq v4 Ultra Low Input RNA Kit for Sequencing and libraries were prepared using the Nextera XT DNA library prep kit and sequenced on an Illumina HiSeq 2500 sequencer.   cell type:Vagus motor neurons|developmental stage:38 hpf|genotype:Tgisl1:Kaede GSM4029964 GSM4029964: 9 RA; Danio rerio; RNA Seq GSM4029964   1 The posterior hindbrain was manually dissected in calcium free Ringer's solution with MESAB and dissected tissue was dissociated to single cell suspension by pipetting in 0.25%Trypsin EDTA for 5 minutes. dissociated cells were transferred into cold DPBS + 1%BSA + 2g/mL DAPI. Cells were then sorted on an BD FACS ARIA II flow cytometer. Kaede+ DAPI cells were collected in lysis buffer from the RNA isolation kit and immediately processed. RNA was isolated using the RNAqueous Micro Total RNA Isolation Kit cDNA was amplified using the SMART Seq v4 Ultra Low Input RNA Kit for Sequencing and libraries were prepared using the Nextera XT DNA library prep kit and sequenced on an Illumina HiSeq 2500 sequencer. GEO Accession:GSM4029964 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP218233     9_RA.R1.fastq.gz 9_RA.R2.fastq.gz fastq fastq 2752434100.0 27524341.0 GSM4029964 r1 0:50 1:50 A:742948333;C:630419013;G:638493678;T:739745278;N:827798 50 50     742948333 630419013 638493678 739745278 827798 SRX6708754 SRS5262469 SRA938976 GEO Fred Hutchinson Cancer Research Center 2 0.91252 0.91511 0.0935 0.09935 0.7303 0.73612 0.48109 0.47973 50 50 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2019-08-13 Pharyngula Embryo Brain Nervous System
53606 53606 SRR9961220 SRX6708753 SRS5262468 SRP218233 PRJNA560048 Gene expression changes in Retinoic Acid treated zebrafish Vagus motor neurons GSE135781 Transcriptome Analysis Weprofiled the transcriptomes of DMSO treated control and Retinoic Acid treated zebrafish Vagus motor neurons at 38 hpf to identifiy genes that are differentially expressed between these two treatments. Overall design: We obtained cells by dissecting the hindbrains of Tgisl1:Kaede expressing embryos dissociating to single cell suspension and sorting for Kaede positive cells by flow cytometry. We sequenced 3 replicates of 4500 10000 cells per condition.   pubmed:32302545   6 RA GSM4029963   tissue:Vagus motor neurons|cell type:Vagus motor neurons|developmental stage:38 hpf|genotype:Tgisl1:Kaede 6 RA Image analysis and base calling were performed using Illumina's Real Time Analysis v1.18 software followed by 'demultiplexing' of indexed reads and generation of FASTQ files using Illumina's bcl2fastq v1.8.4 Reads of low quality were filtered out prior to alignment to GRCz11 using STAR 2.5.2a in 2 pass mode. Counts were generated from STAR alignments at the gene level using featureCounts from the Subread package v1.5.0. Genome build: GRCz11 Supplementary files format and content: tab delimited text files include counts generated at the gene level by featureCounts Vagus motor neurons Embryos were treated 0.2mM PTU as well as with 50nM Retinoic Acid in DMSO or the equivalent volumen of DMSO as a control beginning at 24hpf. The posterior hindbrain was manually dissected in calcium free Ringer’s solution with MESAB and dissected tissue was dissociated to single cell suspension by pipetting in 0.25%Trypsin EDTA for 5 minutes. dissociated cells were transferred into cold DPBS + 1%BSA + 2g/mL DAPI. Cells were then sorted on an BD FACS ARIA II flow cytometer. Kaede+ DAPI cells were collected in lysis buffer from the RNA isolation kit and immediately processed. RNA was isolated using the RNAqueous Micro Total RNA Isolation Kit cDNA was amplified using the SMART Seq v4 Ultra Low Input RNA Kit for Sequencing and libraries were prepared using the Nextera XT DNA library prep kit and sequenced on an Illumina HiSeq 2500 sequencer.   cell type:Vagus motor neurons|developmental stage:38 hpf|genotype:Tgisl1:Kaede GSM4029963 GSM4029963: 6 RA; Danio rerio; RNA Seq GSM4029963   1 The posterior hindbrain was manually dissected in calcium free Ringer's solution with MESAB and dissected tissue was dissociated to single cell suspension by pipetting in 0.25%Trypsin EDTA for 5 minutes. dissociated cells were transferred into cold DPBS + 1%BSA + 2g/mL DAPI. Cells were then sorted on an BD FACS ARIA II flow cytometer. Kaede+ DAPI cells were collected in lysis buffer from the RNA isolation kit and immediately processed. RNA was isolated using the RNAqueous Micro Total RNA Isolation Kit cDNA was amplified using the SMART Seq v4 Ultra Low Input RNA Kit for Sequencing and libraries were prepared using the Nextera XT DNA library prep kit and sequenced on an Illumina HiSeq 2500 sequencer. GEO Accession:GSM4029963 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP218233     6_RA.R1.fastq.gz 6_RA.R2.fastq.gz fastq fastq 1950219200.0 19502192.0 GSM4029963 r1 0:50 1:50 A:524892877;C:449943700;G:454069669;T:520743134;N:569820 50 50     524892877 449943700 454069669 520743134 569820 SRX6708753 SRS5262468 SRA938976 GEO Fred Hutchinson Cancer Research Center 2 0.91139 0.91465 0.08909 0.0985 0.72665 0.73539 0.48694 0.49354 50 50 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2019-08-13 Pharyngula Embryo Brain Nervous System
53607 53607 SRR9961219 SRX6708752 SRS5262467 SRP218233 PRJNA560048 Gene expression changes in Retinoic Acid treated zebrafish Vagus motor neurons GSE135781 Transcriptome Analysis Weprofiled the transcriptomes of DMSO treated control and Retinoic Acid treated zebrafish Vagus motor neurons at 38 hpf to identifiy genes that are differentially expressed between these two treatments. Overall design: We obtained cells by dissecting the hindbrains of Tgisl1:Kaede expressing embryos dissociating to single cell suspension and sorting for Kaede positive cells by flow cytometry. We sequenced 3 replicates of 4500 10000 cells per condition.   pubmed:32302545   10 DMSO GSM4029962   tissue:Vagus motor neurons|cell type:Vagus motor neurons|developmental stage:38 hpf|genotype:Tgisl1:Kaede 10 DMSO Image analysis and base calling were performed using Illumina's Real Time Analysis v1.18 software followed by 'demultiplexing' of indexed reads and generation of FASTQ files using Illumina's bcl2fastq v1.8.4 Reads of low quality were filtered out prior to alignment to GRCz11 using STAR 2.5.2a in 2 pass mode. Counts were generated from STAR alignments at the gene level using featureCounts from the Subread package v1.5.0. Genome build: GRCz11 Supplementary files format and content: tab delimited text files include counts generated at the gene level by featureCounts Vagus motor neurons Embryos were treated 0.2mM PTU as well as with 50nM Retinoic Acid in DMSO or the equivalent volumen of DMSO as a control beginning at 24hpf. The posterior hindbrain was manually dissected in calcium free Ringer’s solution with MESAB and dissected tissue was dissociated to single cell suspension by pipetting in 0.25%Trypsin EDTA for 5 minutes. dissociated cells were transferred into cold DPBS + 1%BSA + 2g/mL DAPI. Cells were then sorted on an BD FACS ARIA II flow cytometer. Kaede+ DAPI cells were collected in lysis buffer from the RNA isolation kit and immediately processed. RNA was isolated using the RNAqueous Micro Total RNA Isolation Kit cDNA was amplified using the SMART Seq v4 Ultra Low Input RNA Kit for Sequencing and libraries were prepared using the Nextera XT DNA library prep kit and sequenced on an Illumina HiSeq 2500 sequencer.   cell type:Vagus motor neurons|developmental stage:38 hpf|genotype:Tgisl1:Kaede GSM4029962 GSM4029962: 10 DMSO; Danio rerio; RNA Seq GSM4029962   1 The posterior hindbrain was manually dissected in calcium free Ringer's solution with MESAB and dissected tissue was dissociated to single cell suspension by pipetting in 0.25%Trypsin EDTA for 5 minutes. dissociated cells were transferred into cold DPBS + 1%BSA + 2g/mL DAPI. Cells were then sorted on an BD FACS ARIA II flow cytometer. Kaede+ DAPI cells were collected in lysis buffer from the RNA isolation kit and immediately processed. RNA was isolated using the RNAqueous Micro Total RNA Isolation Kit cDNA was amplified using the SMART Seq v4 Ultra Low Input RNA Kit for Sequencing and libraries were prepared using the Nextera XT DNA library prep kit and sequenced on an Illumina HiSeq 2500 sequencer. GEO Accession:GSM4029962 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP218233     10_DMSO.R1.fastq.gz 10_DMSO.R2.fastq.gz fastq fastq 2564610000.0 25646100.0 GSM4029962 r1 0:50 1:50 A:695263400;C:585667319;G:591832017;T:691080534;N:766730 50 50     695263400 585667319 591832017 691080534 766730 SRX6708752 SRS5262467 SRA938976 GEO Fred Hutchinson Cancer Research Center 2 0.89865 0.90128 0.09345 0.1017 0.73805 0.74683 0.4764 0.47485 50 50 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2019-08-13 Pharyngula Embryo Brain Nervous System
53608 53608 SRR9961218 SRX6708751 SRS5262466 SRP218233 PRJNA560048 Gene expression changes in Retinoic Acid treated zebrafish Vagus motor neurons GSE135781 Transcriptome Analysis Weprofiled the transcriptomes of DMSO treated control and Retinoic Acid treated zebrafish Vagus motor neurons at 38 hpf to identifiy genes that are differentially expressed between these two treatments. Overall design: We obtained cells by dissecting the hindbrains of Tgisl1:Kaede expressing embryos dissociating to single cell suspension and sorting for Kaede positive cells by flow cytometry. We sequenced 3 replicates of 4500 10000 cells per condition.   pubmed:32302545   4 DMSO GSM4029961   tissue:Vagus motor neurons|cell type:Vagus motor neurons|developmental stage:38 hpf|genotype:Tgisl1:Kaede 4 DMSO Image analysis and base calling were performed using Illumina's Real Time Analysis v1.18 software followed by 'demultiplexing' of indexed reads and generation of FASTQ files using Illumina's bcl2fastq v1.8.4 Reads of low quality were filtered out prior to alignment to GRCz11 using STAR 2.5.2a in 2 pass mode. Counts were generated from STAR alignments at the gene level using featureCounts from the Subread package v1.5.0. Genome build: GRCz11 Supplementary files format and content: tab delimited text files include counts generated at the gene level by featureCounts Vagus motor neurons Embryos were treated 0.2mM PTU as well as with 50nM Retinoic Acid in DMSO or the equivalent volumen of DMSO as a control beginning at 24hpf. The posterior hindbrain was manually dissected in calcium free Ringer’s solution with MESAB and dissected tissue was dissociated to single cell suspension by pipetting in 0.25%Trypsin EDTA for 5 minutes. dissociated cells were transferred into cold DPBS + 1%BSA + 2g/mL DAPI. Cells were then sorted on an BD FACS ARIA II flow cytometer. Kaede+ DAPI cells were collected in lysis buffer from the RNA isolation kit and immediately processed. RNA was isolated using the RNAqueous Micro Total RNA Isolation Kit cDNA was amplified using the SMART Seq v4 Ultra Low Input RNA Kit for Sequencing and libraries were prepared using the Nextera XT DNA library prep kit and sequenced on an Illumina HiSeq 2500 sequencer.   cell type:Vagus motor neurons|developmental stage:38 hpf|genotype:Tgisl1:Kaede GSM4029961 GSM4029961: 4 DMSO; Danio rerio; RNA Seq GSM4029961   1 The posterior hindbrain was manually dissected in calcium free Ringer's solution with MESAB and dissected tissue was dissociated to single cell suspension by pipetting in 0.25%Trypsin EDTA for 5 minutes. dissociated cells were transferred into cold DPBS + 1%BSA + 2g/mL DAPI. Cells were then sorted on an BD FACS ARIA II flow cytometer. Kaede+ DAPI cells were collected in lysis buffer from the RNA isolation kit and immediately processed. RNA was isolated using the RNAqueous Micro Total RNA Isolation Kit cDNA was amplified using the SMART Seq v4 Ultra Low Input RNA Kit for Sequencing and libraries were prepared using the Nextera XT DNA library prep kit and sequenced on an Illumina HiSeq 2500 sequencer. GEO Accession:GSM4029961 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP218233     4_DMSO.R1.fastq.gz 4_DMSO.R2.fastq.gz fastq fastq 2944532300.0 29445323.0 GSM4029961 r1 0:50 1:50 A:794249480;C:674151778;G:684114554;T:791128243;N:888245 50 50     794249480 674151778 684114554 791128243 888245 SRX6708751 SRS5262466 SRA938976 GEO Fred Hutchinson Cancer Research Center 2 0.89952 0.9014 0.0972 0.10304 0.73166 0.73862 0.47176 0.47741 50 50 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2019-08-13 Pharyngula Embryo Brain Nervous System
53609 53609 SRR9961217 SRX6708750 SRS5262465 SRP218233 PRJNA560048 Gene expression changes in Retinoic Acid treated zebrafish Vagus motor neurons GSE135781 Transcriptome Analysis Weprofiled the transcriptomes of DMSO treated control and Retinoic Acid treated zebrafish Vagus motor neurons at 38 hpf to identifiy genes that are differentially expressed between these two treatments. Overall design: We obtained cells by dissecting the hindbrains of Tgisl1:Kaede expressing embryos dissociating to single cell suspension and sorting for Kaede positive cells by flow cytometry. We sequenced 3 replicates of 4500 10000 cells per condition.   pubmed:32302545   1 DMSO GSM4029960   tissue:Vagus motor neurons|cell type:Vagus motor neurons|developmental stage:38 hpf|genotype:Tgisl1:Kaede 1 DMSO Image analysis and base calling were performed using Illumina's Real Time Analysis v1.18 software followed by 'demultiplexing' of indexed reads and generation of FASTQ files using Illumina's bcl2fastq v1.8.4 Reads of low quality were filtered out prior to alignment to GRCz11 using STAR 2.5.2a in 2 pass mode. Counts were generated from STAR alignments at the gene level using featureCounts from the Subread package v1.5.0. Genome build: GRCz11 Supplementary files format and content: tab delimited text files include counts generated at the gene level by featureCounts Vagus motor neurons Embryos were treated 0.2mM PTU as well as with 50nM Retinoic Acid in DMSO or the equivalent volumen of DMSO as a control beginning at 24hpf. The posterior hindbrain was manually dissected in calcium free Ringer’s solution with MESAB and dissected tissue was dissociated to single cell suspension by pipetting in 0.25%Trypsin EDTA for 5 minutes. dissociated cells were transferred into cold DPBS + 1%BSA + 2g/mL DAPI. Cells were then sorted on an BD FACS ARIA II flow cytometer. Kaede+ DAPI cells were collected in lysis buffer from the RNA isolation kit and immediately processed. RNA was isolated using the RNAqueous Micro Total RNA Isolation Kit cDNA was amplified using the SMART Seq v4 Ultra Low Input RNA Kit for Sequencing and libraries were prepared using the Nextera XT DNA library prep kit and sequenced on an Illumina HiSeq 2500 sequencer.   cell type:Vagus motor neurons|developmental stage:38 hpf|genotype:Tgisl1:Kaede GSM4029960 GSM4029960: 1 DMSO; Danio rerio; RNA Seq GSM4029960   1 The posterior hindbrain was manually dissected in calcium free Ringer's solution with MESAB and dissected tissue was dissociated to single cell suspension by pipetting in 0.25%Trypsin EDTA for 5 minutes. dissociated cells were transferred into cold DPBS + 1%BSA + 2g/mL DAPI. Cells were then sorted on an BD FACS ARIA II flow cytometer. Kaede+ DAPI cells were collected in lysis buffer from the RNA isolation kit and immediately processed. RNA was isolated using the RNAqueous Micro Total RNA Isolation Kit cDNA was amplified using the SMART Seq v4 Ultra Low Input RNA Kit for Sequencing and libraries were prepared using the Nextera XT DNA library prep kit and sequenced on an Illumina HiSeq 2500 sequencer. GEO Accession:GSM4029960 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP218233     1_DMSO.R1.fastq.gz 1_DMSO.R2.fastq.gz fastq fastq 2672431200.0 26724312.0 GSM4029960 r1 0:50 1:50 A:730227451;C:600836649;G:608011607;T:732560809;N:794684 50 50     730227451 600836649 608011607 732560809 794684 SRX6708750 SRS5262465 SRA938976 GEO Fred Hutchinson Cancer Research Center 2 0.89002 0.89327 0.11786 0.12268 0.73379 0.73874 0.47942 0.48107 50 50 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2019-08-13 Pharyngula Embryo Brain Nervous System
55625 55625 SRR10586541 SRX7267032 SRS5761556 SRP234693 PRJNA593443 A single cell transcriptome atlas of the developing zebrafish hindbrain [fgfr1] GSE141426 Transcriptome Analysis RNA seq profile of transgenic hindbrains expressing heat shock induced constitutively activated fgfR1 Tghsp70:ca fgfr1 and compared to heat shocked counterparts Method: 22hpf embryos were heat shocked for 30min at 38.5°C and then incubated for 2hr at 28.5°C . post hindbrains were microdissected and the RNA was extracted. fgfR1 overexpression was checked by qPCR and samples were selected for sequencing Overall design: 4 control heat shoked samples and 4 constitutively active fgfr1 were deep sequenced parent bioproject:PRJNA593433 pubmed:32094115   CA fgfr1 4 GSM4202679   source name:Dissected hindbrain and surrounding tissues|tissue:Dissected hindbrain and surrounding tissues|Stage:24 25hpf|strain:Tghsp70:ca fgfr1|genotype:constitutively active fgfr1|growth:28.5°C until 22hpf 30min at 38.5°C 2hr 28.5°C CA fgfr1 4 Reads were and aligned against zebrafish genome GRCz10 and Ensembl release 86 transcript annotations using STAR v2.5.1b via the transcript quantification software RSEM v1.2.31 RSEM estimated gene level counts were rounded to integers Genome build: GRCz10 Supplementary files format and content: Tab delimited counts matrix with row representing genes and columns representing samples. Dissected hindbrain and surrounding tissues   Embryos were decorionated and deyolked in DMEM with high Glucose no Glutamine no Calcium 11530556 Gibco; hindbrains were micro dissected using 0.33mm micro fine sterile needles; RNA was isolated using Quick RNA Microprep kit Zymo Research. Samples were prepared with the Clontech SMARTer kit 634926 TaKaRa for cDNA amplification followed by NexteraXT Illumina for library preparation.   tissue:Dissected hindbrain and surrounding tissues|Stage:24 25hpf|strain:Tghsp70:ca fgfr1|genotype:constitutively active fgfr1|growth:28.5°C until 22hpf 30min at 38.5°C 2hr 28.5°C GSM4202679 GSM4202679: CA fgfr1 4; Danio rerio; RNA Seq GSM4202679   1 Embryos were decorionated and deyolked in DMEM with high Glucose no Glutamine no Calcium 11530556 Gibco; hindbrains were micro dissected using 0.33mm micro fine sterile needles; RNA was isolated using Quick RNA Microprep kit Zymo Research. Samples were prepared with the Clontech SMARTer kit 634926 TaKaRa for cDNA amplification followed by NexteraXT Illumina for library preparation. GEO Accession:GSM4202679 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP234693     TAM488A8_S14_L002_R1_001.fastq.gz fastq 3045400484.0 40071059.0 GSM4202679 r1 0:76 1:0 A:821910580;C:692018977;G:680268603;T:850797187;N:405137 76 0     821910580 692018977 680268603 850797187 405137 SRX7267032 SRS5761556 SRA1006559 GEO The Francis Crick Institute 1 0.92302   0.0648   0.71991   0.46896   76   B   usable mapping rate illumina hiseq_era full_length cdna_unspecified smarter bulk unknown unknown   United Kingdom 2019-12-04 Pharyngula Embryo Brain Nervous System
55626 55626 SRR10586540 SRX7267030 SRS5761555 SRP234693 PRJNA593443 A single cell transcriptome atlas of the developing zebrafish hindbrain [fgfr1] GSE141426 Transcriptome Analysis RNA seq profile of transgenic hindbrains expressing heat shock induced constitutively activated fgfR1 Tghsp70:ca fgfr1 and compared to heat shocked counterparts Method: 22hpf embryos were heat shocked for 30min at 38.5°C and then incubated for 2hr at 28.5°C . post hindbrains were microdissected and the RNA was extracted. fgfR1 overexpression was checked by qPCR and samples were selected for sequencing Overall design: 4 control heat shoked samples and 4 constitutively active fgfr1 were deep sequenced parent bioproject:PRJNA593433 pubmed:32094115   CA fgfr1 3 GSM4202678   source name:Dissected hindbrain and surrounding tissues|tissue:Dissected hindbrain and surrounding tissues|Stage:24 25hpf|strain:Tghsp70:ca fgfr1|genotype:constitutively active fgfr1|growth:28.5°C until 22hpf 30min at 38.5°C 2hr 28.5°C CA fgfr1 3 Reads were and aligned against zebrafish genome GRCz10 and Ensembl release 86 transcript annotations using STAR v2.5.1b via the transcript quantification software RSEM v1.2.31 RSEM estimated gene level counts were rounded to integers Genome build: GRCz10 Supplementary files format and content: Tab delimited counts matrix with row representing genes and columns representing samples. Dissected hindbrain and surrounding tissues   Embryos were decorionated and deyolked in DMEM with high Glucose no Glutamine no Calcium 11530556 Gibco; hindbrains were micro dissected using 0.33mm micro fine sterile needles; RNA was isolated using Quick RNA Microprep kit Zymo Research. Samples were prepared with the Clontech SMARTer kit 634926 TaKaRa for cDNA amplification followed by NexteraXT Illumina for library preparation.   tissue:Dissected hindbrain and surrounding tissues|Stage:24 25hpf|strain:Tghsp70:ca fgfr1|genotype:constitutively active fgfr1|growth:28.5°C until 22hpf 30min at 38.5°C 2hr 28.5°C GSM4202678 GSM4202678: CA fgfr1 3; Danio rerio; RNA Seq GSM4202678   1 Embryos were decorionated and deyolked in DMEM with high Glucose no Glutamine no Calcium 11530556 Gibco; hindbrains were micro dissected using 0.33mm micro fine sterile needles; RNA was isolated using Quick RNA Microprep kit Zymo Research. Samples were prepared with the Clontech SMARTer kit 634926 TaKaRa for cDNA amplification followed by NexteraXT Illumina for library preparation. GEO Accession:GSM4202678 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP234693     TAM488A7_S13_L002_R1_001.fastq.gz fastq 3489328416.0 45912216.0 GSM4202678 r1 0:76 1:0 A:938147636;C:798355890;G:783472993;T:968887339;N:464558 76 0     938147636 798355890 783472993 968887339 464558 SRX7267030 SRS5761555 SRA1006559 GEO The Francis Crick Institute 1 0.92315   0.06062   0.72314   0.46217   76   B   usable mapping rate illumina hiseq_era full_length cdna_unspecified smarter bulk unknown unknown   United Kingdom 2019-12-04 Pharyngula Embryo Brain Nervous System
55627 55627 SRR10586539 SRX7267028 SRS5761554 SRP234693 PRJNA593443 A single cell transcriptome atlas of the developing zebrafish hindbrain [fgfr1] GSE141426 Transcriptome Analysis RNA seq profile of transgenic hindbrains expressing heat shock induced constitutively activated fgfR1 Tghsp70:ca fgfr1 and compared to heat shocked counterparts Method: 22hpf embryos were heat shocked for 30min at 38.5°C and then incubated for 2hr at 28.5°C . post hindbrains were microdissected and the RNA was extracted. fgfR1 overexpression was checked by qPCR and samples were selected for sequencing Overall design: 4 control heat shoked samples and 4 constitutively active fgfr1 were deep sequenced parent bioproject:PRJNA593433 pubmed:32094115   CA fgfr1 2 GSM4202677   source name:Dissected hindbrain and surrounding tissues|tissue:Dissected hindbrain and surrounding tissues|Stage:24 25hpf|strain:Tghsp70:ca fgfr1|genotype:constitutively active fgfr1|growth:28.5°C until 22hpf 30min at 38.5°C 2hr 28.5°C CA fgfr1 2 Reads were and aligned against zebrafish genome GRCz10 and Ensembl release 86 transcript annotations using STAR v2.5.1b via the transcript quantification software RSEM v1.2.31 RSEM estimated gene level counts were rounded to integers Genome build: GRCz10 Supplementary files format and content: Tab delimited counts matrix with row representing genes and columns representing samples. Dissected hindbrain and surrounding tissues   Embryos were decorionated and deyolked in DMEM with high Glucose no Glutamine no Calcium 11530556 Gibco; hindbrains were micro dissected using 0.33mm micro fine sterile needles; RNA was isolated using Quick RNA Microprep kit Zymo Research. Samples were prepared with the Clontech SMARTer kit 634926 TaKaRa for cDNA amplification followed by NexteraXT Illumina for library preparation.   tissue:Dissected hindbrain and surrounding tissues|Stage:24 25hpf|strain:Tghsp70:ca fgfr1|genotype:constitutively active fgfr1|growth:28.5°C until 22hpf 30min at 38.5°C 2hr 28.5°C GSM4202677 GSM4202677: CA fgfr1 2; Danio rerio; RNA Seq GSM4202677   1 Embryos were decorionated and deyolked in DMEM with high Glucose no Glutamine no Calcium 11530556 Gibco; hindbrains were micro dissected using 0.33mm micro fine sterile needles; RNA was isolated using Quick RNA Microprep kit Zymo Research. Samples were prepared with the Clontech SMARTer kit 634926 TaKaRa for cDNA amplification followed by NexteraXT Illumina for library preparation. GEO Accession:GSM4202677 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP234693     TAM488A6_S12_L002_R1_001.fastq.gz fastq 3537086892.0 46540617.0 GSM4202677 r1 0:76 1:0 A:957729349;C:804805887;G:786907851;T:987172559;N:471246 76 0     957729349 804805887 786907851 987172559 471246 SRX7267028 SRS5761554 SRA1006559 GEO The Francis Crick Institute 1 0.9237   0.05836   0.73344   0.45676   76   B   usable mapping rate illumina hiseq_era full_length cdna_unspecified smarter bulk unknown unknown   United Kingdom 2019-12-04 Pharyngula Embryo Brain Nervous System
55628 55628 SRR10586538 SRX7267026 SRS5761553 SRP234693 PRJNA593443 A single cell transcriptome atlas of the developing zebrafish hindbrain [fgfr1] GSE141426 Transcriptome Analysis RNA seq profile of transgenic hindbrains expressing heat shock induced constitutively activated fgfR1 Tghsp70:ca fgfr1 and compared to heat shocked counterparts Method: 22hpf embryos were heat shocked for 30min at 38.5°C and then incubated for 2hr at 28.5°C . post hindbrains were microdissected and the RNA was extracted. fgfR1 overexpression was checked by qPCR and samples were selected for sequencing Overall design: 4 control heat shoked samples and 4 constitutively active fgfr1 were deep sequenced parent bioproject:PRJNA593433 pubmed:32094115   CA fgfr1 1 GSM4202676   source name:Dissected hindbrain and surrounding tissues|tissue:Dissected hindbrain and surrounding tissues|Stage:24 25hpf|strain:Tghsp70:ca fgfr1|genotype:constitutively active fgfr1|growth:28.5°C until 22hpf 30min at 38.5°C 2hr 28.5°C CA fgfr1 1 Reads were and aligned against zebrafish genome GRCz10 and Ensembl release 86 transcript annotations using STAR v2.5.1b via the transcript quantification software RSEM v1.2.31 RSEM estimated gene level counts were rounded to integers Genome build: GRCz10 Supplementary files format and content: Tab delimited counts matrix with row representing genes and columns representing samples. Dissected hindbrain and surrounding tissues   Embryos were decorionated and deyolked in DMEM with high Glucose no Glutamine no Calcium 11530556 Gibco; hindbrains were micro dissected using 0.33mm micro fine sterile needles; RNA was isolated using Quick RNA Microprep kit Zymo Research. Samples were prepared with the Clontech SMARTer kit 634926 TaKaRa for cDNA amplification followed by NexteraXT Illumina for library preparation.   tissue:Dissected hindbrain and surrounding tissues|Stage:24 25hpf|strain:Tghsp70:ca fgfr1|genotype:constitutively active fgfr1|growth:28.5°C until 22hpf 30min at 38.5°C 2hr 28.5°C GSM4202676 GSM4202676: CA fgfr1 1; Danio rerio; RNA Seq GSM4202676   1 Embryos were decorionated and deyolked in DMEM with high Glucose no Glutamine no Calcium 11530556 Gibco; hindbrains were micro dissected using 0.33mm micro fine sterile needles; RNA was isolated using Quick RNA Microprep kit Zymo Research. Samples were prepared with the Clontech SMARTer kit 634926 TaKaRa for cDNA amplification followed by NexteraXT Illumina for library preparation. GEO Accession:GSM4202676 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP234693     TAM488A5_S11_L002_R1_001.fastq.gz fastq 4003882844.0 52682669.0 GSM4202676 r1 0:76 1:0 A:1081567814;C:910668493;G:898715541;T:1112399278;N:531718 76 0     1081567814 910668493 898715541 1112399278 531718 SRX7267026 SRS5761553 SRA1006559 GEO The Francis Crick Institute 1 0.92935   0.06164   0.7276   0.45966   76   B   usable mapping rate illumina hiseq_era full_length cdna_unspecified smarter bulk unknown unknown   United Kingdom 2019-12-04 Pharyngula Embryo Brain Nervous System
55629 55629 SRR10586537 SRX7267024 SRS5761552 SRP234693 PRJNA593443 A single cell transcriptome atlas of the developing zebrafish hindbrain [fgfr1] GSE141426 Transcriptome Analysis RNA seq profile of transgenic hindbrains expressing heat shock induced constitutively activated fgfR1 Tghsp70:ca fgfr1 and compared to heat shocked counterparts Method: 22hpf embryos were heat shocked for 30min at 38.5°C and then incubated for 2hr at 28.5°C . post hindbrains were microdissected and the RNA was extracted. fgfR1 overexpression was checked by qPCR and samples were selected for sequencing Overall design: 4 control heat shoked samples and 4 constitutively active fgfr1 were deep sequenced parent bioproject:PRJNA593433 pubmed:32094115   Cnt4 GSM4202675   source name:Dissected hindbrain and surrounding tissues|tissue:Dissected hindbrain and surrounding tissues|Stage:24 25hpf|strain:Tghsp70:ca fgfr1|genotype:wt|growth:28.5°C until 22hpf 30min at 38.5°C 2hr 28.5°C Cnt4 Reads were and aligned against zebrafish genome GRCz10 and Ensembl release 86 transcript annotations using STAR v2.5.1b via the transcript quantification software RSEM v1.2.31 RSEM estimated gene level counts were rounded to integers Genome build: GRCz10 Supplementary files format and content: Tab delimited counts matrix with row representing genes and columns representing samples. Dissected hindbrain and surrounding tissues   Embryos were decorionated and deyolked in DMEM with high Glucose no Glutamine no Calcium 11530556 Gibco; hindbrains were micro dissected using 0.33mm micro fine sterile needles; RNA was isolated using Quick RNA Microprep kit Zymo Research. Samples were prepared with the Clontech SMARTer kit 634926 TaKaRa for cDNA amplification followed by NexteraXT Illumina for library preparation.   tissue:Dissected hindbrain and surrounding tissues|Stage:24 25hpf|strain:Tghsp70:ca fgfr1|genotype:wt|growth:28.5°C until 22hpf 30min at 38.5°C 2hr 28.5°C GSM4202675 GSM4202675: Cnt4; Danio rerio; RNA Seq GSM4202675   1 Embryos were decorionated and deyolked in DMEM with high Glucose no Glutamine no Calcium 11530556 Gibco; hindbrains were micro dissected using 0.33mm micro fine sterile needles; RNA was isolated using Quick RNA Microprep kit Zymo Research. Samples were prepared with the Clontech SMARTer kit 634926 TaKaRa for cDNA amplification followed by NexteraXT Illumina for library preparation. GEO Accession:GSM4202675 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP234693     TAM488A4_S10_L002_R1_001.fastq.gz fastq 3501222416.0 46068716.0 GSM4202675 r1 0:76 1:0 A:935177317;C:808682245;G:798852592;T:958041399;N:468863 76 0     935177317 808682245 798852592 958041399 468863 SRX7267024 SRS5761552 SRA1006559 GEO The Francis Crick Institute 1 0.92931   0.06509   0.70958   0.4542   76   B   usable mapping rate illumina hiseq_era full_length cdna_unspecified smarter bulk unknown unknown   United Kingdom 2019-12-04 Pharyngula Embryo Brain Nervous System
55630 55630 SRR10586536 SRX7267022 SRS5761551 SRP234693 PRJNA593443 A single cell transcriptome atlas of the developing zebrafish hindbrain [fgfr1] GSE141426 Transcriptome Analysis RNA seq profile of transgenic hindbrains expressing heat shock induced constitutively activated fgfR1 Tghsp70:ca fgfr1 and compared to heat shocked counterparts Method: 22hpf embryos were heat shocked for 30min at 38.5°C and then incubated for 2hr at 28.5°C . post hindbrains were microdissected and the RNA was extracted. fgfR1 overexpression was checked by qPCR and samples were selected for sequencing Overall design: 4 control heat shoked samples and 4 constitutively active fgfr1 were deep sequenced parent bioproject:PRJNA593433 pubmed:32094115   Cnt3 GSM4202674   source name:Dissected hindbrain and surrounding tissues|tissue:Dissected hindbrain and surrounding tissues|Stage:24 25hpf|strain:Tghsp70:ca fgfr1|genotype:wt|growth:28.5°C until 22hpf 30min at 38.5°C 2hr 28.5°C Cnt3 Reads were and aligned against zebrafish genome GRCz10 and Ensembl release 86 transcript annotations using STAR v2.5.1b via the transcript quantification software RSEM v1.2.31 RSEM estimated gene level counts were rounded to integers Genome build: GRCz10 Supplementary files format and content: Tab delimited counts matrix with row representing genes and columns representing samples. Dissected hindbrain and surrounding tissues   Embryos were decorionated and deyolked in DMEM with high Glucose no Glutamine no Calcium 11530556 Gibco; hindbrains were micro dissected using 0.33mm micro fine sterile needles; RNA was isolated using Quick RNA Microprep kit Zymo Research. Samples were prepared with the Clontech SMARTer kit 634926 TaKaRa for cDNA amplification followed by NexteraXT Illumina for library preparation.   tissue:Dissected hindbrain and surrounding tissues|Stage:24 25hpf|strain:Tghsp70:ca fgfr1|genotype:wt|growth:28.5°C until 22hpf 30min at 38.5°C 2hr 28.5°C GSM4202674 GSM4202674: Cnt3; Danio rerio; RNA Seq GSM4202674   1 Embryos were decorionated and deyolked in DMEM with high Glucose no Glutamine no Calcium 11530556 Gibco; hindbrains were micro dissected using 0.33mm micro fine sterile needles; RNA was isolated using Quick RNA Microprep kit Zymo Research. Samples were prepared with the Clontech SMARTer kit 634926 TaKaRa for cDNA amplification followed by NexteraXT Illumina for library preparation. GEO Accession:GSM4202674 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP234693     TAM488A3_S9_L002_R1_001.fastq.gz fastq 3504033276.0 46105701.0 GSM4202674 r1 0:76 1:0 A:934473986;C:809615131;G:799926710;T:959549608;N:467841 76 0     934473986 809615131 799926710 959549608 467841 SRX7267022 SRS5761551 SRA1006559 GEO The Francis Crick Institute 1 0.92775   0.06388   0.71376   0.45447   76   B   usable mapping rate illumina hiseq_era full_length cdna_unspecified smarter bulk unknown unknown   United Kingdom 2019-12-04 Pharyngula Embryo Brain Nervous System
55631 55631 SRR10586535 SRX7267020 SRS5761550 SRP234693 PRJNA593443 A single cell transcriptome atlas of the developing zebrafish hindbrain [fgfr1] GSE141426 Transcriptome Analysis RNA seq profile of transgenic hindbrains expressing heat shock induced constitutively activated fgfR1 Tghsp70:ca fgfr1 and compared to heat shocked counterparts Method: 22hpf embryos were heat shocked for 30min at 38.5°C and then incubated for 2hr at 28.5°C . post hindbrains were microdissected and the RNA was extracted. fgfR1 overexpression was checked by qPCR and samples were selected for sequencing Overall design: 4 control heat shoked samples and 4 constitutively active fgfr1 were deep sequenced parent bioproject:PRJNA593433 pubmed:32094115   Cnt2 GSM4202673   source name:Dissected hindbrain and surrounding tissues|tissue:Dissected hindbrain and surrounding tissues|Stage:24 25hpf|strain:Tghsp70:ca fgfr1|genotype:wt|growth:28.5°C until 22hpf 30min at 38.5°C 2hr 28.5°C Cnt2 Reads were and aligned against zebrafish genome GRCz10 and Ensembl release 86 transcript annotations using STAR v2.5.1b via the transcript quantification software RSEM v1.2.31 RSEM estimated gene level counts were rounded to integers Genome build: GRCz10 Supplementary files format and content: Tab delimited counts matrix with row representing genes and columns representing samples. Dissected hindbrain and surrounding tissues   Embryos were decorionated and deyolked in DMEM with high Glucose no Glutamine no Calcium 11530556 Gibco; hindbrains were micro dissected using 0.33mm micro fine sterile needles; RNA was isolated using Quick RNA Microprep kit Zymo Research. Samples were prepared with the Clontech SMARTer kit 634926 TaKaRa for cDNA amplification followed by NexteraXT Illumina for library preparation.   tissue:Dissected hindbrain and surrounding tissues|Stage:24 25hpf|strain:Tghsp70:ca fgfr1|genotype:wt|growth:28.5°C until 22hpf 30min at 38.5°C 2hr 28.5°C GSM4202673 GSM4202673: Cnt2; Danio rerio; RNA Seq GSM4202673   1 Embryos were decorionated and deyolked in DMEM with high Glucose no Glutamine no Calcium 11530556 Gibco; hindbrains were micro dissected using 0.33mm micro fine sterile needles; RNA was isolated using Quick RNA Microprep kit Zymo Research. Samples were prepared with the Clontech SMARTer kit 634926 TaKaRa for cDNA amplification followed by NexteraXT Illumina for library preparation. GEO Accession:GSM4202673 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP234693     TAM488A2_S8_L002_R1_001.fastq.gz fastq 2853636220.0 37547845.0 GSM4202673 r1 0:76 1:0 A:771888090;C:643180373;G:635425286;T:802759894;N:382577 76 0     771888090 643180373 635425286 802759894 382577 SRX7267020 SRS5761550 SRA1006559 GEO The Francis Crick Institute 1 0.91568   0.08274   0.71703   0.4603   76   B   usable mapping rate illumina hiseq_era full_length cdna_unspecified smarter bulk unknown unknown   United Kingdom 2019-12-04 Pharyngula Embryo Brain Nervous System
55632 55632 SRR10586534 SRX7267018 SRS5761549 SRP234693 PRJNA593443 A single cell transcriptome atlas of the developing zebrafish hindbrain [fgfr1] GSE141426 Transcriptome Analysis RNA seq profile of transgenic hindbrains expressing heat shock induced constitutively activated fgfR1 Tghsp70:ca fgfr1 and compared to heat shocked counterparts Method: 22hpf embryos were heat shocked for 30min at 38.5°C and then incubated for 2hr at 28.5°C . post hindbrains were microdissected and the RNA was extracted. fgfR1 overexpression was checked by qPCR and samples were selected for sequencing Overall design: 4 control heat shoked samples and 4 constitutively active fgfr1 were deep sequenced parent bioproject:PRJNA593433 pubmed:32094115   Cnt1 GSM4202672   source name:Dissected hindbrain and surrounding tissues|tissue:Dissected hindbrain and surrounding tissues|Stage:24 25hpf|strain:Tghsp70:ca fgfr1|genotype:wt|growth:28.5°C until 22hpf 30min at 38.5°C 2hr 28.5°C Cnt1 Reads were and aligned against zebrafish genome GRCz10 and Ensembl release 86 transcript annotations using STAR v2.5.1b via the transcript quantification software RSEM v1.2.31 RSEM estimated gene level counts were rounded to integers Genome build: GRCz10 Supplementary files format and content: Tab delimited counts matrix with row representing genes and columns representing samples. Dissected hindbrain and surrounding tissues   Embryos were decorionated and deyolked in DMEM with high Glucose no Glutamine no Calcium 11530556 Gibco; hindbrains were micro dissected using 0.33mm micro fine sterile needles; RNA was isolated using Quick RNA Microprep kit Zymo Research. Samples were prepared with the Clontech SMARTer kit 634926 TaKaRa for cDNA amplification followed by NexteraXT Illumina for library preparation.   tissue:Dissected hindbrain and surrounding tissues|Stage:24 25hpf|strain:Tghsp70:ca fgfr1|genotype:wt|growth:28.5°C until 22hpf 30min at 38.5°C 2hr 28.5°C GSM4202672 GSM4202672: Cnt1; Danio rerio; RNA Seq GSM4202672   1 Embryos were decorionated and deyolked in DMEM with high Glucose no Glutamine no Calcium 11530556 Gibco; hindbrains were micro dissected using 0.33mm micro fine sterile needles; RNA was isolated using Quick RNA Microprep kit Zymo Research. Samples were prepared with the Clontech SMARTer kit 634926 TaKaRa for cDNA amplification followed by NexteraXT Illumina for library preparation. GEO Accession:GSM4202672 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP234693     TAM488A1_S7_L002_R1_001.fastq.gz fastq 2680453804.0 35269129.0 GSM4202672 r1 0:76 1:0 A:723489298;C:605414444;G:589417935;T:761780151;N:351976 76 0     723489298 605414444 589417935 761780151 351976 SRX7267018 SRS5761549 SRA1006559 GEO The Francis Crick Institute 1 0.91076   0.05355   0.74123   0.47074   76   B   usable mapping rate illumina hiseq_era full_length cdna_unspecified smarter bulk unknown unknown   United Kingdom 2019-12-04 Pharyngula Embryo Brain Nervous System
55633 55633 SRR10586533 SRX7266970 SRS5761504 SRP234692 PRJNA593444 A single cell transcriptome atlas of the developing zebrafish hindbrain [Fgf20a] GSE141425 Transcriptome Analysis RNA seq profile of Fgf20a homozygous mutant hindbrains compared with wilde type hindbrains Method: 24hpf hindbrains were microdissected and the RNA was extracted. Qulity of dissection was monitored by qPCR and samples were selected for sequencing Overall design: 4 control wt Cnt and 3 Fgf20aHOM were deep sequenced parent bioproject:PRJNA593433 pubmed:32094115   Fgf20aHOM 3 GSM4202671   source name:Dissected hindbrain and surrounding tissues|tissue:Dissected hindbrain and surrounding tissues|Stage:24hpf|strain:Fgf20a HOM|genotype:Fgf20a HOM|growth:28.5°C Fgf20aHOM 3 Reads were and aligned against zebrafish genome GRCz10 and Ensembl release 86 transcript annotations using STAR v2.5.1b via the transcript quantification software RSEM v1.2.31 RSEM estimated gene level counts were rounded to integers Genome build: GRCz10 Supplementary files format and content: Tab delimited counts matrix with row representing genes and columns representing samples. Dissected hindbrain and surrounding tissues   Embryos were decorionated and deyolked in DMEM with high Glucose no Glutamine no Calcium 11530556 Gibco; hindbrains were micro dissected using 0.33mm micro fine sterile needles; RNA was isolated using Quick RNA Microprep kit Zymo Research Samples were prepared with the Ovation® RNA Seq System V2 7102 NuGEN for cDNA amplification followed by NexteraXT Illumina for library preparation.   tissue:Dissected hindbrain and surrounding tissues|Stage:24hpf|strain:Fgf20a HOM|genotype:Fgf20a HOM|growth:28.5°C GSM4202671 GSM4202671: Fgf20aHOM 3; Danio rerio; RNA Seq GSM4202671   1 Embryos were decorionated and deyolked in DMEM with high Glucose no Glutamine no Calcium 11530556 Gibco; hindbrains were micro dissected using 0.33mm micro fine sterile needles; RNA was isolated using Quick RNA Microprep kit Zymo Research Samples were prepared with the Ovation® RNA Seq System V2 7102 NuGEN for cDNA amplification followed by NexteraXT Illumina for library preparation. GEO Accession:GSM4202671 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP234692     MT_F4_1.fastq.gz MT_F4_2.fastq.gz fastq fastq 11158354500.0 74389030.0 GSM4202671 r1 0:75 1:75 A:3016461951;C:2575288055;G:2562564003;T:3002459050;N:1581441 75 75     3016461951 2575288055 2562564003 3002459050 1581441 SRX7266970 SRS5761504 SRA1006558 GEO The Francis Crick Institute 2 0.93163 0.9323 0.06582 0.06885 0.72884 0.74073 0.46953 0.4749 75 75 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2019-12-04 Pharyngula Embryo Brain Nervous System
55634 55634 SRR10586532 SRX7266968 SRS5761502 SRP234692 PRJNA593444 A single cell transcriptome atlas of the developing zebrafish hindbrain [Fgf20a] GSE141425 Transcriptome Analysis RNA seq profile of Fgf20a homozygous mutant hindbrains compared with wilde type hindbrains Method: 24hpf hindbrains were microdissected and the RNA was extracted. Qulity of dissection was monitored by qPCR and samples were selected for sequencing Overall design: 4 control wt Cnt and 3 Fgf20aHOM were deep sequenced parent bioproject:PRJNA593433 pubmed:32094115   Fgf20aHOM 2 GSM4202670   source name:Dissected hindbrain and surrounding tissues|tissue:Dissected hindbrain and surrounding tissues|Stage:24hpf|strain:Fgf20a HOM|genotype:Fgf20a HOM|growth:28.5°C Fgf20aHOM 2 Reads were and aligned against zebrafish genome GRCz10 and Ensembl release 86 transcript annotations using STAR v2.5.1b via the transcript quantification software RSEM v1.2.31 RSEM estimated gene level counts were rounded to integers Genome build: GRCz10 Supplementary files format and content: Tab delimited counts matrix with row representing genes and columns representing samples. Dissected hindbrain and surrounding tissues   Embryos were decorionated and deyolked in DMEM with high Glucose no Glutamine no Calcium 11530556 Gibco; hindbrains were micro dissected using 0.33mm micro fine sterile needles; RNA was isolated using Quick RNA Microprep kit Zymo Research Samples were prepared with the Ovation® RNA Seq System V2 7102 NuGEN for cDNA amplification followed by NexteraXT Illumina for library preparation.   tissue:Dissected hindbrain and surrounding tissues|Stage:24hpf|strain:Fgf20a HOM|genotype:Fgf20a HOM|growth:28.5°C GSM4202670 GSM4202670: Fgf20aHOM 2; Danio rerio; RNA Seq GSM4202670   1 Embryos were decorionated and deyolked in DMEM with high Glucose no Glutamine no Calcium 11530556 Gibco; hindbrains were micro dissected using 0.33mm micro fine sterile needles; RNA was isolated using Quick RNA Microprep kit Zymo Research Samples were prepared with the Ovation® RNA Seq System V2 7102 NuGEN for cDNA amplification followed by NexteraXT Illumina for library preparation. GEO Accession:GSM4202670 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP234692     MT_F3_2.fastq.gz MT_F3_1.fastq.gz fastq fastq 11147902050.0 74319347.0 GSM4202670 r1 0:75 1:75 A:3006939166;C:2572909227;G:2560537164;T:3005930748;N:1585745 75 75     3006939166 2572909227 2560537164 3005930748 1585745 SRX7266968 SRS5761502 SRA1006558 GEO The Francis Crick Institute 2 0.92992 0.93097 0.06109 0.06395 0.73432 0.74491 0.46862 0.47434 75 75 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2019-12-04 Pharyngula Embryo Brain Nervous System
55635 55635 SRR10586531 SRX7266966 SRS5761500 SRP234692 PRJNA593444 A single cell transcriptome atlas of the developing zebrafish hindbrain [Fgf20a] GSE141425 Transcriptome Analysis RNA seq profile of Fgf20a homozygous mutant hindbrains compared with wilde type hindbrains Method: 24hpf hindbrains were microdissected and the RNA was extracted. Qulity of dissection was monitored by qPCR and samples were selected for sequencing Overall design: 4 control wt Cnt and 3 Fgf20aHOM were deep sequenced parent bioproject:PRJNA593433 pubmed:32094115   Fgf20aHOM 1 GSM4202669   source name:Dissected hindbrain and surrounding tissues|tissue:Dissected hindbrain and surrounding tissues|Stage:24hpf|strain:Fgf20a HOM|genotype:Fgf20a HOM|growth:28.5°C Fgf20aHOM 1 Reads were and aligned against zebrafish genome GRCz10 and Ensembl release 86 transcript annotations using STAR v2.5.1b via the transcript quantification software RSEM v1.2.31 RSEM estimated gene level counts were rounded to integers Genome build: GRCz10 Supplementary files format and content: Tab delimited counts matrix with row representing genes and columns representing samples. Dissected hindbrain and surrounding tissues   Embryos were decorionated and deyolked in DMEM with high Glucose no Glutamine no Calcium 11530556 Gibco; hindbrains were micro dissected using 0.33mm micro fine sterile needles; RNA was isolated using Quick RNA Microprep kit Zymo Research Samples were prepared with the Ovation® RNA Seq System V2 7102 NuGEN for cDNA amplification followed by NexteraXT Illumina for library preparation.   tissue:Dissected hindbrain and surrounding tissues|Stage:24hpf|strain:Fgf20a HOM|genotype:Fgf20a HOM|growth:28.5°C GSM4202669 GSM4202669: Fgf20aHOM 1; Danio rerio; RNA Seq GSM4202669   1 Embryos were decorionated and deyolked in DMEM with high Glucose no Glutamine no Calcium 11530556 Gibco; hindbrains were micro dissected using 0.33mm micro fine sterile needles; RNA was isolated using Quick RNA Microprep kit Zymo Research Samples were prepared with the Ovation® RNA Seq System V2 7102 NuGEN for cDNA amplification followed by NexteraXT Illumina for library preparation. GEO Accession:GSM4202669 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP234692     MT_F2_1.fastq.gz MT_F2_2.fastq.gz fastq fastq 12024861900.0 80165746.0 GSM4202669 r1 0:75 1:75 A:3237520037;C:2774421770;G:2759094034;T:3252089500;N:1736559 75 75     3237520037 2774421770 2759094034 3252089500 1736559 SRX7266966 SRS5761500 SRA1006558 GEO The Francis Crick Institute 2 0.92645 0.92985 0.07758 0.08151 0.72525 0.73568 0.46508 0.46721 75 75 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2019-12-04 Pharyngula Embryo Brain Nervous System
55636 55636 SRR10586530 SRX7266964 SRS5761498 SRP234692 PRJNA593444 A single cell transcriptome atlas of the developing zebrafish hindbrain [Fgf20a] GSE141425 Transcriptome Analysis RNA seq profile of Fgf20a homozygous mutant hindbrains compared with wilde type hindbrains Method: 24hpf hindbrains were microdissected and the RNA was extracted. Qulity of dissection was monitored by qPCR and samples were selected for sequencing Overall design: 4 control wt Cnt and 3 Fgf20aHOM were deep sequenced parent bioproject:PRJNA593433 pubmed:32094115   Cnt 4 GSM4202668   source name:Dissected hindbrain and surrounding tissues|tissue:Dissected hindbrain and surrounding tissues|Stage:24hpf|strain:LondonAB|genotype:wt|growth:28.5°C Cnt 4 Reads were and aligned against zebrafish genome GRCz10 and Ensembl release 86 transcript annotations using STAR v2.5.1b via the transcript quantification software RSEM v1.2.31 RSEM estimated gene level counts were rounded to integers Genome build: GRCz10 Supplementary files format and content: Tab delimited counts matrix with row representing genes and columns representing samples. Dissected hindbrain and surrounding tissues   Embryos were decorionated and deyolked in DMEM with high Glucose no Glutamine no Calcium 11530556 Gibco; hindbrains were micro dissected using 0.33mm micro fine sterile needles; RNA was isolated using Quick RNA Microprep kit Zymo Research Samples were prepared with the Ovation® RNA Seq System V2 7102 NuGEN for cDNA amplification followed by NexteraXT Illumina for library preparation.   tissue:Dissected hindbrain and surrounding tissues|Stage:24hpf|strain:LondonAB|genotype:wt|growth:28.5°C GSM4202668 GSM4202668: Cnt 4; Danio rerio; RNA Seq GSM4202668   1 Embryos were decorionated and deyolked in DMEM with high Glucose no Glutamine no Calcium 11530556 Gibco; hindbrains were micro dissected using 0.33mm micro fine sterile needles; RNA was isolated using Quick RNA Microprep kit Zymo Research Samples were prepared with the Ovation® RNA Seq System V2 7102 NuGEN for cDNA amplification followed by NexteraXT Illumina for library preparation. GEO Accession:GSM4202668 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP234692     MT_C4_2.fastq.gz MT_C4_1.fastq.gz fastq fastq 14240675550.0 94937837.0 GSM4202668 r1 0:75 1:75 A:3887408926;C:3255744621;G:3242638143;T:3853080420;N:1803440 75 75     3887408926 3255744621 3242638143 3853080420 1803440 SRX7266964 SRS5761498 SRA1006558 GEO The Francis Crick Institute 2 0.93355 0.93519 0.04859 0.05117 0.74416 0.75617 0.47017 0.43891 75 75 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2019-12-04 Pharyngula Embryo Brain Nervous System
55637 55637 SRR10586529 SRX7266962 SRS5761496 SRP234692 PRJNA593444 A single cell transcriptome atlas of the developing zebrafish hindbrain [Fgf20a] GSE141425 Transcriptome Analysis RNA seq profile of Fgf20a homozygous mutant hindbrains compared with wilde type hindbrains Method: 24hpf hindbrains were microdissected and the RNA was extracted. Qulity of dissection was monitored by qPCR and samples were selected for sequencing Overall design: 4 control wt Cnt and 3 Fgf20aHOM were deep sequenced parent bioproject:PRJNA593433 pubmed:32094115   Cnt 3 GSM4202667   source name:Dissected hindbrain and surrounding tissues|tissue:Dissected hindbrain and surrounding tissues|Stage:24hpf|strain:LondonAB|genotype:wt|growth:28.5°C Cnt 3 Reads were and aligned against zebrafish genome GRCz10 and Ensembl release 86 transcript annotations using STAR v2.5.1b via the transcript quantification software RSEM v1.2.31 RSEM estimated gene level counts were rounded to integers Genome build: GRCz10 Supplementary files format and content: Tab delimited counts matrix with row representing genes and columns representing samples. Dissected hindbrain and surrounding tissues   Embryos were decorionated and deyolked in DMEM with high Glucose no Glutamine no Calcium 11530556 Gibco; hindbrains were micro dissected using 0.33mm micro fine sterile needles; RNA was isolated using Quick RNA Microprep kit Zymo Research Samples were prepared with the Ovation® RNA Seq System V2 7102 NuGEN for cDNA amplification followed by NexteraXT Illumina for library preparation.   tissue:Dissected hindbrain and surrounding tissues|Stage:24hpf|strain:LondonAB|genotype:wt|growth:28.5°C GSM4202667 GSM4202667: Cnt 3; Danio rerio; RNA Seq GSM4202667   1 Embryos were decorionated and deyolked in DMEM with high Glucose no Glutamine no Calcium 11530556 Gibco; hindbrains were micro dissected using 0.33mm micro fine sterile needles; RNA was isolated using Quick RNA Microprep kit Zymo Research Samples were prepared with the Ovation® RNA Seq System V2 7102 NuGEN for cDNA amplification followed by NexteraXT Illumina for library preparation. GEO Accession:GSM4202667 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP234692     MT_C3_1.fastq.gz MT_C3_2.fastq.gz fastq fastq 13419895350.0 89465969.0 GSM4202667 r1 0:75 1:75 A:3648325732;C:3079934528;G:3067595771;T:3622362214;N:1677105 75 75     3648325732 3079934528 3067595771 3622362214 1677105 SRX7266962 SRS5761496 SRA1006558 GEO The Francis Crick Institute 2 0.9319 0.93156 0.05953 0.06316 0.72705 0.74077 0.48017 0.4764 75 75 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2019-12-04 Pharyngula Embryo Brain Nervous System
55638 55638 SRR10586528 SRX7266960 SRS5761494 SRP234692 PRJNA593444 A single cell transcriptome atlas of the developing zebrafish hindbrain [Fgf20a] GSE141425 Transcriptome Analysis RNA seq profile of Fgf20a homozygous mutant hindbrains compared with wilde type hindbrains Method: 24hpf hindbrains were microdissected and the RNA was extracted. Qulity of dissection was monitored by qPCR and samples were selected for sequencing Overall design: 4 control wt Cnt and 3 Fgf20aHOM were deep sequenced parent bioproject:PRJNA593433 pubmed:32094115   Cnt 2 GSM4202666   source name:Dissected hindbrain and surrounding tissues|tissue:Dissected hindbrain and surrounding tissues|Stage:24hpf|strain:LondonAB|genotype:wt|growth:28.5°C Cnt 2 Reads were and aligned against zebrafish genome GRCz10 and Ensembl release 86 transcript annotations using STAR v2.5.1b via the transcript quantification software RSEM v1.2.31 RSEM estimated gene level counts were rounded to integers Genome build: GRCz10 Supplementary files format and content: Tab delimited counts matrix with row representing genes and columns representing samples. Dissected hindbrain and surrounding tissues   Embryos were decorionated and deyolked in DMEM with high Glucose no Glutamine no Calcium 11530556 Gibco; hindbrains were micro dissected using 0.33mm micro fine sterile needles; RNA was isolated using Quick RNA Microprep kit Zymo Research Samples were prepared with the Ovation® RNA Seq System V2 7102 NuGEN for cDNA amplification followed by NexteraXT Illumina for library preparation.   tissue:Dissected hindbrain and surrounding tissues|Stage:24hpf|strain:LondonAB|genotype:wt|growth:28.5°C GSM4202666 GSM4202666: Cnt 2; Danio rerio; RNA Seq GSM4202666   1 Embryos were decorionated and deyolked in DMEM with high Glucose no Glutamine no Calcium 11530556 Gibco; hindbrains were micro dissected using 0.33mm micro fine sterile needles; RNA was isolated using Quick RNA Microprep kit Zymo Research Samples were prepared with the Ovation® RNA Seq System V2 7102 NuGEN for cDNA amplification followed by NexteraXT Illumina for library preparation. GEO Accession:GSM4202666 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP234692     MT_C2_1.fastq.gz MT_C2_2.fastq.gz fastq fastq 13384473450.0 89229823.0 GSM4202666 r1 0:75 1:75 A:3648519008;C:3057477428;G:3043763915;T:3633023284;N:1689815 75 75     3648519008 3057477428 3043763915 3633023284 1689815 SRX7266960 SRS5761494 SRA1006558 GEO The Francis Crick Institute 2 0.93086 0.93239 0.06636 0.07075 0.73026 0.74221 0.47916 0.47798 75 75 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2019-12-04 Pharyngula Embryo Brain Nervous System
55639 55639 SRR10586527 SRX7266958 SRS5761492 SRP234692 PRJNA593444 A single cell transcriptome atlas of the developing zebrafish hindbrain [Fgf20a] GSE141425 Transcriptome Analysis RNA seq profile of Fgf20a homozygous mutant hindbrains compared with wilde type hindbrains Method: 24hpf hindbrains were microdissected and the RNA was extracted. Qulity of dissection was monitored by qPCR and samples were selected for sequencing Overall design: 4 control wt Cnt and 3 Fgf20aHOM were deep sequenced parent bioproject:PRJNA593433 pubmed:32094115   Cnt 1 GSM4202665   source name:Dissected hindbrain and surrounding tissues|tissue:Dissected hindbrain and surrounding tissues|Stage:24hpf|strain:LondonAB|genotype:wt|growth:28.5°C Cnt 1 Reads were and aligned against zebrafish genome GRCz10 and Ensembl release 86 transcript annotations using STAR v2.5.1b via the transcript quantification software RSEM v1.2.31 RSEM estimated gene level counts were rounded to integers Genome build: GRCz10 Supplementary files format and content: Tab delimited counts matrix with row representing genes and columns representing samples. Dissected hindbrain and surrounding tissues   Embryos were decorionated and deyolked in DMEM with high Glucose no Glutamine no Calcium 11530556 Gibco; hindbrains were micro dissected using 0.33mm micro fine sterile needles; RNA was isolated using Quick RNA Microprep kit Zymo Research Samples were prepared with the Ovation® RNA Seq System V2 7102 NuGEN for cDNA amplification followed by NexteraXT Illumina for library preparation.   tissue:Dissected hindbrain and surrounding tissues|Stage:24hpf|strain:LondonAB|genotype:wt|growth:28.5°C GSM4202665 GSM4202665: Cnt 1; Danio rerio; RNA Seq GSM4202665   1 Embryos were decorionated and deyolked in DMEM with high Glucose no Glutamine no Calcium 11530556 Gibco; hindbrains were micro dissected using 0.33mm micro fine sterile needles; RNA was isolated using Quick RNA Microprep kit Zymo Research Samples were prepared with the Ovation® RNA Seq System V2 7102 NuGEN for cDNA amplification followed by NexteraXT Illumina for library preparation. GEO Accession:GSM4202665 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP234692     MT_C1_1.fastq.gz MT_C1_2.fastq.gz fastq fastq 12665118300.0 84434122.0 GSM4202665 r1 0:75 1:75 A:3438373419;C:2921877813;G:2892018591;T:3411258211;N:1590266 75 75     3438373419 2921877813 2892018591 3411258211 1590266 SRX7266958 SRS5761492 SRA1006558 GEO The Francis Crick Institute 2 0.93498 0.93472 0.06357 0.0675 0.73072 0.74497 0.46679 0.47424 75 75 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2019-12-04 Pharyngula Embryo Brain Nervous System
55640 55640 SRR10586526 SRX7266919 SRS5761461 SRP234691 PRJNA593445 A single cell transcriptome atlas of the developing zebrafish hindbrain [scRNA Seq] GSE141427 Transcriptome Analysis Purpose: The goal of this study is to understand the progressive patterning of neurogenesis of the developing zebrafish hindbrain. 16hpf 24hpf and 44hpf zebrafish hindbrains were used for single cell RNA sequencing with the aim to uncover hindbrain development. Methods: 40 microdissected hindbrains per each stage were dissociated at loaded into the 10x Genomics Chromium Platform and sequenced using Illumina HiSeq 4000. Conclusions: Our study constitute a resource of hindbrain gene expression during development. We have identified transcriptional programs involved in: rhombomere segmental identity dorso ventral patterning boundary and centre progenitor cells and temporal regulation of neurogenesis. Overall design: 16hpf 24hpf 44hpf hindbrains were used for single cell RNA sequencing 10xGenomics Chromium Platform and sequenced using Illumina HiSeq 4000. parent bioproject:PRJNA593433 pubmed:32094115   44hpf Hindbrain scRNA seq GSM4202682   source name:Dissected hindbrain and surrounding tissues|tissue:Dissected hindbrain and surrounding tissues|Stage:44hpf|strain:LondonAB|genotype:wt|growth:25°C 44hpf Hindbrain scRNA seq 10X’s Cell Ranger software was used to de multiplex Illumina BCL output create fastq files and generate single cell feature counts for each library Three 10X libraries representing the 16hpf 24hpf and 44hpf stages of embryonic development were aggregated using the 10X software “cellranger aggr” function which sub samples reads such that all libraries have the same effective sequencing depth. Genome build: GRCz10 Supplementary files format and content: Tab delimited text file containing aggregated Cell Ranger counts Dissected hindbrain and surrounding tissues   Embryos were decorionated and deyolked in DMEM with high Glucose no Glutamine no Calcium 11530556 Gibco; hindbrains were micro dissected using 0.33mm micro fine sterile needles; 40 tissues per stage were polled together and immediately processed for cell dissociation; samples were incubated with FACS max cell dissociation solution T200100 Amsbio supplemented with 1mg/ml Papain 10108014001 Sigma for 25min at 37°C and resuspended one time during incubation; cells were then transferred to HBSS no calcium no magnesium no phenol red; 11140035 ThermoFisher Scientific supplemented with 5%FBS rock inhibitor Y 27632 Stem Cell Technologies and 1X non essential amino acids 11140035 ThermoFisher Scientific; cells were further disaggregated by pipetting and filtered several times using 20µm strainers 130 101 812 Miltenyi Biotech GmbH RNA libraries were prepared for sequencing using Chromium Single Cell three prime v2 protocol PN 120233 10X Genomics; cDNA amplification involved 12 PCR cycles   tissue:Dissected hindbrain and surrounding tissues|Stage:44hpf|strain:LondonAB|genotype:wt|growth:25°C GSM4202682 GSM4202682: 44hpf Hindbrain scRNA seq; Danio rerio; RNA Seq GSM4202682   1 Embryos were decorionated and deyolked in DMEM with high Glucose no Glutamine no Calcium 11530556 Gibco; hindbrains were micro dissected using 0.33mm micro fine sterile needles; 40 tissues per stage were polled together and immediately processed for cell dissociation; samples were incubated with FACS max cell dissociation solution T200100 Amsbio supplemented with 1mg/ml Papain 10108014001 Sigma for 25min at 37°C and resuspended one time during incubation; cells were then transferred to HBSS no calcium no magnesium no phenol red; 11140035 ThermoFisher Scientific supplemented with 5%FBS rock inhibitor Y 27632 Stem Cell Technologies and 1X non essential amino acids 11140035 ThermoFisher Scientific; cells were further disaggregated by pipetting and filtered several times using 20µm strainers 130 101 812 Miltenyi Biotech GmbH RNA libraries were prepared for sequencing using Chromium Single Cell three prime v2 protocol PN 120233 10X Genomics; cDNA amplification involved 12 PCR cycles GEO Accession:GSM4202682 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP234691   loader:fastq load.py|options: readTypes=TTB read1PairFiles=MT 10X240118 S1 L006 I1 001.fastq.gz read2PairFiles=MT 10X240118 S1 L006 R1 001.fastq.gz read3PairFiles=MT 10X240118 S1 L006 R2 001.fastq.gz MT_10X240118_S1_L006_R2_001.fastq.gz MT_10X240118_S1_L006_R1_001.fastq.gz MT_10X240118_S1_L006_I1_001.fastq.gz fastq fastq fastq 67359962250.0 320761725.0 GSM4202682 r1 0:8 1:101 2:101 A:16212646159;C:11777426351;G:12335518595;T:27032040933;N:2330212 8 101 101   16212646159 11777426351 12335518595 27032040933 2330212 SRX7266919 SRS5761461 SRA1006557 GEO The Francis Crick Institute 1 0.9195   0.12389   0.82593   0.50909   101   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United Kingdom 2019-12-04 Pharyngula Embryo Brain Nervous System
55641 55641 SRR10586525 SRX7266917 SRS5761460 SRP234691 PRJNA593445 A single cell transcriptome atlas of the developing zebrafish hindbrain [scRNA Seq] GSE141427 Transcriptome Analysis Purpose: The goal of this study is to understand the progressive patterning of neurogenesis of the developing zebrafish hindbrain. 16hpf 24hpf and 44hpf zebrafish hindbrains were used for single cell RNA sequencing with the aim to uncover hindbrain development. Methods: 40 microdissected hindbrains per each stage were dissociated at loaded into the 10x Genomics Chromium Platform and sequenced using Illumina HiSeq 4000. Conclusions: Our study constitute a resource of hindbrain gene expression during development. We have identified transcriptional programs involved in: rhombomere segmental identity dorso ventral patterning boundary and centre progenitor cells and temporal regulation of neurogenesis. Overall design: 16hpf 24hpf 44hpf hindbrains were used for single cell RNA sequencing 10xGenomics Chromium Platform and sequenced using Illumina HiSeq 4000. parent bioproject:PRJNA593433 pubmed:32094115   24hpf Hindbrain scRNA seq GSM4202681   source name:Dissected hindbrain and surrounding tissues|tissue:Dissected hindbrain and surrounding tissues|Stage:24hpf|strain:LondonAB|genotype:wt|growth:28.5°C 24hpf Hindbrain scRNA seq 10X’s Cell Ranger software was used to de multiplex Illumina BCL output create fastq files and generate single cell feature counts for each library Three 10X libraries representing the 16hpf 24hpf and 44hpf stages of embryonic development were aggregated using the 10X software “cellranger aggr” function which sub samples reads such that all libraries have the same effective sequencing depth. Genome build: GRCz10 Supplementary files format and content: Tab delimited text file containing aggregated Cell Ranger counts Dissected hindbrain and surrounding tissues   Embryos were decorionated and deyolked in DMEM with high Glucose no Glutamine no Calcium 11530556 Gibco; hindbrains were micro dissected using 0.33mm micro fine sterile needles; 40 tissues per stage were polled together and immediately processed for cell dissociation; samples were incubated with FACS max cell dissociation solution T200100 Amsbio supplemented with 1mg/ml Papain 10108014001 Sigma for 25min at 37°C and resuspended one time during incubation; cells were then transferred to HBSS no calcium no magnesium no phenol red; 11140035 ThermoFisher Scientific supplemented with 5%FBS rock inhibitor Y 27632 Stem Cell Technologies and 1X non essential amino acids 11140035 ThermoFisher Scientific; cells were further disaggregated by pipetting and filtered several times using 20µm strainers 130 101 812 Miltenyi Biotech GmbH RNA libraries were prepared for sequencing using Chromium Single Cell three prime v2 protocol PN 120233 10X Genomics; cDNA amplification involved 12 PCR cycles   tissue:Dissected hindbrain and surrounding tissues|Stage:24hpf|strain:LondonAB|genotype:wt|growth:28.5°C GSM4202681 GSM4202681: 24hpf Hindbrain scRNA seq; Danio rerio; RNA Seq GSM4202681   1 Embryos were decorionated and deyolked in DMEM with high Glucose no Glutamine no Calcium 11530556 Gibco; hindbrains were micro dissected using 0.33mm micro fine sterile needles; 40 tissues per stage were polled together and immediately processed for cell dissociation; samples were incubated with FACS max cell dissociation solution T200100 Amsbio supplemented with 1mg/ml Papain 10108014001 Sigma for 25min at 37°C and resuspended one time during incubation; cells were then transferred to HBSS no calcium no magnesium no phenol red; 11140035 ThermoFisher Scientific supplemented with 5%FBS rock inhibitor Y 27632 Stem Cell Technologies and 1X non essential amino acids 11140035 ThermoFisher Scientific; cells were further disaggregated by pipetting and filtered several times using 20µm strainers 130 101 812 Miltenyi Biotech GmbH RNA libraries were prepared for sequencing using Chromium Single Cell three prime v2 protocol PN 120233 10X Genomics; cDNA amplification involved 12 PCR cycles GEO Accession:GSM4202681 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP234691   loader:fastq load.py|options: readTypes=TTB read1PairFiles=TAM677A2 S7 L008 I1 001.fastq.gz read2PairFiles=TAM677A2 S7 L008 R1 001.fastq.gz read3PairFiles=TAM677A2 S7 L008 R2 001.fastq.gz TAM677A2_S7_L008_I1_001.fastq.gz TAM677A2_S7_L008_R1_001.fastq.gz TAM677A2_S7_L008_R2_001.fastq.gz fastq fastq fastq 71824244730.0 342020213.0 GSM4202681 r1 0:8 1:101 2:101 A:16595981302;C:11865598791;G:12955979417;T:30401981747;N:4703473 8 101 101   16595981302 11865598791 12955979417 30401981747 4703473 SRX7266917 SRS5761460 SRA1006557 GEO The Francis Crick Institute 1 0.92906   0.11719   0.80982   0.52506   101   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United Kingdom 2019-12-04 Pharyngula Embryo Brain Nervous System
61265 61265 SRR12661716 SRX9142583 SRS7383887 SRP282920 PRJNA664124 Emergence of neuronal diversity during vertebrate brain development GSE158142 Transcriptome Analysis Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT   pubmed:33068532   zBr36hpf2 S7 GSM4793200   source name:zebrafish brain|tissue:brain|developmental stage:36hpf zBr36hpf2 S7 Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as *b in raw files and the processing was done using the combination of all data processed data files have comb* prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: *barcodes.tsv files contain 10X Genomics cell barcodes *genes.tsv files contain gene names *matrix.mtx contain transcriptome count data *web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD*.rds files are the processed R objects for performing URD cell trajectory analysis. tree*.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont… zebrafish brain   Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing   tissue:brain|developmental stage:36hpf GSM4793200 GSM4793200: zBr36hpf2 S7; Danio rerio; RNA Seq GSM4793200   1 Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing GEO Accession:GSM4793200 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP282920   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=zBr36hpf2 S7 L001 I1 001.fastq.gz read2PairFiles=zBr36hpf2 S7 L001 R1 001.fastq.gz read3PairFiles=zBr36hpf2 S7 L001 R2 001.fastq.gz zBr36hpf2_S7_L001_I1_001.fastq.gz zBr36hpf2_S7_L001_R1_001.fastq.gz zBr36hpf2_S7_L001_R2_001.fastq.gz fastq fastq fastq 1354796416.0 14726048.0 GSM4793200 r1 0:8 1:26 2:58 A:361641217;C:295707879;G:331919755;T:363556787;N:1970778 8 26 58   361641217 295707879 331919755 363556787 1970778 SRX9142583 SRS7383887 SRA1127180 GEO Harvard University 1 0.94293   0.09579   0.80659   0.48535   58   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2020-09-17 Pharyngula Embryo Brain Nervous System
61266 61266 SRR12661717 SRX9142583 SRS7383887 SRP282920 PRJNA664124 Emergence of neuronal diversity during vertebrate brain development GSE158142 Transcriptome Analysis Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT   pubmed:33068532   zBr36hpf2 S7 GSM4793200   source name:zebrafish brain|tissue:brain|developmental stage:36hpf zBr36hpf2 S7 Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as *b in raw files and the processing was done using the combination of all data processed data files have comb* prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: *barcodes.tsv files contain 10X Genomics cell barcodes *genes.tsv files contain gene names *matrix.mtx contain transcriptome count data *web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD*.rds files are the processed R objects for performing URD cell trajectory analysis. tree*.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont… zebrafish brain   Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing   tissue:brain|developmental stage:36hpf GSM4793200 GSM4793200: zBr36hpf2 S7; Danio rerio; RNA Seq GSM4793200   1 Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing GEO Accession:GSM4793200 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP282920   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=zBr36hpf2 S7 L002 I1 001.fastq.gz read2PairFiles=zBr36hpf2 S7 L002 R1 001.fastq.gz read3PairFiles=zBr36hpf2 S7 L002 R2 001.fastq.gz zBr36hpf2_S7_L002_I1_001.fastq.gz zBr36hpf2_S7_L002_R1_001.fastq.gz zBr36hpf2_S7_L002_R2_001.fastq.gz fastq fastq fastq 1358239516.0 14763473.0 GSM4793200 r2 0:8 1:26 2:58 A:361906449;C:296366138;G:333591075;T:364374247;N:2001607 8 26 58   361906449 296366138 333591075 364374247 2001607 SRX9142583 SRS7383887 SRA1127180 GEO Harvard University 1 0.94081   0.09328   0.80497   0.48086   58   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2020-09-17 Pharyngula Embryo Brain Nervous System
61267 61267 SRR12661718 SRX9142583 SRS7383887 SRP282920 PRJNA664124 Emergence of neuronal diversity during vertebrate brain development GSE158142 Transcriptome Analysis Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT   pubmed:33068532   zBr36hpf2 S7 GSM4793200   source name:zebrafish brain|tissue:brain|developmental stage:36hpf zBr36hpf2 S7 Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as *b in raw files and the processing was done using the combination of all data processed data files have comb* prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: *barcodes.tsv files contain 10X Genomics cell barcodes *genes.tsv files contain gene names *matrix.mtx contain transcriptome count data *web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD*.rds files are the processed R objects for performing URD cell trajectory analysis. tree*.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont… zebrafish brain   Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing   tissue:brain|developmental stage:36hpf GSM4793200 GSM4793200: zBr36hpf2 S7; Danio rerio; RNA Seq GSM4793200   1 Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing GEO Accession:GSM4793200 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP282920   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=zBr36hpf2 S7 L003 I1 001.fastq.gz read2PairFiles=zBr36hpf2 S7 L003 R1 001.fastq.gz read3PairFiles=zBr36hpf2 S7 L003 R2 001.fastq.gz zBr36hpf2_S7_L003_I1_001.fastq.gz zBr36hpf2_S7_L003_R1_001.fastq.gz zBr36hpf2_S7_L003_R2_001.fastq.gz fastq fastq fastq 1370706988.0 14898989.0 GSM4793200 r3 0:8 1:26 2:58 A:364455570;C:298700749;G:338352913;T:367620807;N:1576949 8 26 58   364455570 298700749 338352913 367620807 1576949 SRX9142583 SRS7383887 SRA1127180 GEO Harvard University 1 0.94035   0.09554   0.80474   0.48964   58   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2020-09-17 Pharyngula Embryo Brain Nervous System
61268 61268 SRR12661719 SRX9142583 SRS7383887 SRP282920 PRJNA664124 Emergence of neuronal diversity during vertebrate brain development GSE158142 Transcriptome Analysis Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT   pubmed:33068532   zBr36hpf2 S7 GSM4793200   source name:zebrafish brain|tissue:brain|developmental stage:36hpf zBr36hpf2 S7 Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as *b in raw files and the processing was done using the combination of all data processed data files have comb* prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: *barcodes.tsv files contain 10X Genomics cell barcodes *genes.tsv files contain gene names *matrix.mtx contain transcriptome count data *web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD*.rds files are the processed R objects for performing URD cell trajectory analysis. tree*.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont… zebrafish brain   Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing   tissue:brain|developmental stage:36hpf GSM4793200 GSM4793200: zBr36hpf2 S7; Danio rerio; RNA Seq GSM4793200   1 Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing GEO Accession:GSM4793200 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP282920   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=zBr36hpf2 S7 L004 I1 001.fastq.gz read2PairFiles=zBr36hpf2 S7 L004 R1 001.fastq.gz read3PairFiles=zBr36hpf2 S7 L004 R2 001.fastq.gz zBr36hpf2_S7_L004_I1_001.fastq.gz zBr36hpf2_S7_L004_R1_001.fastq.gz zBr36hpf2_S7_L004_R2_001.fastq.gz fastq fastq fastq 1366604800.0 14854400.0 GSM4793200 r4 0:8 1:26 2:58 A:364547650;C:298236417;G:335364562;T:366845359;N:1610812 8 26 58   364547650 298236417 335364562 366845359 1610812 SRX9142583 SRS7383887 SRA1127180 GEO Harvard University 1 0.94169   0.09572   0.8076   0.49419   58   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2020-09-17 Pharyngula Embryo Brain Nervous System
61269 61269 SRR12661720 SRX9142583 SRS7383887 SRP282920 PRJNA664124 Emergence of neuronal diversity during vertebrate brain development GSE158142 Transcriptome Analysis Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT   pubmed:33068532   zBr36hpf2 S7 GSM4793200   source name:zebrafish brain|tissue:brain|developmental stage:36hpf zBr36hpf2 S7 Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as *b in raw files and the processing was done using the combination of all data processed data files have comb* prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: *barcodes.tsv files contain 10X Genomics cell barcodes *genes.tsv files contain gene names *matrix.mtx contain transcriptome count data *web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD*.rds files are the processed R objects for performing URD cell trajectory analysis. tree*.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont… zebrafish brain   Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing   tissue:brain|developmental stage:36hpf GSM4793200 GSM4793200: zBr36hpf2 S7; Danio rerio; RNA Seq GSM4793200   1 Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing GEO Accession:GSM4793200 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP282920   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=zBr36hpf2b S7 L001 I1 001.fastq.gz read2PairFiles=zBr36hpf2b S7 L001 R1 001.fastq.gz read3PairFiles=zBr36hpf2b S7 L001 R2 001.fastq.gz zBr36hpf2b_S7_L001_I1_001.fastq.gz zBr36hpf2b_S7_L001_R1_001.fastq.gz zBr36hpf2b_S7_L001_R2_001.fastq.gz fastq fastq fastq 1405330268.0 15275329.0 GSM4793200 r5 0:8 1:26 2:58 A:375342661;C:306451867;G:346478190;T:376672948;N:384602 8 26 58   375342661 306451867 346478190 376672948 384602 SRX9142583 SRS7383887 SRA1127180 GEO Harvard University 1 0.94163   0.09494   0.80813   0.4829   58   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2020-09-17 Pharyngula Embryo Brain Nervous System
61270 61270 SRR12661721 SRX9142583 SRS7383887 SRP282920 PRJNA664124 Emergence of neuronal diversity during vertebrate brain development GSE158142 Transcriptome Analysis Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT   pubmed:33068532   zBr36hpf2 S7 GSM4793200   source name:zebrafish brain|tissue:brain|developmental stage:36hpf zBr36hpf2 S7 Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as *b in raw files and the processing was done using the combination of all data processed data files have comb* prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: *barcodes.tsv files contain 10X Genomics cell barcodes *genes.tsv files contain gene names *matrix.mtx contain transcriptome count data *web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD*.rds files are the processed R objects for performing URD cell trajectory analysis. tree*.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont… zebrafish brain   Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing   tissue:brain|developmental stage:36hpf GSM4793200 GSM4793200: zBr36hpf2 S7; Danio rerio; RNA Seq GSM4793200   1 Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing GEO Accession:GSM4793200 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP282920   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=zBr36hpf2b S7 L002 I1 001.fastq.gz read2PairFiles=zBr36hpf2b S7 L002 R1 001.fastq.gz read3PairFiles=zBr36hpf2b S7 L002 R2 001.fastq.gz zBr36hpf2b_S7_L002_I1_001.fastq.gz zBr36hpf2b_S7_L002_R1_001.fastq.gz zBr36hpf2b_S7_L002_R2_001.fastq.gz fastq fastq fastq 1394928748.0 15162269.0 GSM4793200 r6 0:8 1:26 2:58 A:372974203;C:304436911;G:343375665;T:373791458;N:350511 8 26 58   372974203 304436911 343375665 373791458 350511 SRX9142583 SRS7383887 SRA1127180 GEO Harvard University 1 0.9424   0.0951   0.80689   0.48817   58   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2020-09-17 Pharyngula Embryo Brain Nervous System
61271 61271 SRR12661722 SRX9142583 SRS7383887 SRP282920 PRJNA664124 Emergence of neuronal diversity during vertebrate brain development GSE158142 Transcriptome Analysis Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT   pubmed:33068532   zBr36hpf2 S7 GSM4793200   source name:zebrafish brain|tissue:brain|developmental stage:36hpf zBr36hpf2 S7 Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as *b in raw files and the processing was done using the combination of all data processed data files have comb* prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: *barcodes.tsv files contain 10X Genomics cell barcodes *genes.tsv files contain gene names *matrix.mtx contain transcriptome count data *web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD*.rds files are the processed R objects for performing URD cell trajectory analysis. tree*.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont… zebrafish brain   Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing   tissue:brain|developmental stage:36hpf GSM4793200 GSM4793200: zBr36hpf2 S7; Danio rerio; RNA Seq GSM4793200   1 Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing GEO Accession:GSM4793200 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP282920   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=zBr36hpf2b S7 L003 I1 001.fastq.gz read2PairFiles=zBr36hpf2b S7 L003 R1 001.fastq.gz read3PairFiles=zBr36hpf2b S7 L003 R2 001.fastq.gz zBr36hpf2b_S7_L003_I1_001.fastq.gz zBr36hpf2b_S7_L003_R1_001.fastq.gz zBr36hpf2b_S7_L003_R2_001.fastq.gz fastq fastq fastq 1395591792.0 15169476.0 GSM4793200 r7 0:8 1:26 2:58 A:372521506;C:304137483;G:344538336;T:374208291;N:186176 8 26 58   372521506 304137483 344538336 374208291 186176 SRX9142583 SRS7383887 SRA1127180 GEO Harvard University 1 0.94224   0.09336   0.80886   0.48266   58   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2020-09-17 Pharyngula Embryo Brain Nervous System
61272 61272 SRR12661723 SRX9142583 SRS7383887 SRP282920 PRJNA664124 Emergence of neuronal diversity during vertebrate brain development GSE158142 Transcriptome Analysis Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT   pubmed:33068532   zBr36hpf2 S7 GSM4793200   source name:zebrafish brain|tissue:brain|developmental stage:36hpf zBr36hpf2 S7 Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as *b in raw files and the processing was done using the combination of all data processed data files have comb* prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: *barcodes.tsv files contain 10X Genomics cell barcodes *genes.tsv files contain gene names *matrix.mtx contain transcriptome count data *web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD*.rds files are the processed R objects for performing URD cell trajectory analysis. tree*.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont… zebrafish brain   Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing   tissue:brain|developmental stage:36hpf GSM4793200 GSM4793200: zBr36hpf2 S7; Danio rerio; RNA Seq GSM4793200   1 Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing GEO Accession:GSM4793200 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP282920   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=zBr36hpf2b S7 L004 I1 001.fastq.gz read2PairFiles=zBr36hpf2b S7 L004 R1 001.fastq.gz read3PairFiles=zBr36hpf2b S7 L004 R2 001.fastq.gz zBr36hpf2b_S7_L004_I1_001.fastq.gz zBr36hpf2b_S7_L004_R1_001.fastq.gz zBr36hpf2b_S7_L004_R2_001.fastq.gz fastq fastq fastq 1284456068.0 13961479.0 GSM4793200 r8 0:8 1:26 2:58 A:345006052;C:280180152;G:313982801;T:345126707;N:160356 8 26 58   345006052 280180152 313982801 345126707 160356 SRX9142583 SRS7383887 SRA1127180 GEO Harvard University 1 0.9426   0.09636   0.81373   0.48776   58   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2020-09-17 Pharyngula Embryo Brain Nervous System
61273 61273 SRR12661708 SRX9142582 SRS7383886 SRP282920 PRJNA664124 Emergence of neuronal diversity during vertebrate brain development GSE158142 Transcriptome Analysis Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT   pubmed:33068532   zBr36hpf1 S8 GSM4793199   source name:zebrafish brain|tissue:brain|developmental stage:36hpf zBr36hpf1 S8 Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as *b in raw files and the processing was done using the combination of all data processed data files have comb* prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: *barcodes.tsv files contain 10X Genomics cell barcodes *genes.tsv files contain gene names *matrix.mtx contain transcriptome count data *web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD*.rds files are the processed R objects for performing URD cell trajectory analysis. tree*.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont… zebrafish brain   Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing   tissue:brain|developmental stage:36hpf GSM4793199 GSM4793199: zBr36hpf1 S8; Danio rerio; RNA Seq GSM4793199   1 Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing GEO Accession:GSM4793199 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP282920   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=zBr36hpf1 S8 L001 I1 001.fastq.gz read2PairFiles=zBr36hpf1 S8 L001 R1 001.fastq.gz read3PairFiles=zBr36hpf1 S8 L001 R2 001.fastq.gz zBr36hpf1_S8_L001_I1_001.fastq.gz zBr36hpf1_S8_L001_R1_001.fastq.gz zBr36hpf1_S8_L001_R2_001.fastq.gz fastq fastq fastq 1311331568.0 14253604.0 GSM4793199 r1 0:8 1:26 2:58 A:349311358;C:289871823;G:320764029;T:349490594;N:1893764 8 26 58   349311358 289871823 320764029 349490594 1893764 SRX9142582 SRS7383886 SRA1127180 GEO Harvard University 1 0.94285   0.09707   0.80543   0.50628   58   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2020-09-17 Pharyngula Embryo Brain Nervous System
61274 61274 SRR12661709 SRX9142582 SRS7383886 SRP282920 PRJNA664124 Emergence of neuronal diversity during vertebrate brain development GSE158142 Transcriptome Analysis Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT   pubmed:33068532   zBr36hpf1 S8 GSM4793199   source name:zebrafish brain|tissue:brain|developmental stage:36hpf zBr36hpf1 S8 Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as *b in raw files and the processing was done using the combination of all data processed data files have comb* prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: *barcodes.tsv files contain 10X Genomics cell barcodes *genes.tsv files contain gene names *matrix.mtx contain transcriptome count data *web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD*.rds files are the processed R objects for performing URD cell trajectory analysis. tree*.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont… zebrafish brain   Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing   tissue:brain|developmental stage:36hpf GSM4793199 GSM4793199: zBr36hpf1 S8; Danio rerio; RNA Seq GSM4793199   1 Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing GEO Accession:GSM4793199 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP282920   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=zBr36hpf1 S8 L002 I1 001.fastq.gz read2PairFiles=zBr36hpf1 S8 L002 R1 001.fastq.gz read3PairFiles=zBr36hpf1 S8 L002 R2 001.fastq.gz zBr36hpf1_S8_L002_I1_001.fastq.gz zBr36hpf1_S8_L002_R1_001.fastq.gz zBr36hpf1_S8_L002_R2_001.fastq.gz fastq fastq fastq 1314508604.0 14288137.0 GSM4793199 r2 0:8 1:26 2:58 A:349593185;C:290464605;G:322339344;T:350190708;N:1920762 8 26 58   349593185 290464605 322339344 350190708 1920762 SRX9142582 SRS7383886 SRA1127180 GEO Harvard University 1 0.94186   0.09781   0.806   0.49005   58   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2020-09-17 Pharyngula Embryo Brain Nervous System
61275 61275 SRR12661710 SRX9142582 SRS7383886 SRP282920 PRJNA664124 Emergence of neuronal diversity during vertebrate brain development GSE158142 Transcriptome Analysis Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT   pubmed:33068532   zBr36hpf1 S8 GSM4793199   source name:zebrafish brain|tissue:brain|developmental stage:36hpf zBr36hpf1 S8 Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as *b in raw files and the processing was done using the combination of all data processed data files have comb* prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: *barcodes.tsv files contain 10X Genomics cell barcodes *genes.tsv files contain gene names *matrix.mtx contain transcriptome count data *web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD*.rds files are the processed R objects for performing URD cell trajectory analysis. tree*.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont… zebrafish brain   Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing   tissue:brain|developmental stage:36hpf GSM4793199 GSM4793199: zBr36hpf1 S8; Danio rerio; RNA Seq GSM4793199   1 Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing GEO Accession:GSM4793199 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP282920   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=zBr36hpf1 S8 L003 I1 001.fastq.gz read2PairFiles=zBr36hpf1 S8 L003 R1 001.fastq.gz read3PairFiles=zBr36hpf1 S8 L003 R2 001.fastq.gz zBr36hpf1_S8_L003_I1_001.fastq.gz zBr36hpf1_S8_L003_R1_001.fastq.gz zBr36hpf1_S8_L003_R2_001.fastq.gz fastq fastq fastq 1323431500.0 14385125.0 GSM4793199 r3 0:8 1:26 2:58 A:351235327;C:292146627;G:326032256;T:352503850;N:1513440 8 26 58   351235327 292146627 326032256 352503850 1513440 SRX9142582 SRS7383886 SRA1127180 GEO Harvard University 1 0.94259   0.09668   0.80456   0.4837   58   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2020-09-17 Pharyngula Embryo Brain Nervous System
61276 61276 SRR12661711 SRX9142582 SRS7383886 SRP282920 PRJNA664124 Emergence of neuronal diversity during vertebrate brain development GSE158142 Transcriptome Analysis Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT   pubmed:33068532   zBr36hpf1 S8 GSM4793199   source name:zebrafish brain|tissue:brain|developmental stage:36hpf zBr36hpf1 S8 Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as *b in raw files and the processing was done using the combination of all data processed data files have comb* prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: *barcodes.tsv files contain 10X Genomics cell barcodes *genes.tsv files contain gene names *matrix.mtx contain transcriptome count data *web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD*.rds files are the processed R objects for performing URD cell trajectory analysis. tree*.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont… zebrafish brain   Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing   tissue:brain|developmental stage:36hpf GSM4793199 GSM4793199: zBr36hpf1 S8; Danio rerio; RNA Seq GSM4793199   1 Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing GEO Accession:GSM4793199 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP282920   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=zBr36hpf1 S8 L004 I1 001.fastq.gz read2PairFiles=zBr36hpf1 S8 L004 R1 001.fastq.gz read3PairFiles=zBr36hpf1 S8 L004 R2 001.fastq.gz zBr36hpf1_S8_L004_I1_001.fastq.gz zBr36hpf1_S8_L004_R1_001.fastq.gz zBr36hpf1_S8_L004_R2_001.fastq.gz fastq fastq fastq 1323552940.0 14386445.0 GSM4793199 r4 0:8 1:26 2:58 A:352361534;C:292521995;G:324227981;T:352876234;N:1565196 8 26 58   352361534 292521995 324227981 352876234 1565196 SRX9142582 SRS7383886 SRA1127180 GEO Harvard University 1 0.94286   0.09605   0.80436   0.49703   58   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2020-09-17 Pharyngula Embryo Brain Nervous System
61277 61277 SRR12661712 SRX9142582 SRS7383886 SRP282920 PRJNA664124 Emergence of neuronal diversity during vertebrate brain development GSE158142 Transcriptome Analysis Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT   pubmed:33068532   zBr36hpf1 S8 GSM4793199   source name:zebrafish brain|tissue:brain|developmental stage:36hpf zBr36hpf1 S8 Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as *b in raw files and the processing was done using the combination of all data processed data files have comb* prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: *barcodes.tsv files contain 10X Genomics cell barcodes *genes.tsv files contain gene names *matrix.mtx contain transcriptome count data *web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD*.rds files are the processed R objects for performing URD cell trajectory analysis. tree*.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont… zebrafish brain   Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing   tissue:brain|developmental stage:36hpf GSM4793199 GSM4793199: zBr36hpf1 S8; Danio rerio; RNA Seq GSM4793199   1 Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing GEO Accession:GSM4793199 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP282920   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=zBr36hpf1b S8 L001 I1 001.fastq.gz read2PairFiles=zBr36hpf1b S8 L001 R1 001.fastq.gz read3PairFiles=zBr36hpf1b S8 L001 R2 001.fastq.gz zBr36hpf1b_S8_L001_I1_001.fastq.gz zBr36hpf1b_S8_L001_R1_001.fastq.gz zBr36hpf1b_S8_L001_R2_001.fastq.gz fastq fastq fastq 1352165032.0 14697446.0 GSM4793199 r5 0:8 1:26 2:58 A:360326597;C:298694884;G:332801734;T:359971929;N:369888 8 26 58   360326597 298694884 332801734 359971929 369888 SRX9142582 SRS7383886 SRA1127180 GEO Harvard University 1 0.94237   0.09683   0.80768   0.48464   58   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2020-09-17 Pharyngula Embryo Brain Nervous System
61278 61278 SRR12661713 SRX9142582 SRS7383886 SRP282920 PRJNA664124 Emergence of neuronal diversity during vertebrate brain development GSE158142 Transcriptome Analysis Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT   pubmed:33068532   zBr36hpf1 S8 GSM4793199   source name:zebrafish brain|tissue:brain|developmental stage:36hpf zBr36hpf1 S8 Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as *b in raw files and the processing was done using the combination of all data processed data files have comb* prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: *barcodes.tsv files contain 10X Genomics cell barcodes *genes.tsv files contain gene names *matrix.mtx contain transcriptome count data *web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD*.rds files are the processed R objects for performing URD cell trajectory analysis. tree*.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont… zebrafish brain   Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing   tissue:brain|developmental stage:36hpf GSM4793199 GSM4793199: zBr36hpf1 S8; Danio rerio; RNA Seq GSM4793199   1 Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing GEO Accession:GSM4793199 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP282920   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=zBr36hpf1b S8 L002 I1 001.fastq.gz read2PairFiles=zBr36hpf1b S8 L002 R1 001.fastq.gz read3PairFiles=zBr36hpf1b S8 L002 R2 001.fastq.gz zBr36hpf1b_S8_L002_I1_001.fastq.gz zBr36hpf1b_S8_L002_R1_001.fastq.gz zBr36hpf1b_S8_L002_R2_001.fastq.gz fastq fastq fastq 1344669976.0 14615978.0 GSM4793199 r6 0:8 1:26 2:58 A:358739497;C:297264368;G:330471655;T:357861866;N:332590 8 26 58   358739497 297264368 330471655 357861866 332590 SRX9142582 SRS7383886 SRA1127180 GEO Harvard University 1 0.94299   0.09714   0.80793   0.49394   58   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2020-09-17 Pharyngula Embryo Brain Nervous System
61279 61279 SRR12661714 SRX9142582 SRS7383886 SRP282920 PRJNA664124 Emergence of neuronal diversity during vertebrate brain development GSE158142 Transcriptome Analysis Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT   pubmed:33068532   zBr36hpf1 S8 GSM4793199   source name:zebrafish brain|tissue:brain|developmental stage:36hpf zBr36hpf1 S8 Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as *b in raw files and the processing was done using the combination of all data processed data files have comb* prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: *barcodes.tsv files contain 10X Genomics cell barcodes *genes.tsv files contain gene names *matrix.mtx contain transcriptome count data *web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD*.rds files are the processed R objects for performing URD cell trajectory analysis. tree*.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont… zebrafish brain   Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing   tissue:brain|developmental stage:36hpf GSM4793199 GSM4793199: zBr36hpf1 S8; Danio rerio; RNA Seq GSM4793199   1 Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing GEO Accession:GSM4793199 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP282920   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=zBr36hpf1b S8 L003 I1 001.fastq.gz read2PairFiles=zBr36hpf1b S8 L003 R1 001.fastq.gz read3PairFiles=zBr36hpf1b S8 L003 R2 001.fastq.gz zBr36hpf1b_S8_L003_I1_001.fastq.gz zBr36hpf1b_S8_L003_R1_001.fastq.gz zBr36hpf1b_S8_L003_R2_001.fastq.gz fastq fastq fastq 1340447268.0 14570079.0 GSM4793199 r7 0:8 1:26 2:58 A:356994310;C:295934792;G:330308810;T:357032061;N:177295 8 26 58   356994310 295934792 330308810 357032061 177295 SRX9142582 SRS7383886 SRA1127180 GEO Harvard University 1 0.94211   0.0964   0.80868   0.49803   58   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2020-09-17 Pharyngula Embryo Brain Nervous System
61280 61280 SRR12661715 SRX9142582 SRS7383886 SRP282920 PRJNA664124 Emergence of neuronal diversity during vertebrate brain development GSE158142 Transcriptome Analysis Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT   pubmed:33068532   zBr36hpf1 S8 GSM4793199   source name:zebrafish brain|tissue:brain|developmental stage:36hpf zBr36hpf1 S8 Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as *b in raw files and the processing was done using the combination of all data processed data files have comb* prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: *barcodes.tsv files contain 10X Genomics cell barcodes *genes.tsv files contain gene names *matrix.mtx contain transcriptome count data *web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD*.rds files are the processed R objects for performing URD cell trajectory analysis. tree*.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont… zebrafish brain   Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing   tissue:brain|developmental stage:36hpf GSM4793199 GSM4793199: zBr36hpf1 S8; Danio rerio; RNA Seq GSM4793199   1 Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing GEO Accession:GSM4793199 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP282920   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=zBr36hpf1b S8 L004 I1 001.fastq.gz read2PairFiles=zBr36hpf1b S8 L004 R1 001.fastq.gz read3PairFiles=zBr36hpf1b S8 L004 R2 001.fastq.gz zBr36hpf1b_S8_L004_I1_001.fastq.gz zBr36hpf1b_S8_L004_R1_001.fastq.gz zBr36hpf1b_S8_L004_R2_001.fastq.gz fastq fastq fastq 1233239116.0 13404773.0 GSM4793199 r8 0:8 1:26 2:58 A:330431166;C:272462685;G:301048391;T:329148018;N:148856 8 26 58   330431166 272462685 301048391 329148018 148856 SRX9142582 SRS7383886 SRA1127180 GEO Harvard University 1 0.94278   0.09641   0.81012   0.49678   58   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2020-09-17 Pharyngula Embryo Brain Nervous System
61281 61281 SRR12661704 SRX9142581 SRS7383885 SRP282920 PRJNA664124 Emergence of neuronal diversity during vertebrate brain development GSE158142 Transcriptome Analysis Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT   pubmed:33068532   zBr24hpf3 S2 GSM4793198   source name:zebrafish brain|tissue:brain|developmental stage:24hpf zBr24hpf3 S2 Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as *b in raw files and the processing was done using the combination of all data processed data files have comb* prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: *barcodes.tsv files contain 10X Genomics cell barcodes *genes.tsv files contain gene names *matrix.mtx contain transcriptome count data *web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD*.rds files are the processed R objects for performing URD cell trajectory analysis. tree*.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont… zebrafish brain   Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing   tissue:brain|developmental stage:24hpf GSM4793198 GSM4793198: zBr24hpf3 S2; Danio rerio; RNA Seq GSM4793198   1 Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing GEO Accession:GSM4793198 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP282920   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=zBr24hpf3 S2 L001 I1 001.fastq.gz read2PairFiles=zBr24hpf3 S2 L001 R1 001.fastq.gz read3PairFiles=zBr24hpf3 S2 L001 R2 001.fastq.gz zBr24hpf3_S2_L001_I1_001.fastq.gz zBr24hpf3_S2_L001_R1_001.fastq.gz zBr24hpf3_S2_L001_R2_001.fastq.gz fastq fastq fastq 1911367160.0 20775730.0 GSM4793198 r1 0:8 1:26 2:58 A:518555517;C:428251265;G:480738767;T:483105990;N:715621 8 26 58   518555517 428251265 480738767 483105990 715621 SRX9142581 SRS7383885 SRA1127180 GEO Harvard University 1 0.94875   0.07782   0.83017   0.48957   58   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2020-09-17 Pharyngula Embryo Brain Nervous System
61282 61282 SRR12661705 SRX9142581 SRS7383885 SRP282920 PRJNA664124 Emergence of neuronal diversity during vertebrate brain development GSE158142 Transcriptome Analysis Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT   pubmed:33068532   zBr24hpf3 S2 GSM4793198   source name:zebrafish brain|tissue:brain|developmental stage:24hpf zBr24hpf3 S2 Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as *b in raw files and the processing was done using the combination of all data processed data files have comb* prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: *barcodes.tsv files contain 10X Genomics cell barcodes *genes.tsv files contain gene names *matrix.mtx contain transcriptome count data *web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD*.rds files are the processed R objects for performing URD cell trajectory analysis. tree*.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont… zebrafish brain   Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing   tissue:brain|developmental stage:24hpf GSM4793198 GSM4793198: zBr24hpf3 S2; Danio rerio; RNA Seq GSM4793198   1 Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing GEO Accession:GSM4793198 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP282920   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=zBr24hpf3 S2 L002 I1 001.fastq.gz read2PairFiles=zBr24hpf3 S2 L002 R1 001.fastq.gz read3PairFiles=zBr24hpf3 S2 L002 R2 001.fastq.gz zBr24hpf3_S2_L002_I1_001.fastq.gz zBr24hpf3_S2_L002_R1_001.fastq.gz zBr24hpf3_S2_L002_R2_001.fastq.gz fastq fastq fastq 1768561540.0 19223495.0 GSM4793198 r2 0:8 1:26 2:58 A:492211957;C:396800414;G:429629025;T:449274681;N:645463 8 26 58   492211957 396800414 429629025 449274681 645463 SRX9142581 SRS7383885 SRA1127180 GEO Harvard University 1 0.94574   0.08385   0.84964   0.47837   58   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2020-09-17 Pharyngula Embryo Brain Nervous System
61283 61283 SRR12661706 SRX9142581 SRS7383885 SRP282920 PRJNA664124 Emergence of neuronal diversity during vertebrate brain development GSE158142 Transcriptome Analysis Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT   pubmed:33068532   zBr24hpf3 S2 GSM4793198   source name:zebrafish brain|tissue:brain|developmental stage:24hpf zBr24hpf3 S2 Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as *b in raw files and the processing was done using the combination of all data processed data files have comb* prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: *barcodes.tsv files contain 10X Genomics cell barcodes *genes.tsv files contain gene names *matrix.mtx contain transcriptome count data *web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD*.rds files are the processed R objects for performing URD cell trajectory analysis. tree*.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont… zebrafish brain   Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing   tissue:brain|developmental stage:24hpf GSM4793198 GSM4793198: zBr24hpf3 S2; Danio rerio; RNA Seq GSM4793198   1 Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing GEO Accession:GSM4793198 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP282920   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=zBr24hpf3 S2 L003 I1 001.fastq.gz read2PairFiles=zBr24hpf3 S2 L003 R1 001.fastq.gz read3PairFiles=zBr24hpf3 S2 L003 R2 001.fastq.gz zBr24hpf3_S2_L003_I1_001.fastq.gz zBr24hpf3_S2_L003_R1_001.fastq.gz zBr24hpf3_S2_L003_R2_001.fastq.gz fastq fastq fastq 1785914856.0 19412118.0 GSM4793198 r3 0:8 1:26 2:58 A:493608499;C:399868847;G:438420362;T:453669924;N:347224 8 26 58   493608499 399868847 438420362 453669924 347224 SRX9142581 SRS7383885 SRA1127180 GEO Harvard University 1 0.94782   0.08226   0.84137   0.46993   58   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2020-09-17 Pharyngula Embryo Brain Nervous System
61284 61284 SRR12661707 SRX9142581 SRS7383885 SRP282920 PRJNA664124 Emergence of neuronal diversity during vertebrate brain development GSE158142 Transcriptome Analysis Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT   pubmed:33068532   zBr24hpf3 S2 GSM4793198   source name:zebrafish brain|tissue:brain|developmental stage:24hpf zBr24hpf3 S2 Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as *b in raw files and the processing was done using the combination of all data processed data files have comb* prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: *barcodes.tsv files contain 10X Genomics cell barcodes *genes.tsv files contain gene names *matrix.mtx contain transcriptome count data *web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD*.rds files are the processed R objects for performing URD cell trajectory analysis. tree*.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont… zebrafish brain   Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing   tissue:brain|developmental stage:24hpf GSM4793198 GSM4793198: zBr24hpf3 S2; Danio rerio; RNA Seq GSM4793198   1 Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing GEO Accession:GSM4793198 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP282920   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=zBr24hpf3 S2 L004 I1 001.fastq.gz read2PairFiles=zBr24hpf3 S2 L004 R1 001.fastq.gz read3PairFiles=zBr24hpf3 S2 L004 R2 001.fastq.gz zBr24hpf3_S2_L004_I1_001.fastq.gz zBr24hpf3_S2_L004_R1_001.fastq.gz zBr24hpf3_S2_L004_R2_001.fastq.gz fastq fastq fastq 1783165344.0 19382232.0 GSM4793198 r4 0:8 1:26 2:58 A:495573405;C:399567193;G:434183228;T:453517782;N:323736 8 26 58   495573405 399567193 434183228 453517782 323736 SRX9142581 SRS7383885 SRA1127180 GEO Harvard University 1 0.94802   0.08421   0.85131   0.4818   58   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2020-09-17 Pharyngula Embryo Brain Nervous System
61285 61285 SRR12661700 SRX9142580 SRS7383884 SRP282920 PRJNA664124 Emergence of neuronal diversity during vertebrate brain development GSE158142 Transcriptome Analysis Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT   pubmed:33068532   zBr24hpf2 S4 GSM4793197   source name:zebrafish brain|tissue:brain|developmental stage:24hpf zBr24hpf2 S4 Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as *b in raw files and the processing was done using the combination of all data processed data files have comb* prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: *barcodes.tsv files contain 10X Genomics cell barcodes *genes.tsv files contain gene names *matrix.mtx contain transcriptome count data *web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD*.rds files are the processed R objects for performing URD cell trajectory analysis. tree*.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont… zebrafish brain   Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing   tissue:brain|developmental stage:24hpf GSM4793197 GSM4793197: zBr24hpf2 S4; Danio rerio; RNA Seq GSM4793197   1 Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing GEO Accession:GSM4793197 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP282920   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=zBr24hpf2 S4 L001 I1 001.fastq.gz read2PairFiles=zBr24hpf2 S4 L001 R1 001.fastq.gz read3PairFiles=zBr24hpf2 S4 L001 R2 001.fastq.gz zBr24hpf2_S4_L001_I1_001.fastq.gz zBr24hpf2_S4_L001_R1_001.fastq.gz zBr24hpf2_S4_L001_R2_001.fastq.gz fastq fastq fastq 1610567916.0 17506173.0 GSM4793197 r1 0:8 1:26 2:58 A:440549008;C:355249104;G:389445387;T:424941131;N:383286 8 26 58   440549008 355249104 389445387 424941131 383286 SRX9142580 SRS7383884 SRA1127180 GEO Harvard University 1 0.93926   0.11249   0.82012   0.48613   58   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2020-09-17 Pharyngula Embryo Brain Nervous System
61286 61286 SRR12661701 SRX9142580 SRS7383884 SRP282920 PRJNA664124 Emergence of neuronal diversity during vertebrate brain development GSE158142 Transcriptome Analysis Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT   pubmed:33068532   zBr24hpf2 S4 GSM4793197   source name:zebrafish brain|tissue:brain|developmental stage:24hpf zBr24hpf2 S4 Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as *b in raw files and the processing was done using the combination of all data processed data files have comb* prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: *barcodes.tsv files contain 10X Genomics cell barcodes *genes.tsv files contain gene names *matrix.mtx contain transcriptome count data *web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD*.rds files are the processed R objects for performing URD cell trajectory analysis. tree*.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont… zebrafish brain   Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing   tissue:brain|developmental stage:24hpf GSM4793197 GSM4793197: zBr24hpf2 S4; Danio rerio; RNA Seq GSM4793197   1 Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing GEO Accession:GSM4793197 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP282920   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=zBr24hpf2 S4 L002 I1 001.fastq.gz read2PairFiles=zBr24hpf2 S4 L002 R1 001.fastq.gz read3PairFiles=zBr24hpf2 S4 L002 R2 001.fastq.gz zBr24hpf2_S4_L002_I1_001.fastq.gz zBr24hpf2_S4_L002_R1_001.fastq.gz zBr24hpf2_S4_L002_R2_001.fastq.gz fastq fastq fastq 1584562552.0 17223506.0 GSM4793197 r2 0:8 1:26 2:58 A:436038687;C:349679779;G:380784321;T:417744447;N:315318 8 26 58   436038687 349679779 380784321 417744447 315318 SRX9142580 SRS7383884 SRA1127180 GEO Harvard University 1 0.93966   0.1161   0.82217   0.47132   58   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2020-09-17 Pharyngula Embryo Brain Nervous System
61287 61287 SRR12661702 SRX9142580 SRS7383884 SRP282920 PRJNA664124 Emergence of neuronal diversity during vertebrate brain development GSE158142 Transcriptome Analysis Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT   pubmed:33068532   zBr24hpf2 S4 GSM4793197   source name:zebrafish brain|tissue:brain|developmental stage:24hpf zBr24hpf2 S4 Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as *b in raw files and the processing was done using the combination of all data processed data files have comb* prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: *barcodes.tsv files contain 10X Genomics cell barcodes *genes.tsv files contain gene names *matrix.mtx contain transcriptome count data *web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD*.rds files are the processed R objects for performing URD cell trajectory analysis. tree*.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont… zebrafish brain   Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing   tissue:brain|developmental stage:24hpf GSM4793197 GSM4793197: zBr24hpf2 S4; Danio rerio; RNA Seq GSM4793197   1 Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing GEO Accession:GSM4793197 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP282920   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=zBr24hpf2 S4 L003 I1 001.fastq.gz read2PairFiles=zBr24hpf2 S4 L003 R1 001.fastq.gz read3PairFiles=zBr24hpf2 S4 L003 R2 001.fastq.gz zBr24hpf2_S4_L003_I1_001.fastq.gz zBr24hpf2_S4_L003_R1_001.fastq.gz zBr24hpf2_S4_L003_R2_001.fastq.gz fastq fastq fastq 1564085008.0 17000924.0 GSM4793197 r3 0:8 1:26 2:58 A:428352345;C:344229050;G:377948837;T:413305594;N:249182 8 26 58   428352345 344229050 377948837 413305594 249182 SRX9142580 SRS7383884 SRA1127180 GEO Harvard University 1 0.93914   0.11487   0.82361   0.4832   58   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2020-09-17 Pharyngula Embryo Brain Nervous System
61288 61288 SRR12661703 SRX9142580 SRS7383884 SRP282920 PRJNA664124 Emergence of neuronal diversity during vertebrate brain development GSE158142 Transcriptome Analysis Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT   pubmed:33068532   zBr24hpf2 S4 GSM4793197   source name:zebrafish brain|tissue:brain|developmental stage:24hpf zBr24hpf2 S4 Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as *b in raw files and the processing was done using the combination of all data processed data files have comb* prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: *barcodes.tsv files contain 10X Genomics cell barcodes *genes.tsv files contain gene names *matrix.mtx contain transcriptome count data *web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD*.rds files are the processed R objects for performing URD cell trajectory analysis. tree*.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont… zebrafish brain   Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing   tissue:brain|developmental stage:24hpf GSM4793197 GSM4793197: zBr24hpf2 S4; Danio rerio; RNA Seq GSM4793197   1 Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing GEO Accession:GSM4793197 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP282920   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=zBr24hpf2 S4 L004 I1 001.fastq.gz read2PairFiles=zBr24hpf2 S4 L004 R1 001.fastq.gz read3PairFiles=zBr24hpf2 S4 L004 R2 001.fastq.gz zBr24hpf2_S4_L004_I1_001.fastq.gz zBr24hpf2_S4_L004_R1_001.fastq.gz zBr24hpf2_S4_L004_R2_001.fastq.gz fastq fastq fastq 1618721692.0 17594801.0 GSM4793197 r4 0:8 1:26 2:58 A:441946732;C:356875026;G:392950304;T:426747266;N:202364 8 26 58   441946732 356875026 392950304 426747266 202364 SRX9142580 SRS7383884 SRA1127180 GEO Harvard University 1 0.93904   0.11095   0.8196   0.47549   58   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2020-09-17 Pharyngula Embryo Brain Nervous System
61289 61289 SRR12661696 SRX9142579 SRS7383883 SRP282920 PRJNA664124 Emergence of neuronal diversity during vertebrate brain development GSE158142 Transcriptome Analysis Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT   pubmed:33068532   zBr24hpf1 S3 GSM4793196   source name:zebrafish brain|tissue:brain|developmental stage:24hpf zBr24hpf1 S3 Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as *b in raw files and the processing was done using the combination of all data processed data files have comb* prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: *barcodes.tsv files contain 10X Genomics cell barcodes *genes.tsv files contain gene names *matrix.mtx contain transcriptome count data *web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD*.rds files are the processed R objects for performing URD cell trajectory analysis. tree*.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont… zebrafish brain   Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing   tissue:brain|developmental stage:24hpf GSM4793196 GSM4793196: zBr24hpf1 S3; Danio rerio; RNA Seq GSM4793196   1 Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing GEO Accession:GSM4793196 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP282920   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=zBr24hpf1 S3 L001 I1 001.fastq.gz read2PairFiles=zBr24hpf1 S3 L001 R1 001.fastq.gz read3PairFiles=zBr24hpf1 S3 L001 R2 001.fastq.gz zBr24hpf1_S3_L001_I1_001.fastq.gz zBr24hpf1_S3_L001_R1_001.fastq.gz zBr24hpf1_S3_L001_R2_001.fastq.gz fastq fastq fastq 1540025904.0 16739412.0 GSM4793196 r1 0:8 1:26 2:58 A:420531344;C:344603786;G:372689090;T:401831664;N:370020 8 26 58   420531344 344603786 372689090 401831664 370020 SRX9142579 SRS7383883 SRA1127180 GEO Harvard University 1 0.93908   0.11195   0.82252   0.48589   58   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2020-09-17 Pharyngula Embryo Brain Nervous System
61290 61290 SRR12661697 SRX9142579 SRS7383883 SRP282920 PRJNA664124 Emergence of neuronal diversity during vertebrate brain development GSE158142 Transcriptome Analysis Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT   pubmed:33068532   zBr24hpf1 S3 GSM4793196   source name:zebrafish brain|tissue:brain|developmental stage:24hpf zBr24hpf1 S3 Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as *b in raw files and the processing was done using the combination of all data processed data files have comb* prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: *barcodes.tsv files contain 10X Genomics cell barcodes *genes.tsv files contain gene names *matrix.mtx contain transcriptome count data *web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD*.rds files are the processed R objects for performing URD cell trajectory analysis. tree*.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont… zebrafish brain   Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing   tissue:brain|developmental stage:24hpf GSM4793196 GSM4793196: zBr24hpf1 S3; Danio rerio; RNA Seq GSM4793196   1 Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing GEO Accession:GSM4793196 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP282920   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=zBr24hpf1 S3 L002 I1 001.fastq.gz read2PairFiles=zBr24hpf1 S3 L002 R1 001.fastq.gz read3PairFiles=zBr24hpf1 S3 L002 R2 001.fastq.gz zBr24hpf1_S3_L002_I1_001.fastq.gz zBr24hpf1_S3_L002_R1_001.fastq.gz zBr24hpf1_S3_L002_R2_001.fastq.gz fastq fastq fastq 1516047116.0 16478773.0 GSM4793196 r2 0:8 1:26 2:58 A:416452609;C:339452130;G:364607393;T:395226361;N:308623 8 26 58   416452609 339452130 364607393 395226361 308623 SRX9142579 SRS7383883 SRA1127180 GEO Harvard University 1 0.94016   0.11299   0.82315   0.49117   58   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2020-09-17 Pharyngula Embryo Brain Nervous System
61291 61291 SRR12661698 SRX9142579 SRS7383883 SRP282920 PRJNA664124 Emergence of neuronal diversity during vertebrate brain development GSE158142 Transcriptome Analysis Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT   pubmed:33068532   zBr24hpf1 S3 GSM4793196   source name:zebrafish brain|tissue:brain|developmental stage:24hpf zBr24hpf1 S3 Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as *b in raw files and the processing was done using the combination of all data processed data files have comb* prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: *barcodes.tsv files contain 10X Genomics cell barcodes *genes.tsv files contain gene names *matrix.mtx contain transcriptome count data *web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD*.rds files are the processed R objects for performing URD cell trajectory analysis. tree*.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont… zebrafish brain   Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing   tissue:brain|developmental stage:24hpf GSM4793196 GSM4793196: zBr24hpf1 S3; Danio rerio; RNA Seq GSM4793196   1 Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing GEO Accession:GSM4793196 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP282920   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=zBr24hpf1 S3 L003 I1 001.fastq.gz read2PairFiles=zBr24hpf1 S3 L003 R1 001.fastq.gz read3PairFiles=zBr24hpf1 S3 L003 R2 001.fastq.gz zBr24hpf1_S3_L003_I1_001.fastq.gz zBr24hpf1_S3_L003_R1_001.fastq.gz zBr24hpf1_S3_L003_R2_001.fastq.gz fastq fastq fastq 1489844964.0 16193967.0 GSM4793196 r3 0:8 1:26 2:58 A:407319455;C:332619231;G:360252453;T:389416862;N:236963 8 26 58   407319455 332619231 360252453 389416862 236963 SRX9142579 SRS7383883 SRA1127180 GEO Harvard University 1 0.93915   0.11239   0.81945   0.49251   58   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2020-09-17 Pharyngula Embryo Brain Nervous System
61292 61292 SRR12661699 SRX9142579 SRS7383883 SRP282920 PRJNA664124 Emergence of neuronal diversity during vertebrate brain development GSE158142 Transcriptome Analysis Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT   pubmed:33068532   zBr24hpf1 S3 GSM4793196   source name:zebrafish brain|tissue:brain|developmental stage:24hpf zBr24hpf1 S3 Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as *b in raw files and the processing was done using the combination of all data processed data files have comb* prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: *barcodes.tsv files contain 10X Genomics cell barcodes *genes.tsv files contain gene names *matrix.mtx contain transcriptome count data *web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD*.rds files are the processed R objects for performing URD cell trajectory analysis. tree*.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont… zebrafish brain   Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing   tissue:brain|developmental stage:24hpf GSM4793196 GSM4793196: zBr24hpf1 S3; Danio rerio; RNA Seq GSM4793196   1 Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing GEO Accession:GSM4793196 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP282920   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=zBr24hpf1 S3 L004 I1 001.fastq.gz read2PairFiles=zBr24hpf1 S3 L004 R1 001.fastq.gz read3PairFiles=zBr24hpf1 S3 L004 R2 001.fastq.gz zBr24hpf1_S3_L004_I1_001.fastq.gz zBr24hpf1_S3_L004_R1_001.fastq.gz zBr24hpf1_S3_L004_R2_001.fastq.gz fastq fastq fastq 1546038104.0 16804762.0 GSM4793196 r4 0:8 1:26 2:58 A:421307490;C:345861740;G:375609488;T:403067619;N:191767 8 26 58   421307490 345861740 375609488 403067619 191767 SRX9142579 SRS7383883 SRA1127180 GEO Harvard University 1 0.94111   0.10957   0.81769   0.47888   58   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2020-09-17 Pharyngula Embryo Brain Nervous System
65104 65104 SRR14923954 SRX11237257 SRS9283132 SRP325759 PRJNA741770 Single cell profiling of cranial neural crest diversification across a vertebrate lifetime GSE178969 Other The cranial neural crest CNC is a vertebrate specific population that generates a huge diversity of derivatives including the bulk of the connective and skeletal tissues of the head. How neural crest cells generate the appropriate cell types for distinct head regions over time remains unresolved. Here we profile RNA expression scRNAseq and chromatin accessibility snATACseq of the zebrafish cranial neural crest lineage at single cell resolution from embryos to adults. Overall design: To recover the cell heterogeneity and lineage information in the span of a life time of a fish we collected the converted cells from embryonic stages 1.5 2 dpf larval stage 3 5 and 14 dpf juvenile stage 60 dpf to adult stage 150 or 210 dpf. We used a cranial neural crest converted zebrafish line 28.5Sox10:Cre;bactin:BFP to DsRed to permanantly convert and label the CNCC derived cells. The converted cells were collected and subjected to single cell sequencing for both their transcriptome and open chromatin region using Chromium platform of 10X Genomic. For biological and technical control we include replicates for both scRNAseq and snATACseq at various stages. We include an additional line fli1a:eGFP/sox10:dsRed for a biological and positive control of CNCC of 1.5 dpf sample.   pubmed:35013168   scRNAseq fliIa eGFP Sox10 dsRed 1.5dpf rep 1 GSM5402429   tissue:Cranial neural crest derived cells|cell type:Cranial neural crest derived cells|transgene1:Tgfli1a:eGFPy1|transgene2:Tgsox10:DsRed Expressel10|developmental stage:1.5 dpf|facs markers:DAPI / dsRed+/eGFP+ scRNAseq fliIa eGFP Sox10 dsRed 1.5dpf rep 1 For scRNAseq libraries Cellranger v3.0.0 10X Genomics was used for demultiplexing alignment and raw count matrix generation. The alignment was performed against zebrafish genome index built with GRCz11.fa and GRCz11.98.gtf. For snATACseq libraries Cellranger ATAC v1.2.0 10X Genomics was used for alignment against zebrafish genome index built with GRCz11.fa JASPAR2020 and GRCz11.98.gtf peak calling and peak by cell count matrix generation with default parameters. QC step for the library was performed along with the Cellranger or Cellranger ATAC alignment process. We performed a second round of peak calling for our snATACseq data using package Snaptools and SnapATAC. We first removed cell debris low quality cells and cell duplicates by setting cutoffs based on percentage of reads in peaks > 30 for 60 dpf > 45 for 210 dpf and > 50 for the rest and fragment number within peaks 5 000 – 30 000 for 5 dpf 1 000 – 11 000 for 14 dpf and 1 000 – 20 000 for the rest. To  recover every aligned fragment we binned the genome into 5 kb sections and constructed the bin by cell matrices bmats for each library by Snaptools from the positional sorted bam files generated by cellranger atac. The cells were filtered dimensionally reduced by diffusion map and clustered with inputs of the first 34 dimensions followed the SnapATAC vignette. The specific peaks were called for each cluster by the wrapped MACS2 function in SnapATAC with parameter gsize = 1.5e9 shift = 100 ext = 200 and qval = 5e 2. The finalized and refined peak profile was derived by collapsing and merging all 175 individual peak files to about 450K peaks. The count matrices of both scRNAseq and snATACseq data were analyzed by R package Seurat and Signac. The count matrices of each sample were aggregated if there is any replicate. For scRNAseq data the matrices are normalized NormalizeData and scaled for the top 2 000 variable genes FindVariableFeatures and ScaleData. The scaled matrices were dimensional reduced to 50 principal components 60 component… Cranial neural crest derived cells   Dissected heads from converted Sox10:cre; bactin:loxP eGFP loxP DsRed fish were incubated in fresh Ringer’s solution 5 10 min followed by mechanical and enzymatic dissociation by pipetting every 5 minutes in protease solution 0.25% trypsin Life Technologies 15090 046 1 mM EDTA and 400 mg/ml Collagenase D Sigma 11088882001 in PBS and incubated at 28.5°C for 20 30 minutes or until full dissociation. Reaction was stopped by 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted 2000 rpm 5 minute 4 °C and resuspended in suspension media 1% FBS 0.8 mM CaCl2 50 U/ml penicillin and 0.05 mg/ml streptomycin Sigma Aldrich St. Louis MO in phenol red free Leibovitz’s L15 medium Life Technologies twice. Final volumes of 500 µl resuspended cells were placed on ice and sorted by fluorescence activated cell sorting FACS to isolate live cells that excluded the cytoplasmic stain Zombie green BioLegend 423111 or the nuclear stain DAPI. Live cells were sorted into PBS solution containing 0.04% BSA and loaded to 10X Genomics microfluidic chips. The version 2 of Chromium Single Cell three prime Reagent Kits was used for RNA extraction. For snATACseq library construction we used the same cell dissociation and sorting protocol as for scRNAseq with isolation of live cells that excluded the cytoplasmic stain Zombie green product information. Nuclei isolation was performed per manufacturer’s instructions 10X Genomic protocol CG000169. Cells were incubated with lysis buffer on ice for 90 second followed by integrity check of nuclei under fluorescence microscope with DAPI before library synthesis. For scRNAseq the cell lysis polyA pull down tagging with cell barcode and RNA:DNA hybrid synthesis were performed in the GEMs per manufacturer's instruction. GEMs containing barcoded single cell cDNA were lysis for further fragmentation and ligation of illumina P5 and P7 ends. Libraries were sequenced to depths of at least 1 000 000 reads per cell for each library. For snATACseq the open chroma… The Institutional Animal Care and Use Committee of the University of Southern California approved all animal experiments Protocol 20771. Zebrafish embryos Danio rerio were raised in embryo media at 28.5°C. For adults in the institute vivarium according to Protocol 20771. cell type:Cranial neural crest derived cells|transgene1:Tgfli1a:eGFPy1|transgene2:Tgsox10:DsRed Expressel10|developmental stage:1.5 dpf|facs markers:DAPI / dsRed+/eGFP+ GSM5402429 GSM5402429: scRNAseq fliIa eGFP Sox10 dsRed 1.5dpf rep 1; Danio rerio; RNA Seq GSM5402429   1 Dissected heads from converted Sox10:cre; bactin:loxP eGFP loxP DsRed fish were incubated in fresh Ringer's solution 5 10 min followed by mechanical and enzymatic dissociation by pipetting every 5 minutes in protease solution 0.25% trypsin Life Technologies 15090 046 1 mM EDTA and 400 mg/ml Collagenase D Sigma 11088882001 in PBS and incubated at 28.5°C for 20 30 minutes or until full dissociation. Reaction was stopped by 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted 2000 rpm 5 minute 4 °C and resuspended in suspension media 1% FBS 0.8 mM CaCl2 50 U/ml penicillin and 0.05 mg/ml streptomycin Sigma Aldrich St. Louis MO in phenol red free Leibovitz's L15 medium Life Technologies twice. Final volumes of 500 µl resuspended cells were placed on ice and sorted by fluorescence activated cell sorting FACS to isolate live cells that excluded the cytoplasmic stain Zombie green BioLegend 423111 or the nuclear stain DAPI. Live cells were sorted into PBS solution containing 0.04% BSA and loaded to 10X Genomics microfluidic chips. The version 2 of Chromium Single Cell three prime Reagent Kits was used for RNA extraction. For snATACseq library construction we used the same cell dissociation and sorting protocol as for scRNAseq with isolation of live cells that excluded the cytoplasmic stain Zombie green product information. Nuclei isolation was performed per manufacturer's instructions 10X Genomic protocol CG000169. Cells were incubated with lysis buffer on ice for 90 second followed by integrity check of nuclei under fluorescence microscope with DAPI before library synthesis. For scRNAseq the cell lysis polyA pull down tagging with cell barcode and RNA:DNA hybrid synthesis were performed in the GEMs per manufacturer's instruction. GEMs containing barcoded single cell cDNA were lysis for further fragmentation and ligation of illumina P5 and P7 ends. Libraries were sequenced to depths of at least 1 000 000 reads per cell for each library. For snATACseq the open chroma… GEO Accession:GSM5402429 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 550   SRP325759     scRNAseq_fliIa_eGFP_Sox10_dsRed_1.5dpf_rep_1_S5_L001_R1_001.fastq.gz scRNAseq_fliIa_eGFP_Sox10_dsRed_1.5dpf_rep_1_S5_L001_R2_001.fastq.gz fastq fastq 8491189961.0 67691516.0 GSM5402429 r1 0:27 1:98.44 A:2357122563;C:1869226920;G:2114433016;T:2119986585;N:30420877 27 98     2357122563 1869226920 2114433016 2119986585 30420877 SRX11237257 SRS9283132 SRA1250944 GEO Crump Lab, Stem Cell, USC 2 0.0011 0.94535 0.00032 0.09684 0.9975 0.85076 0.51724 0.49889 27 97 T B sc-like readlen illumina nextseq unknown poly_a unknown sc single_cell_droplet 10x   United States 2021-06-27 Pharyngula Embryo Brain Nervous System
65105 65105 SRR14923955 SRX11237257 SRS9283132 SRP325759 PRJNA741770 Single cell profiling of cranial neural crest diversification across a vertebrate lifetime GSE178969 Other The cranial neural crest CNC is a vertebrate specific population that generates a huge diversity of derivatives including the bulk of the connective and skeletal tissues of the head. How neural crest cells generate the appropriate cell types for distinct head regions over time remains unresolved. Here we profile RNA expression scRNAseq and chromatin accessibility snATACseq of the zebrafish cranial neural crest lineage at single cell resolution from embryos to adults. Overall design: To recover the cell heterogeneity and lineage information in the span of a life time of a fish we collected the converted cells from embryonic stages 1.5 2 dpf larval stage 3 5 and 14 dpf juvenile stage 60 dpf to adult stage 150 or 210 dpf. We used a cranial neural crest converted zebrafish line 28.5Sox10:Cre;bactin:BFP to DsRed to permanantly convert and label the CNCC derived cells. The converted cells were collected and subjected to single cell sequencing for both their transcriptome and open chromatin region using Chromium platform of 10X Genomic. For biological and technical control we include replicates for both scRNAseq and snATACseq at various stages. We include an additional line fli1a:eGFP/sox10:dsRed for a biological and positive control of CNCC of 1.5 dpf sample.   pubmed:35013168   scRNAseq fliIa eGFP Sox10 dsRed 1.5dpf rep 1 GSM5402429   tissue:Cranial neural crest derived cells|cell type:Cranial neural crest derived cells|transgene1:Tgfli1a:eGFPy1|transgene2:Tgsox10:DsRed Expressel10|developmental stage:1.5 dpf|facs markers:DAPI / dsRed+/eGFP+ scRNAseq fliIa eGFP Sox10 dsRed 1.5dpf rep 1 For scRNAseq libraries Cellranger v3.0.0 10X Genomics was used for demultiplexing alignment and raw count matrix generation. The alignment was performed against zebrafish genome index built with GRCz11.fa and GRCz11.98.gtf. For snATACseq libraries Cellranger ATAC v1.2.0 10X Genomics was used for alignment against zebrafish genome index built with GRCz11.fa JASPAR2020 and GRCz11.98.gtf peak calling and peak by cell count matrix generation with default parameters. QC step for the library was performed along with the Cellranger or Cellranger ATAC alignment process. We performed a second round of peak calling for our snATACseq data using package Snaptools and SnapATAC. We first removed cell debris low quality cells and cell duplicates by setting cutoffs based on percentage of reads in peaks > 30 for 60 dpf > 45 for 210 dpf and > 50 for the rest and fragment number within peaks 5 000 – 30 000 for 5 dpf 1 000 – 11 000 for 14 dpf and 1 000 – 20 000 for the rest. To  recover every aligned fragment we binned the genome into 5 kb sections and constructed the bin by cell matrices bmats for each library by Snaptools from the positional sorted bam files generated by cellranger atac. The cells were filtered dimensionally reduced by diffusion map and clustered with inputs of the first 34 dimensions followed the SnapATAC vignette. The specific peaks were called for each cluster by the wrapped MACS2 function in SnapATAC with parameter gsize = 1.5e9 shift = 100 ext = 200 and qval = 5e 2. The finalized and refined peak profile was derived by collapsing and merging all 175 individual peak files to about 450K peaks. The count matrices of both scRNAseq and snATACseq data were analyzed by R package Seurat and Signac. The count matrices of each sample were aggregated if there is any replicate. For scRNAseq data the matrices are normalized NormalizeData and scaled for the top 2 000 variable genes FindVariableFeatures and ScaleData. The scaled matrices were dimensional reduced to 50 principal components 60 component… Cranial neural crest derived cells   Dissected heads from converted Sox10:cre; bactin:loxP eGFP loxP DsRed fish were incubated in fresh Ringer’s solution 5 10 min followed by mechanical and enzymatic dissociation by pipetting every 5 minutes in protease solution 0.25% trypsin Life Technologies 15090 046 1 mM EDTA and 400 mg/ml Collagenase D Sigma 11088882001 in PBS and incubated at 28.5°C for 20 30 minutes or until full dissociation. Reaction was stopped by 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted 2000 rpm 5 minute 4 °C and resuspended in suspension media 1% FBS 0.8 mM CaCl2 50 U/ml penicillin and 0.05 mg/ml streptomycin Sigma Aldrich St. Louis MO in phenol red free Leibovitz’s L15 medium Life Technologies twice. Final volumes of 500 µl resuspended cells were placed on ice and sorted by fluorescence activated cell sorting FACS to isolate live cells that excluded the cytoplasmic stain Zombie green BioLegend 423111 or the nuclear stain DAPI. Live cells were sorted into PBS solution containing 0.04% BSA and loaded to 10X Genomics microfluidic chips. The version 2 of Chromium Single Cell three prime Reagent Kits was used for RNA extraction. For snATACseq library construction we used the same cell dissociation and sorting protocol as for scRNAseq with isolation of live cells that excluded the cytoplasmic stain Zombie green product information. Nuclei isolation was performed per manufacturer’s instructions 10X Genomic protocol CG000169. Cells were incubated with lysis buffer on ice for 90 second followed by integrity check of nuclei under fluorescence microscope with DAPI before library synthesis. For scRNAseq the cell lysis polyA pull down tagging with cell barcode and RNA:DNA hybrid synthesis were performed in the GEMs per manufacturer's instruction. GEMs containing barcoded single cell cDNA were lysis for further fragmentation and ligation of illumina P5 and P7 ends. Libraries were sequenced to depths of at least 1 000 000 reads per cell for each library. For snATACseq the open chroma… The Institutional Animal Care and Use Committee of the University of Southern California approved all animal experiments Protocol 20771. Zebrafish embryos Danio rerio were raised in embryo media at 28.5°C. For adults in the institute vivarium according to Protocol 20771. cell type:Cranial neural crest derived cells|transgene1:Tgfli1a:eGFPy1|transgene2:Tgsox10:DsRed Expressel10|developmental stage:1.5 dpf|facs markers:DAPI / dsRed+/eGFP+ GSM5402429 GSM5402429: scRNAseq fliIa eGFP Sox10 dsRed 1.5dpf rep 1; Danio rerio; RNA Seq GSM5402429   1 Dissected heads from converted Sox10:cre; bactin:loxP eGFP loxP DsRed fish were incubated in fresh Ringer's solution 5 10 min followed by mechanical and enzymatic dissociation by pipetting every 5 minutes in protease solution 0.25% trypsin Life Technologies 15090 046 1 mM EDTA and 400 mg/ml Collagenase D Sigma 11088882001 in PBS and incubated at 28.5°C for 20 30 minutes or until full dissociation. Reaction was stopped by 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted 2000 rpm 5 minute 4 °C and resuspended in suspension media 1% FBS 0.8 mM CaCl2 50 U/ml penicillin and 0.05 mg/ml streptomycin Sigma Aldrich St. Louis MO in phenol red free Leibovitz's L15 medium Life Technologies twice. Final volumes of 500 µl resuspended cells were placed on ice and sorted by fluorescence activated cell sorting FACS to isolate live cells that excluded the cytoplasmic stain Zombie green BioLegend 423111 or the nuclear stain DAPI. Live cells were sorted into PBS solution containing 0.04% BSA and loaded to 10X Genomics microfluidic chips. The version 2 of Chromium Single Cell three prime Reagent Kits was used for RNA extraction. For snATACseq library construction we used the same cell dissociation and sorting protocol as for scRNAseq with isolation of live cells that excluded the cytoplasmic stain Zombie green product information. Nuclei isolation was performed per manufacturer's instructions 10X Genomic protocol CG000169. Cells were incubated with lysis buffer on ice for 90 second followed by integrity check of nuclei under fluorescence microscope with DAPI before library synthesis. For scRNAseq the cell lysis polyA pull down tagging with cell barcode and RNA:DNA hybrid synthesis were performed in the GEMs per manufacturer's instruction. GEMs containing barcoded single cell cDNA were lysis for further fragmentation and ligation of illumina P5 and P7 ends. Libraries were sequenced to depths of at least 1 000 000 reads per cell for each library. For snATACseq the open chroma… GEO Accession:GSM5402429 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 550   SRP325759     scRNAseq_fliIa_eGFP_Sox10_dsRed_1.5dpf_rep_1_S6_L002_R1_001.fastq.gz scRNAseq_fliIa_eGFP_Sox10_dsRed_1.5dpf_rep_1_S6_L002_R2_001.fastq.gz fastq fastq 7077449567.0 56420723.0 GSM5402429 r2 0:27 1:98.44 A:1968441069;C:1556988032;G:1756721147;T:1769895777;N:25403542 27 98     1968441069 1556988032 1756721147 1769895777 25403542 SRX11237257 SRS9283132 SRA1250944 GEO Crump Lab, Stem Cell, USC 2 0.00128 0.94634 0.00051 0.09752 0.9976 0.85295 0.62857 0.46295 27 99 T B sc-like readlen illumina nextseq unknown poly_a unknown sc single_cell_droplet 10x   United States 2021-06-27 Pharyngula Embryo Brain Nervous System
65106 65106 SRR14923956 SRX11237257 SRS9283132 SRP325759 PRJNA741770 Single cell profiling of cranial neural crest diversification across a vertebrate lifetime GSE178969 Other The cranial neural crest CNC is a vertebrate specific population that generates a huge diversity of derivatives including the bulk of the connective and skeletal tissues of the head. How neural crest cells generate the appropriate cell types for distinct head regions over time remains unresolved. Here we profile RNA expression scRNAseq and chromatin accessibility snATACseq of the zebrafish cranial neural crest lineage at single cell resolution from embryos to adults. Overall design: To recover the cell heterogeneity and lineage information in the span of a life time of a fish we collected the converted cells from embryonic stages 1.5 2 dpf larval stage 3 5 and 14 dpf juvenile stage 60 dpf to adult stage 150 or 210 dpf. We used a cranial neural crest converted zebrafish line 28.5Sox10:Cre;bactin:BFP to DsRed to permanantly convert and label the CNCC derived cells. The converted cells were collected and subjected to single cell sequencing for both their transcriptome and open chromatin region using Chromium platform of 10X Genomic. For biological and technical control we include replicates for both scRNAseq and snATACseq at various stages. We include an additional line fli1a:eGFP/sox10:dsRed for a biological and positive control of CNCC of 1.5 dpf sample.   pubmed:35013168   scRNAseq fliIa eGFP Sox10 dsRed 1.5dpf rep 1 GSM5402429   tissue:Cranial neural crest derived cells|cell type:Cranial neural crest derived cells|transgene1:Tgfli1a:eGFPy1|transgene2:Tgsox10:DsRed Expressel10|developmental stage:1.5 dpf|facs markers:DAPI / dsRed+/eGFP+ scRNAseq fliIa eGFP Sox10 dsRed 1.5dpf rep 1 For scRNAseq libraries Cellranger v3.0.0 10X Genomics was used for demultiplexing alignment and raw count matrix generation. The alignment was performed against zebrafish genome index built with GRCz11.fa and GRCz11.98.gtf. For snATACseq libraries Cellranger ATAC v1.2.0 10X Genomics was used for alignment against zebrafish genome index built with GRCz11.fa JASPAR2020 and GRCz11.98.gtf peak calling and peak by cell count matrix generation with default parameters. QC step for the library was performed along with the Cellranger or Cellranger ATAC alignment process. We performed a second round of peak calling for our snATACseq data using package Snaptools and SnapATAC. We first removed cell debris low quality cells and cell duplicates by setting cutoffs based on percentage of reads in peaks > 30 for 60 dpf > 45 for 210 dpf and > 50 for the rest and fragment number within peaks 5 000 – 30 000 for 5 dpf 1 000 – 11 000 for 14 dpf and 1 000 – 20 000 for the rest. To  recover every aligned fragment we binned the genome into 5 kb sections and constructed the bin by cell matrices bmats for each library by Snaptools from the positional sorted bam files generated by cellranger atac. The cells were filtered dimensionally reduced by diffusion map and clustered with inputs of the first 34 dimensions followed the SnapATAC vignette. The specific peaks were called for each cluster by the wrapped MACS2 function in SnapATAC with parameter gsize = 1.5e9 shift = 100 ext = 200 and qval = 5e 2. The finalized and refined peak profile was derived by collapsing and merging all 175 individual peak files to about 450K peaks. The count matrices of both scRNAseq and snATACseq data were analyzed by R package Seurat and Signac. The count matrices of each sample were aggregated if there is any replicate. For scRNAseq data the matrices are normalized NormalizeData and scaled for the top 2 000 variable genes FindVariableFeatures and ScaleData. The scaled matrices were dimensional reduced to 50 principal components 60 component… Cranial neural crest derived cells   Dissected heads from converted Sox10:cre; bactin:loxP eGFP loxP DsRed fish were incubated in fresh Ringer’s solution 5 10 min followed by mechanical and enzymatic dissociation by pipetting every 5 minutes in protease solution 0.25% trypsin Life Technologies 15090 046 1 mM EDTA and 400 mg/ml Collagenase D Sigma 11088882001 in PBS and incubated at 28.5°C for 20 30 minutes or until full dissociation. Reaction was stopped by 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted 2000 rpm 5 minute 4 °C and resuspended in suspension media 1% FBS 0.8 mM CaCl2 50 U/ml penicillin and 0.05 mg/ml streptomycin Sigma Aldrich St. Louis MO in phenol red free Leibovitz’s L15 medium Life Technologies twice. Final volumes of 500 µl resuspended cells were placed on ice and sorted by fluorescence activated cell sorting FACS to isolate live cells that excluded the cytoplasmic stain Zombie green BioLegend 423111 or the nuclear stain DAPI. Live cells were sorted into PBS solution containing 0.04% BSA and loaded to 10X Genomics microfluidic chips. The version 2 of Chromium Single Cell three prime Reagent Kits was used for RNA extraction. For snATACseq library construction we used the same cell dissociation and sorting protocol as for scRNAseq with isolation of live cells that excluded the cytoplasmic stain Zombie green product information. Nuclei isolation was performed per manufacturer’s instructions 10X Genomic protocol CG000169. Cells were incubated with lysis buffer on ice for 90 second followed by integrity check of nuclei under fluorescence microscope with DAPI before library synthesis. For scRNAseq the cell lysis polyA pull down tagging with cell barcode and RNA:DNA hybrid synthesis were performed in the GEMs per manufacturer's instruction. GEMs containing barcoded single cell cDNA were lysis for further fragmentation and ligation of illumina P5 and P7 ends. Libraries were sequenced to depths of at least 1 000 000 reads per cell for each library. For snATACseq the open chroma… The Institutional Animal Care and Use Committee of the University of Southern California approved all animal experiments Protocol 20771. Zebrafish embryos Danio rerio were raised in embryo media at 28.5°C. For adults in the institute vivarium according to Protocol 20771. cell type:Cranial neural crest derived cells|transgene1:Tgfli1a:eGFPy1|transgene2:Tgsox10:DsRed Expressel10|developmental stage:1.5 dpf|facs markers:DAPI / dsRed+/eGFP+ GSM5402429 GSM5402429: scRNAseq fliIa eGFP Sox10 dsRed 1.5dpf rep 1; Danio rerio; RNA Seq GSM5402429   1 Dissected heads from converted Sox10:cre; bactin:loxP eGFP loxP DsRed fish were incubated in fresh Ringer's solution 5 10 min followed by mechanical and enzymatic dissociation by pipetting every 5 minutes in protease solution 0.25% trypsin Life Technologies 15090 046 1 mM EDTA and 400 mg/ml Collagenase D Sigma 11088882001 in PBS and incubated at 28.5°C for 20 30 minutes or until full dissociation. Reaction was stopped by 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted 2000 rpm 5 minute 4 °C and resuspended in suspension media 1% FBS 0.8 mM CaCl2 50 U/ml penicillin and 0.05 mg/ml streptomycin Sigma Aldrich St. Louis MO in phenol red free Leibovitz's L15 medium Life Technologies twice. Final volumes of 500 µl resuspended cells were placed on ice and sorted by fluorescence activated cell sorting FACS to isolate live cells that excluded the cytoplasmic stain Zombie green BioLegend 423111 or the nuclear stain DAPI. Live cells were sorted into PBS solution containing 0.04% BSA and loaded to 10X Genomics microfluidic chips. The version 2 of Chromium Single Cell three prime Reagent Kits was used for RNA extraction. For snATACseq library construction we used the same cell dissociation and sorting protocol as for scRNAseq with isolation of live cells that excluded the cytoplasmic stain Zombie green product information. Nuclei isolation was performed per manufacturer's instructions 10X Genomic protocol CG000169. Cells were incubated with lysis buffer on ice for 90 second followed by integrity check of nuclei under fluorescence microscope with DAPI before library synthesis. For scRNAseq the cell lysis polyA pull down tagging with cell barcode and RNA:DNA hybrid synthesis were performed in the GEMs per manufacturer's instruction. GEMs containing barcoded single cell cDNA were lysis for further fragmentation and ligation of illumina P5 and P7 ends. Libraries were sequenced to depths of at least 1 000 000 reads per cell for each library. For snATACseq the open chroma… GEO Accession:GSM5402429 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 550   SRP325759     scRNAseq_fliIa_eGFP_Sox10_dsRed_1.5dpf_rep_1_S7_L003_R1_001.fastq.gz scRNAseq_fliIa_eGFP_Sox10_dsRed_1.5dpf_rep_1_S7_L003_R2_001.fastq.gz fastq fastq 5225950053.0 41661265.0 GSM5402429 r3 0:27 1:98.44 A:1453509288;C:1149078976;G:1297083462;T:1307516032;N:18762295 27 98     1453509288 1149078976 1297083462 1307516032 18762295 SRX11237257 SRS9283132 SRA1250944 GEO Crump Lab, Stem Cell, USC 2 0.00123 0.9459 0.0005 0.09718 0.9976 0.84987 0.55303 0.48991 27 98 T B sc-like readlen illumina nextseq unknown poly_a unknown sc single_cell_droplet 10x   United States 2021-06-27 Pharyngula Embryo Brain Nervous System
65107 65107 SRR14923957 SRX11237257 SRS9283132 SRP325759 PRJNA741770 Single cell profiling of cranial neural crest diversification across a vertebrate lifetime GSE178969 Other The cranial neural crest CNC is a vertebrate specific population that generates a huge diversity of derivatives including the bulk of the connective and skeletal tissues of the head. How neural crest cells generate the appropriate cell types for distinct head regions over time remains unresolved. Here we profile RNA expression scRNAseq and chromatin accessibility snATACseq of the zebrafish cranial neural crest lineage at single cell resolution from embryos to adults. Overall design: To recover the cell heterogeneity and lineage information in the span of a life time of a fish we collected the converted cells from embryonic stages 1.5 2 dpf larval stage 3 5 and 14 dpf juvenile stage 60 dpf to adult stage 150 or 210 dpf. We used a cranial neural crest converted zebrafish line 28.5Sox10:Cre;bactin:BFP to DsRed to permanantly convert and label the CNCC derived cells. The converted cells were collected and subjected to single cell sequencing for both their transcriptome and open chromatin region using Chromium platform of 10X Genomic. For biological and technical control we include replicates for both scRNAseq and snATACseq at various stages. We include an additional line fli1a:eGFP/sox10:dsRed for a biological and positive control of CNCC of 1.5 dpf sample.   pubmed:35013168   scRNAseq fliIa eGFP Sox10 dsRed 1.5dpf rep 1 GSM5402429   tissue:Cranial neural crest derived cells|cell type:Cranial neural crest derived cells|transgene1:Tgfli1a:eGFPy1|transgene2:Tgsox10:DsRed Expressel10|developmental stage:1.5 dpf|facs markers:DAPI / dsRed+/eGFP+ scRNAseq fliIa eGFP Sox10 dsRed 1.5dpf rep 1 For scRNAseq libraries Cellranger v3.0.0 10X Genomics was used for demultiplexing alignment and raw count matrix generation. The alignment was performed against zebrafish genome index built with GRCz11.fa and GRCz11.98.gtf. For snATACseq libraries Cellranger ATAC v1.2.0 10X Genomics was used for alignment against zebrafish genome index built with GRCz11.fa JASPAR2020 and GRCz11.98.gtf peak calling and peak by cell count matrix generation with default parameters. QC step for the library was performed along with the Cellranger or Cellranger ATAC alignment process. We performed a second round of peak calling for our snATACseq data using package Snaptools and SnapATAC. We first removed cell debris low quality cells and cell duplicates by setting cutoffs based on percentage of reads in peaks > 30 for 60 dpf > 45 for 210 dpf and > 50 for the rest and fragment number within peaks 5 000 – 30 000 for 5 dpf 1 000 – 11 000 for 14 dpf and 1 000 – 20 000 for the rest. To  recover every aligned fragment we binned the genome into 5 kb sections and constructed the bin by cell matrices bmats for each library by Snaptools from the positional sorted bam files generated by cellranger atac. The cells were filtered dimensionally reduced by diffusion map and clustered with inputs of the first 34 dimensions followed the SnapATAC vignette. The specific peaks were called for each cluster by the wrapped MACS2 function in SnapATAC with parameter gsize = 1.5e9 shift = 100 ext = 200 and qval = 5e 2. The finalized and refined peak profile was derived by collapsing and merging all 175 individual peak files to about 450K peaks. The count matrices of both scRNAseq and snATACseq data were analyzed by R package Seurat and Signac. The count matrices of each sample were aggregated if there is any replicate. For scRNAseq data the matrices are normalized NormalizeData and scaled for the top 2 000 variable genes FindVariableFeatures and ScaleData. The scaled matrices were dimensional reduced to 50 principal components 60 component… Cranial neural crest derived cells   Dissected heads from converted Sox10:cre; bactin:loxP eGFP loxP DsRed fish were incubated in fresh Ringer’s solution 5 10 min followed by mechanical and enzymatic dissociation by pipetting every 5 minutes in protease solution 0.25% trypsin Life Technologies 15090 046 1 mM EDTA and 400 mg/ml Collagenase D Sigma 11088882001 in PBS and incubated at 28.5°C for 20 30 minutes or until full dissociation. Reaction was stopped by 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted 2000 rpm 5 minute 4 °C and resuspended in suspension media 1% FBS 0.8 mM CaCl2 50 U/ml penicillin and 0.05 mg/ml streptomycin Sigma Aldrich St. Louis MO in phenol red free Leibovitz’s L15 medium Life Technologies twice. Final volumes of 500 µl resuspended cells were placed on ice and sorted by fluorescence activated cell sorting FACS to isolate live cells that excluded the cytoplasmic stain Zombie green BioLegend 423111 or the nuclear stain DAPI. Live cells were sorted into PBS solution containing 0.04% BSA and loaded to 10X Genomics microfluidic chips. The version 2 of Chromium Single Cell three prime Reagent Kits was used for RNA extraction. For snATACseq library construction we used the same cell dissociation and sorting protocol as for scRNAseq with isolation of live cells that excluded the cytoplasmic stain Zombie green product information. Nuclei isolation was performed per manufacturer’s instructions 10X Genomic protocol CG000169. Cells were incubated with lysis buffer on ice for 90 second followed by integrity check of nuclei under fluorescence microscope with DAPI before library synthesis. For scRNAseq the cell lysis polyA pull down tagging with cell barcode and RNA:DNA hybrid synthesis were performed in the GEMs per manufacturer's instruction. GEMs containing barcoded single cell cDNA were lysis for further fragmentation and ligation of illumina P5 and P7 ends. Libraries were sequenced to depths of at least 1 000 000 reads per cell for each library. For snATACseq the open chroma… The Institutional Animal Care and Use Committee of the University of Southern California approved all animal experiments Protocol 20771. Zebrafish embryos Danio rerio were raised in embryo media at 28.5°C. For adults in the institute vivarium according to Protocol 20771. cell type:Cranial neural crest derived cells|transgene1:Tgfli1a:eGFPy1|transgene2:Tgsox10:DsRed Expressel10|developmental stage:1.5 dpf|facs markers:DAPI / dsRed+/eGFP+ GSM5402429 GSM5402429: scRNAseq fliIa eGFP Sox10 dsRed 1.5dpf rep 1; Danio rerio; RNA Seq GSM5402429   1 Dissected heads from converted Sox10:cre; bactin:loxP eGFP loxP DsRed fish were incubated in fresh Ringer's solution 5 10 min followed by mechanical and enzymatic dissociation by pipetting every 5 minutes in protease solution 0.25% trypsin Life Technologies 15090 046 1 mM EDTA and 400 mg/ml Collagenase D Sigma 11088882001 in PBS and incubated at 28.5°C for 20 30 minutes or until full dissociation. Reaction was stopped by 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted 2000 rpm 5 minute 4 °C and resuspended in suspension media 1% FBS 0.8 mM CaCl2 50 U/ml penicillin and 0.05 mg/ml streptomycin Sigma Aldrich St. Louis MO in phenol red free Leibovitz's L15 medium Life Technologies twice. Final volumes of 500 µl resuspended cells were placed on ice and sorted by fluorescence activated cell sorting FACS to isolate live cells that excluded the cytoplasmic stain Zombie green BioLegend 423111 or the nuclear stain DAPI. Live cells were sorted into PBS solution containing 0.04% BSA and loaded to 10X Genomics microfluidic chips. The version 2 of Chromium Single Cell three prime Reagent Kits was used for RNA extraction. For snATACseq library construction we used the same cell dissociation and sorting protocol as for scRNAseq with isolation of live cells that excluded the cytoplasmic stain Zombie green product information. Nuclei isolation was performed per manufacturer's instructions 10X Genomic protocol CG000169. Cells were incubated with lysis buffer on ice for 90 second followed by integrity check of nuclei under fluorescence microscope with DAPI before library synthesis. For scRNAseq the cell lysis polyA pull down tagging with cell barcode and RNA:DNA hybrid synthesis were performed in the GEMs per manufacturer's instruction. GEMs containing barcoded single cell cDNA were lysis for further fragmentation and ligation of illumina P5 and P7 ends. Libraries were sequenced to depths of at least 1 000 000 reads per cell for each library. For snATACseq the open chroma… GEO Accession:GSM5402429 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 550   SRP325759     scRNAseq_fliIa_eGFP_Sox10_dsRed_1.5dpf_rep_1_S8_L004_R1_001.fastq.gz scRNAseq_fliIa_eGFP_Sox10_dsRed_1.5dpf_rep_1_S8_L004_R2_001.fastq.gz fastq fastq 7144119256.0 56952127.0 GSM5402429 r4 0:27 1:98.44 A:1983943995;C:1567659681;G:1778675605;T:1788400708;N:25439267 27 98     1983943995 1567659681 1778675605 1788400708 25439267 SRX11237257 SRS9283132 SRA1250944 GEO Crump Lab, Stem Cell, USC 2 0.00116 0.9453 0.00039 0.09775 0.99742 0.85036 0.55555 0.50521 27 99 T B sc-like readlen illumina nextseq unknown poly_a unknown sc single_cell_droplet 10x   United States 2021-06-27 Pharyngula Embryo Brain Nervous System
65108 65108 SRR14923950 SRX11237256 SRS9283130 SRP325759 PRJNA741770 Single cell profiling of cranial neural crest diversification across a vertebrate lifetime GSE178969 Other The cranial neural crest CNC is a vertebrate specific population that generates a huge diversity of derivatives including the bulk of the connective and skeletal tissues of the head. How neural crest cells generate the appropriate cell types for distinct head regions over time remains unresolved. Here we profile RNA expression scRNAseq and chromatin accessibility snATACseq of the zebrafish cranial neural crest lineage at single cell resolution from embryos to adults. Overall design: To recover the cell heterogeneity and lineage information in the span of a life time of a fish we collected the converted cells from embryonic stages 1.5 2 dpf larval stage 3 5 and 14 dpf juvenile stage 60 dpf to adult stage 150 or 210 dpf. We used a cranial neural crest converted zebrafish line 28.5Sox10:Cre;bactin:BFP to DsRed to permanantly convert and label the CNCC derived cells. The converted cells were collected and subjected to single cell sequencing for both their transcriptome and open chromatin region using Chromium platform of 10X Genomic. For biological and technical control we include replicates for both scRNAseq and snATACseq at various stages. We include an additional line fli1a:eGFP/sox10:dsRed for a biological and positive control of CNCC of 1.5 dpf sample.   pubmed:35013168   scRNAseq Sox10 Cre bact BtR 1.5dpf rep 1 GSM5402428   tissue:Cranial neural crest derived cells|cell type:Cranial neural crest derived cells|transgene1:TgMmu.Sox10 Mmu.Fos:Crezf384|transgene2:Tgactab2:loxP BFP STOP loxP dsRed|developmental stage:1.5 dpf|facs markers:Zombie / dsRed+ scRNAseq Sox10 Cre bact BtR 1.5dpf rep 1 For scRNAseq libraries Cellranger v3.0.0 10X Genomics was used for demultiplexing alignment and raw count matrix generation. The alignment was performed against zebrafish genome index built with GRCz11.fa and GRCz11.98.gtf. For snATACseq libraries Cellranger ATAC v1.2.0 10X Genomics was used for alignment against zebrafish genome index built with GRCz11.fa JASPAR2020 and GRCz11.98.gtf peak calling and peak by cell count matrix generation with default parameters. QC step for the library was performed along with the Cellranger or Cellranger ATAC alignment process. We performed a second round of peak calling for our snATACseq data using package Snaptools and SnapATAC. We first removed cell debris low quality cells and cell duplicates by setting cutoffs based on percentage of reads in peaks > 30 for 60 dpf > 45 for 210 dpf and > 50 for the rest and fragment number within peaks 5 000 – 30 000 for 5 dpf 1 000 – 11 000 for 14 dpf and 1 000 – 20 000 for the rest. To  recover every aligned fragment we binned the genome into 5 kb sections and constructed the bin by cell matrices bmats for each library by Snaptools from the positional sorted bam files generated by cellranger atac. The cells were filtered dimensionally reduced by diffusion map and clustered with inputs of the first 34 dimensions followed the SnapATAC vignette. The specific peaks were called for each cluster by the wrapped MACS2 function in SnapATAC with parameter gsize = 1.5e9 shift = 100 ext = 200 and qval = 5e 2. The finalized and refined peak profile was derived by collapsing and merging all 175 individual peak files to about 450K peaks. The count matrices of both scRNAseq and snATACseq data were analyzed by R package Seurat and Signac. The count matrices of each sample were aggregated if there is any replicate. For scRNAseq data the matrices are normalized NormalizeData and scaled for the top 2 000 variable genes FindVariableFeatures and ScaleData. The scaled matrices were dimensional reduced to 50 principal components 60 component… Cranial neural crest derived cells   Dissected heads from converted Sox10:cre; bactin:loxP eGFP loxP DsRed fish were incubated in fresh Ringer’s solution 5 10 min followed by mechanical and enzymatic dissociation by pipetting every 5 minutes in protease solution 0.25% trypsin Life Technologies 15090 046 1 mM EDTA and 400 mg/ml Collagenase D Sigma 11088882001 in PBS and incubated at 28.5°C for 20 30 minutes or until full dissociation. Reaction was stopped by 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted 2000 rpm 5 minute 4 °C and resuspended in suspension media 1% FBS 0.8 mM CaCl2 50 U/ml penicillin and 0.05 mg/ml streptomycin Sigma Aldrich St. Louis MO in phenol red free Leibovitz’s L15 medium Life Technologies twice. Final volumes of 500 µl resuspended cells were placed on ice and sorted by fluorescence activated cell sorting FACS to isolate live cells that excluded the cytoplasmic stain Zombie green BioLegend 423111 or the nuclear stain DAPI. Live cells were sorted into PBS solution containing 0.04% BSA and loaded to 10X Genomics microfluidic chips. The version 2 of Chromium Single Cell three prime Reagent Kits was used for RNA extraction. For snATACseq library construction we used the same cell dissociation and sorting protocol as for scRNAseq with isolation of live cells that excluded the cytoplasmic stain Zombie green product information. Nuclei isolation was performed per manufacturer’s instructions 10X Genomic protocol CG000169. Cells were incubated with lysis buffer on ice for 90 second followed by integrity check of nuclei under fluorescence microscope with DAPI before library synthesis. For scRNAseq the cell lysis polyA pull down tagging with cell barcode and RNA:DNA hybrid synthesis were performed in the GEMs per manufacturer's instruction. GEMs containing barcoded single cell cDNA were lysis for further fragmentation and ligation of illumina P5 and P7 ends. Libraries were sequenced to depths of at least 1 000 000 reads per cell for each library. For snATACseq the open chroma… The Institutional Animal Care and Use Committee of the University of Southern California approved all animal experiments Protocol 20771. Zebrafish embryos Danio rerio were raised in embryo media at 28.5°C. For adults in the institute vivarium according to Protocol 20771. cell type:Cranial neural crest derived cells|transgene1:TgMmu.Sox10 Mmu.Fos:Crezf384|transgene2:Tgactab2:loxP BFP STOP loxP dsRed|developmental stage:1.5 dpf|facs markers:Zombie / dsRed+ GSM5402428 GSM5402428: scRNAseq Sox10 Cre bact BtR 1.5dpf rep 1; Danio rerio; RNA Seq GSM5402428   1 Dissected heads from converted Sox10:cre; bactin:loxP eGFP loxP DsRed fish were incubated in fresh Ringer's solution 5 10 min followed by mechanical and enzymatic dissociation by pipetting every 5 minutes in protease solution 0.25% trypsin Life Technologies 15090 046 1 mM EDTA and 400 mg/ml Collagenase D Sigma 11088882001 in PBS and incubated at 28.5°C for 20 30 minutes or until full dissociation. Reaction was stopped by 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted 2000 rpm 5 minute 4 °C and resuspended in suspension media 1% FBS 0.8 mM CaCl2 50 U/ml penicillin and 0.05 mg/ml streptomycin Sigma Aldrich St. Louis MO in phenol red free Leibovitz's L15 medium Life Technologies twice. Final volumes of 500 µl resuspended cells were placed on ice and sorted by fluorescence activated cell sorting FACS to isolate live cells that excluded the cytoplasmic stain Zombie green BioLegend 423111 or the nuclear stain DAPI. Live cells were sorted into PBS solution containing 0.04% BSA and loaded to 10X Genomics microfluidic chips. The version 2 of Chromium Single Cell three prime Reagent Kits was used for RNA extraction. For snATACseq library construction we used the same cell dissociation and sorting protocol as for scRNAseq with isolation of live cells that excluded the cytoplasmic stain Zombie green product information. Nuclei isolation was performed per manufacturer's instructions 10X Genomic protocol CG000169. Cells were incubated with lysis buffer on ice for 90 second followed by integrity check of nuclei under fluorescence microscope with DAPI before library synthesis. For scRNAseq the cell lysis polyA pull down tagging with cell barcode and RNA:DNA hybrid synthesis were performed in the GEMs per manufacturer's instruction. GEMs containing barcoded single cell cDNA were lysis for further fragmentation and ligation of illumina P5 and P7 ends. Libraries were sequenced to depths of at least 1 000 000 reads per cell for each library. For snATACseq the open chroma… GEO Accession:GSM5402428 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 550   SRP325759     scRNAseq_Sox10_Cre_bact_BtR_1.5dpf_rep_1_S1_L001_R1_001.fastq.gz scRNAseq_Sox10_Cre_bact_BtR_1.5dpf_rep_1_S1_L001_R2_001.fastq.gz fastq fastq 12664163429.0 85909948.0 GSM5402428 r1 0:27 1:120.41 A:3416898693;C:2781527625;G:3137817240;T:3313932607;N:13987264 27 120     3416898693 2781527625 3137817240 3313932607 13987264 SRX11237256 SRS9283130 SRA1250944 GEO Crump Lab, Stem Cell, USC 2 0.00651 0.95378 0.00122 0.09059 0.98679 0.8342 0.53698 0.49652 27 120 T B sc-like readlen illumina nextseq unknown poly_a unknown sc single_cell_droplet 10x   United States 2021-06-27 Pharyngula Embryo Brain Nervous System
65109 65109 SRR14923951 SRX11237256 SRS9283130 SRP325759 PRJNA741770 Single cell profiling of cranial neural crest diversification across a vertebrate lifetime GSE178969 Other The cranial neural crest CNC is a vertebrate specific population that generates a huge diversity of derivatives including the bulk of the connective and skeletal tissues of the head. How neural crest cells generate the appropriate cell types for distinct head regions over time remains unresolved. Here we profile RNA expression scRNAseq and chromatin accessibility snATACseq of the zebrafish cranial neural crest lineage at single cell resolution from embryos to adults. Overall design: To recover the cell heterogeneity and lineage information in the span of a life time of a fish we collected the converted cells from embryonic stages 1.5 2 dpf larval stage 3 5 and 14 dpf juvenile stage 60 dpf to adult stage 150 or 210 dpf. We used a cranial neural crest converted zebrafish line 28.5Sox10:Cre;bactin:BFP to DsRed to permanantly convert and label the CNCC derived cells. The converted cells were collected and subjected to single cell sequencing for both their transcriptome and open chromatin region using Chromium platform of 10X Genomic. For biological and technical control we include replicates for both scRNAseq and snATACseq at various stages. We include an additional line fli1a:eGFP/sox10:dsRed for a biological and positive control of CNCC of 1.5 dpf sample.   pubmed:35013168   scRNAseq Sox10 Cre bact BtR 1.5dpf rep 1 GSM5402428   tissue:Cranial neural crest derived cells|cell type:Cranial neural crest derived cells|transgene1:TgMmu.Sox10 Mmu.Fos:Crezf384|transgene2:Tgactab2:loxP BFP STOP loxP dsRed|developmental stage:1.5 dpf|facs markers:Zombie / dsRed+ scRNAseq Sox10 Cre bact BtR 1.5dpf rep 1 For scRNAseq libraries Cellranger v3.0.0 10X Genomics was used for demultiplexing alignment and raw count matrix generation. The alignment was performed against zebrafish genome index built with GRCz11.fa and GRCz11.98.gtf. For snATACseq libraries Cellranger ATAC v1.2.0 10X Genomics was used for alignment against zebrafish genome index built with GRCz11.fa JASPAR2020 and GRCz11.98.gtf peak calling and peak by cell count matrix generation with default parameters. QC step for the library was performed along with the Cellranger or Cellranger ATAC alignment process. We performed a second round of peak calling for our snATACseq data using package Snaptools and SnapATAC. We first removed cell debris low quality cells and cell duplicates by setting cutoffs based on percentage of reads in peaks > 30 for 60 dpf > 45 for 210 dpf and > 50 for the rest and fragment number within peaks 5 000 – 30 000 for 5 dpf 1 000 – 11 000 for 14 dpf and 1 000 – 20 000 for the rest. To  recover every aligned fragment we binned the genome into 5 kb sections and constructed the bin by cell matrices bmats for each library by Snaptools from the positional sorted bam files generated by cellranger atac. The cells were filtered dimensionally reduced by diffusion map and clustered with inputs of the first 34 dimensions followed the SnapATAC vignette. The specific peaks were called for each cluster by the wrapped MACS2 function in SnapATAC with parameter gsize = 1.5e9 shift = 100 ext = 200 and qval = 5e 2. The finalized and refined peak profile was derived by collapsing and merging all 175 individual peak files to about 450K peaks. The count matrices of both scRNAseq and snATACseq data were analyzed by R package Seurat and Signac. The count matrices of each sample were aggregated if there is any replicate. For scRNAseq data the matrices are normalized NormalizeData and scaled for the top 2 000 variable genes FindVariableFeatures and ScaleData. The scaled matrices were dimensional reduced to 50 principal components 60 component… Cranial neural crest derived cells   Dissected heads from converted Sox10:cre; bactin:loxP eGFP loxP DsRed fish were incubated in fresh Ringer’s solution 5 10 min followed by mechanical and enzymatic dissociation by pipetting every 5 minutes in protease solution 0.25% trypsin Life Technologies 15090 046 1 mM EDTA and 400 mg/ml Collagenase D Sigma 11088882001 in PBS and incubated at 28.5°C for 20 30 minutes or until full dissociation. Reaction was stopped by 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted 2000 rpm 5 minute 4 °C and resuspended in suspension media 1% FBS 0.8 mM CaCl2 50 U/ml penicillin and 0.05 mg/ml streptomycin Sigma Aldrich St. Louis MO in phenol red free Leibovitz’s L15 medium Life Technologies twice. Final volumes of 500 µl resuspended cells were placed on ice and sorted by fluorescence activated cell sorting FACS to isolate live cells that excluded the cytoplasmic stain Zombie green BioLegend 423111 or the nuclear stain DAPI. Live cells were sorted into PBS solution containing 0.04% BSA and loaded to 10X Genomics microfluidic chips. The version 2 of Chromium Single Cell three prime Reagent Kits was used for RNA extraction. For snATACseq library construction we used the same cell dissociation and sorting protocol as for scRNAseq with isolation of live cells that excluded the cytoplasmic stain Zombie green product information. Nuclei isolation was performed per manufacturer’s instructions 10X Genomic protocol CG000169. Cells were incubated with lysis buffer on ice for 90 second followed by integrity check of nuclei under fluorescence microscope with DAPI before library synthesis. For scRNAseq the cell lysis polyA pull down tagging with cell barcode and RNA:DNA hybrid synthesis were performed in the GEMs per manufacturer's instruction. GEMs containing barcoded single cell cDNA were lysis for further fragmentation and ligation of illumina P5 and P7 ends. Libraries were sequenced to depths of at least 1 000 000 reads per cell for each library. For snATACseq the open chroma… The Institutional Animal Care and Use Committee of the University of Southern California approved all animal experiments Protocol 20771. Zebrafish embryos Danio rerio were raised in embryo media at 28.5°C. For adults in the institute vivarium according to Protocol 20771. cell type:Cranial neural crest derived cells|transgene1:TgMmu.Sox10 Mmu.Fos:Crezf384|transgene2:Tgactab2:loxP BFP STOP loxP dsRed|developmental stage:1.5 dpf|facs markers:Zombie / dsRed+ GSM5402428 GSM5402428: scRNAseq Sox10 Cre bact BtR 1.5dpf rep 1; Danio rerio; RNA Seq GSM5402428   1 Dissected heads from converted Sox10:cre; bactin:loxP eGFP loxP DsRed fish were incubated in fresh Ringer's solution 5 10 min followed by mechanical and enzymatic dissociation by pipetting every 5 minutes in protease solution 0.25% trypsin Life Technologies 15090 046 1 mM EDTA and 400 mg/ml Collagenase D Sigma 11088882001 in PBS and incubated at 28.5°C for 20 30 minutes or until full dissociation. Reaction was stopped by 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted 2000 rpm 5 minute 4 °C and resuspended in suspension media 1% FBS 0.8 mM CaCl2 50 U/ml penicillin and 0.05 mg/ml streptomycin Sigma Aldrich St. Louis MO in phenol red free Leibovitz's L15 medium Life Technologies twice. Final volumes of 500 µl resuspended cells were placed on ice and sorted by fluorescence activated cell sorting FACS to isolate live cells that excluded the cytoplasmic stain Zombie green BioLegend 423111 or the nuclear stain DAPI. Live cells were sorted into PBS solution containing 0.04% BSA and loaded to 10X Genomics microfluidic chips. The version 2 of Chromium Single Cell three prime Reagent Kits was used for RNA extraction. For snATACseq library construction we used the same cell dissociation and sorting protocol as for scRNAseq with isolation of live cells that excluded the cytoplasmic stain Zombie green product information. Nuclei isolation was performed per manufacturer's instructions 10X Genomic protocol CG000169. Cells were incubated with lysis buffer on ice for 90 second followed by integrity check of nuclei under fluorescence microscope with DAPI before library synthesis. For scRNAseq the cell lysis polyA pull down tagging with cell barcode and RNA:DNA hybrid synthesis were performed in the GEMs per manufacturer's instruction. GEMs containing barcoded single cell cDNA were lysis for further fragmentation and ligation of illumina P5 and P7 ends. Libraries were sequenced to depths of at least 1 000 000 reads per cell for each library. For snATACseq the open chroma… GEO Accession:GSM5402428 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 550   SRP325759     scRNAseq_Sox10_Cre_bact_BtR_1.5dpf_rep_1_S2_L001_R1_001.fastq.gz scRNAseq_Sox10_Cre_bact_BtR_1.5dpf_rep_1_S2_L001_R2_001.fastq.gz fastq fastq 14599490166.0 99034572.0 GSM5402428 r2 0:27 1:120.42 A:3933113520;C:3208819901;G:3626379482;T:3815145641;N:16031622 27 120     3933113520 3208819901 3626379482 3815145641 16031622 SRX11237256 SRS9283130 SRA1250944 GEO Crump Lab, Stem Cell, USC 2 0.00646 0.95432 0.00116 0.08936 0.98695 0.83309 0.54325 0.49157 27 120 T B sc-like readlen illumina nextseq unknown poly_a unknown sc single_cell_droplet 10x   United States 2021-06-27 Pharyngula Embryo Brain Nervous System
65110 65110 SRR14923952 SRX11237256 SRS9283130 SRP325759 PRJNA741770 Single cell profiling of cranial neural crest diversification across a vertebrate lifetime GSE178969 Other The cranial neural crest CNC is a vertebrate specific population that generates a huge diversity of derivatives including the bulk of the connective and skeletal tissues of the head. How neural crest cells generate the appropriate cell types for distinct head regions over time remains unresolved. Here we profile RNA expression scRNAseq and chromatin accessibility snATACseq of the zebrafish cranial neural crest lineage at single cell resolution from embryos to adults. Overall design: To recover the cell heterogeneity and lineage information in the span of a life time of a fish we collected the converted cells from embryonic stages 1.5 2 dpf larval stage 3 5 and 14 dpf juvenile stage 60 dpf to adult stage 150 or 210 dpf. We used a cranial neural crest converted zebrafish line 28.5Sox10:Cre;bactin:BFP to DsRed to permanantly convert and label the CNCC derived cells. The converted cells were collected and subjected to single cell sequencing for both their transcriptome and open chromatin region using Chromium platform of 10X Genomic. For biological and technical control we include replicates for both scRNAseq and snATACseq at various stages. We include an additional line fli1a:eGFP/sox10:dsRed for a biological and positive control of CNCC of 1.5 dpf sample.   pubmed:35013168   scRNAseq Sox10 Cre bact BtR 1.5dpf rep 1 GSM5402428   tissue:Cranial neural crest derived cells|cell type:Cranial neural crest derived cells|transgene1:TgMmu.Sox10 Mmu.Fos:Crezf384|transgene2:Tgactab2:loxP BFP STOP loxP dsRed|developmental stage:1.5 dpf|facs markers:Zombie / dsRed+ scRNAseq Sox10 Cre bact BtR 1.5dpf rep 1 For scRNAseq libraries Cellranger v3.0.0 10X Genomics was used for demultiplexing alignment and raw count matrix generation. The alignment was performed against zebrafish genome index built with GRCz11.fa and GRCz11.98.gtf. For snATACseq libraries Cellranger ATAC v1.2.0 10X Genomics was used for alignment against zebrafish genome index built with GRCz11.fa JASPAR2020 and GRCz11.98.gtf peak calling and peak by cell count matrix generation with default parameters. QC step for the library was performed along with the Cellranger or Cellranger ATAC alignment process. We performed a second round of peak calling for our snATACseq data using package Snaptools and SnapATAC. We first removed cell debris low quality cells and cell duplicates by setting cutoffs based on percentage of reads in peaks > 30 for 60 dpf > 45 for 210 dpf and > 50 for the rest and fragment number within peaks 5 000 – 30 000 for 5 dpf 1 000 – 11 000 for 14 dpf and 1 000 – 20 000 for the rest. To  recover every aligned fragment we binned the genome into 5 kb sections and constructed the bin by cell matrices bmats for each library by Snaptools from the positional sorted bam files generated by cellranger atac. The cells were filtered dimensionally reduced by diffusion map and clustered with inputs of the first 34 dimensions followed the SnapATAC vignette. The specific peaks were called for each cluster by the wrapped MACS2 function in SnapATAC with parameter gsize = 1.5e9 shift = 100 ext = 200 and qval = 5e 2. The finalized and refined peak profile was derived by collapsing and merging all 175 individual peak files to about 450K peaks. The count matrices of both scRNAseq and snATACseq data were analyzed by R package Seurat and Signac. The count matrices of each sample were aggregated if there is any replicate. For scRNAseq data the matrices are normalized NormalizeData and scaled for the top 2 000 variable genes FindVariableFeatures and ScaleData. The scaled matrices were dimensional reduced to 50 principal components 60 component… Cranial neural crest derived cells   Dissected heads from converted Sox10:cre; bactin:loxP eGFP loxP DsRed fish were incubated in fresh Ringer’s solution 5 10 min followed by mechanical and enzymatic dissociation by pipetting every 5 minutes in protease solution 0.25% trypsin Life Technologies 15090 046 1 mM EDTA and 400 mg/ml Collagenase D Sigma 11088882001 in PBS and incubated at 28.5°C for 20 30 minutes or until full dissociation. Reaction was stopped by 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted 2000 rpm 5 minute 4 °C and resuspended in suspension media 1% FBS 0.8 mM CaCl2 50 U/ml penicillin and 0.05 mg/ml streptomycin Sigma Aldrich St. Louis MO in phenol red free Leibovitz’s L15 medium Life Technologies twice. Final volumes of 500 µl resuspended cells were placed on ice and sorted by fluorescence activated cell sorting FACS to isolate live cells that excluded the cytoplasmic stain Zombie green BioLegend 423111 or the nuclear stain DAPI. Live cells were sorted into PBS solution containing 0.04% BSA and loaded to 10X Genomics microfluidic chips. The version 2 of Chromium Single Cell three prime Reagent Kits was used for RNA extraction. For snATACseq library construction we used the same cell dissociation and sorting protocol as for scRNAseq with isolation of live cells that excluded the cytoplasmic stain Zombie green product information. Nuclei isolation was performed per manufacturer’s instructions 10X Genomic protocol CG000169. Cells were incubated with lysis buffer on ice for 90 second followed by integrity check of nuclei under fluorescence microscope with DAPI before library synthesis. For scRNAseq the cell lysis polyA pull down tagging with cell barcode and RNA:DNA hybrid synthesis were performed in the GEMs per manufacturer's instruction. GEMs containing barcoded single cell cDNA were lysis for further fragmentation and ligation of illumina P5 and P7 ends. Libraries were sequenced to depths of at least 1 000 000 reads per cell for each library. For snATACseq the open chroma… The Institutional Animal Care and Use Committee of the University of Southern California approved all animal experiments Protocol 20771. Zebrafish embryos Danio rerio were raised in embryo media at 28.5°C. For adults in the institute vivarium according to Protocol 20771. cell type:Cranial neural crest derived cells|transgene1:TgMmu.Sox10 Mmu.Fos:Crezf384|transgene2:Tgactab2:loxP BFP STOP loxP dsRed|developmental stage:1.5 dpf|facs markers:Zombie / dsRed+ GSM5402428 GSM5402428: scRNAseq Sox10 Cre bact BtR 1.5dpf rep 1; Danio rerio; RNA Seq GSM5402428   1 Dissected heads from converted Sox10:cre; bactin:loxP eGFP loxP DsRed fish were incubated in fresh Ringer's solution 5 10 min followed by mechanical and enzymatic dissociation by pipetting every 5 minutes in protease solution 0.25% trypsin Life Technologies 15090 046 1 mM EDTA and 400 mg/ml Collagenase D Sigma 11088882001 in PBS and incubated at 28.5°C for 20 30 minutes or until full dissociation. Reaction was stopped by 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted 2000 rpm 5 minute 4 °C and resuspended in suspension media 1% FBS 0.8 mM CaCl2 50 U/ml penicillin and 0.05 mg/ml streptomycin Sigma Aldrich St. Louis MO in phenol red free Leibovitz's L15 medium Life Technologies twice. Final volumes of 500 µl resuspended cells were placed on ice and sorted by fluorescence activated cell sorting FACS to isolate live cells that excluded the cytoplasmic stain Zombie green BioLegend 423111 or the nuclear stain DAPI. Live cells were sorted into PBS solution containing 0.04% BSA and loaded to 10X Genomics microfluidic chips. The version 2 of Chromium Single Cell three prime Reagent Kits was used for RNA extraction. For snATACseq library construction we used the same cell dissociation and sorting protocol as for scRNAseq with isolation of live cells that excluded the cytoplasmic stain Zombie green product information. Nuclei isolation was performed per manufacturer's instructions 10X Genomic protocol CG000169. Cells were incubated with lysis buffer on ice for 90 second followed by integrity check of nuclei under fluorescence microscope with DAPI before library synthesis. For scRNAseq the cell lysis polyA pull down tagging with cell barcode and RNA:DNA hybrid synthesis were performed in the GEMs per manufacturer's instruction. GEMs containing barcoded single cell cDNA were lysis for further fragmentation and ligation of illumina P5 and P7 ends. Libraries were sequenced to depths of at least 1 000 000 reads per cell for each library. For snATACseq the open chroma… GEO Accession:GSM5402428 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 550   SRP325759     scRNAseq_Sox10_Cre_bact_BtR_1.5dpf_rep_1_S3_L001_R1_001.fastq.gz scRNAseq_Sox10_Cre_bact_BtR_1.5dpf_rep_1_S3_L001_R2_001.fastq.gz fastq fastq 12846018715.0 87140553.0 GSM5402428 r3 0:27 1:120.42 A:3466641763;C:2821876779;G:3180013901;T:3363481208;N:14005064 27 120     3466641763 2821876779 3180013901 3363481208 14005064 SRX11237256 SRS9283130 SRA1250944 GEO Crump Lab, Stem Cell, USC 2 0.00647 0.95541 0.00109 0.08934 0.98612 0.83268 0.51494 0.49096 27 121 T B sc-like readlen illumina nextseq unknown poly_a unknown sc single_cell_droplet 10x   United States 2021-06-27 Pharyngula Embryo Brain Nervous System
65111 65111 SRR14923953 SRX11237256 SRS9283130 SRP325759 PRJNA741770 Single cell profiling of cranial neural crest diversification across a vertebrate lifetime GSE178969 Other The cranial neural crest CNC is a vertebrate specific population that generates a huge diversity of derivatives including the bulk of the connective and skeletal tissues of the head. How neural crest cells generate the appropriate cell types for distinct head regions over time remains unresolved. Here we profile RNA expression scRNAseq and chromatin accessibility snATACseq of the zebrafish cranial neural crest lineage at single cell resolution from embryos to adults. Overall design: To recover the cell heterogeneity and lineage information in the span of a life time of a fish we collected the converted cells from embryonic stages 1.5 2 dpf larval stage 3 5 and 14 dpf juvenile stage 60 dpf to adult stage 150 or 210 dpf. We used a cranial neural crest converted zebrafish line 28.5Sox10:Cre;bactin:BFP to DsRed to permanantly convert and label the CNCC derived cells. The converted cells were collected and subjected to single cell sequencing for both their transcriptome and open chromatin region using Chromium platform of 10X Genomic. For biological and technical control we include replicates for both scRNAseq and snATACseq at various stages. We include an additional line fli1a:eGFP/sox10:dsRed for a biological and positive control of CNCC of 1.5 dpf sample.   pubmed:35013168   scRNAseq Sox10 Cre bact BtR 1.5dpf rep 1 GSM5402428   tissue:Cranial neural crest derived cells|cell type:Cranial neural crest derived cells|transgene1:TgMmu.Sox10 Mmu.Fos:Crezf384|transgene2:Tgactab2:loxP BFP STOP loxP dsRed|developmental stage:1.5 dpf|facs markers:Zombie / dsRed+ scRNAseq Sox10 Cre bact BtR 1.5dpf rep 1 For scRNAseq libraries Cellranger v3.0.0 10X Genomics was used for demultiplexing alignment and raw count matrix generation. The alignment was performed against zebrafish genome index built with GRCz11.fa and GRCz11.98.gtf. For snATACseq libraries Cellranger ATAC v1.2.0 10X Genomics was used for alignment against zebrafish genome index built with GRCz11.fa JASPAR2020 and GRCz11.98.gtf peak calling and peak by cell count matrix generation with default parameters. QC step for the library was performed along with the Cellranger or Cellranger ATAC alignment process. We performed a second round of peak calling for our snATACseq data using package Snaptools and SnapATAC. We first removed cell debris low quality cells and cell duplicates by setting cutoffs based on percentage of reads in peaks > 30 for 60 dpf > 45 for 210 dpf and > 50 for the rest and fragment number within peaks 5 000 – 30 000 for 5 dpf 1 000 – 11 000 for 14 dpf and 1 000 – 20 000 for the rest. To  recover every aligned fragment we binned the genome into 5 kb sections and constructed the bin by cell matrices bmats for each library by Snaptools from the positional sorted bam files generated by cellranger atac. The cells were filtered dimensionally reduced by diffusion map and clustered with inputs of the first 34 dimensions followed the SnapATAC vignette. The specific peaks were called for each cluster by the wrapped MACS2 function in SnapATAC with parameter gsize = 1.5e9 shift = 100 ext = 200 and qval = 5e 2. The finalized and refined peak profile was derived by collapsing and merging all 175 individual peak files to about 450K peaks. The count matrices of both scRNAseq and snATACseq data were analyzed by R package Seurat and Signac. The count matrices of each sample were aggregated if there is any replicate. For scRNAseq data the matrices are normalized NormalizeData and scaled for the top 2 000 variable genes FindVariableFeatures and ScaleData. The scaled matrices were dimensional reduced to 50 principal components 60 component… Cranial neural crest derived cells   Dissected heads from converted Sox10:cre; bactin:loxP eGFP loxP DsRed fish were incubated in fresh Ringer’s solution 5 10 min followed by mechanical and enzymatic dissociation by pipetting every 5 minutes in protease solution 0.25% trypsin Life Technologies 15090 046 1 mM EDTA and 400 mg/ml Collagenase D Sigma 11088882001 in PBS and incubated at 28.5°C for 20 30 minutes or until full dissociation. Reaction was stopped by 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted 2000 rpm 5 minute 4 °C and resuspended in suspension media 1% FBS 0.8 mM CaCl2 50 U/ml penicillin and 0.05 mg/ml streptomycin Sigma Aldrich St. Louis MO in phenol red free Leibovitz’s L15 medium Life Technologies twice. Final volumes of 500 µl resuspended cells were placed on ice and sorted by fluorescence activated cell sorting FACS to isolate live cells that excluded the cytoplasmic stain Zombie green BioLegend 423111 or the nuclear stain DAPI. Live cells were sorted into PBS solution containing 0.04% BSA and loaded to 10X Genomics microfluidic chips. The version 2 of Chromium Single Cell three prime Reagent Kits was used for RNA extraction. For snATACseq library construction we used the same cell dissociation and sorting protocol as for scRNAseq with isolation of live cells that excluded the cytoplasmic stain Zombie green product information. Nuclei isolation was performed per manufacturer’s instructions 10X Genomic protocol CG000169. Cells were incubated with lysis buffer on ice for 90 second followed by integrity check of nuclei under fluorescence microscope with DAPI before library synthesis. For scRNAseq the cell lysis polyA pull down tagging with cell barcode and RNA:DNA hybrid synthesis were performed in the GEMs per manufacturer's instruction. GEMs containing barcoded single cell cDNA were lysis for further fragmentation and ligation of illumina P5 and P7 ends. Libraries were sequenced to depths of at least 1 000 000 reads per cell for each library. For snATACseq the open chroma… The Institutional Animal Care and Use Committee of the University of Southern California approved all animal experiments Protocol 20771. Zebrafish embryos Danio rerio were raised in embryo media at 28.5°C. For adults in the institute vivarium according to Protocol 20771. cell type:Cranial neural crest derived cells|transgene1:TgMmu.Sox10 Mmu.Fos:Crezf384|transgene2:Tgactab2:loxP BFP STOP loxP dsRed|developmental stage:1.5 dpf|facs markers:Zombie / dsRed+ GSM5402428 GSM5402428: scRNAseq Sox10 Cre bact BtR 1.5dpf rep 1; Danio rerio; RNA Seq GSM5402428   1 Dissected heads from converted Sox10:cre; bactin:loxP eGFP loxP DsRed fish were incubated in fresh Ringer's solution 5 10 min followed by mechanical and enzymatic dissociation by pipetting every 5 minutes in protease solution 0.25% trypsin Life Technologies 15090 046 1 mM EDTA and 400 mg/ml Collagenase D Sigma 11088882001 in PBS and incubated at 28.5°C for 20 30 minutes or until full dissociation. Reaction was stopped by 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted 2000 rpm 5 minute 4 °C and resuspended in suspension media 1% FBS 0.8 mM CaCl2 50 U/ml penicillin and 0.05 mg/ml streptomycin Sigma Aldrich St. Louis MO in phenol red free Leibovitz's L15 medium Life Technologies twice. Final volumes of 500 µl resuspended cells were placed on ice and sorted by fluorescence activated cell sorting FACS to isolate live cells that excluded the cytoplasmic stain Zombie green BioLegend 423111 or the nuclear stain DAPI. Live cells were sorted into PBS solution containing 0.04% BSA and loaded to 10X Genomics microfluidic chips. The version 2 of Chromium Single Cell three prime Reagent Kits was used for RNA extraction. For snATACseq library construction we used the same cell dissociation and sorting protocol as for scRNAseq with isolation of live cells that excluded the cytoplasmic stain Zombie green product information. Nuclei isolation was performed per manufacturer's instructions 10X Genomic protocol CG000169. Cells were incubated with lysis buffer on ice for 90 second followed by integrity check of nuclei under fluorescence microscope with DAPI before library synthesis. For scRNAseq the cell lysis polyA pull down tagging with cell barcode and RNA:DNA hybrid synthesis were performed in the GEMs per manufacturer's instruction. GEMs containing barcoded single cell cDNA were lysis for further fragmentation and ligation of illumina P5 and P7 ends. Libraries were sequenced to depths of at least 1 000 000 reads per cell for each library. For snATACseq the open chroma… GEO Accession:GSM5402428 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 550   SRP325759     scRNAseq_Sox10_Cre_bact_BtR_1.5dpf_rep_1_S4_L001_R1_001.fastq.gz scRNAseq_Sox10_Cre_bact_BtR_1.5dpf_rep_1_S4_L001_R2_001.fastq.gz fastq fastq 8108614905.0 55005025.0 GSM5402428 r4 0:27 1:120.42 A:2194580999;C:1780742152;G:1996005251;T:2128372584;N:8913919 27 120     2194580999 1780742152 1996005251 2128372584 8913919 SRX11237256 SRS9283130 SRA1250944 GEO Crump Lab, Stem Cell, USC 2 0.00658 0.95583 0.00117 0.09133 0.98573 0.83177 0.52554 0.49175 27 121 T B sc-like readlen illumina nextseq unknown poly_a unknown sc single_cell_droplet 10x   United States 2021-06-27 Pharyngula Embryo Brain Nervous System
65478 65478 SRR15321085 SRX11625563 SRS9659654 SRP330794 PRJNA751418 Epigenetic dynamics shaping melanophore and iridophore cell fate in zebrafish GSE181287 Other We charted the global changes in the epigenetic landscape including DNA methylation and chromatin accessibility during neural crest differentiation into melanophores and iridophores in zebrafish to identify epigenetic determinants shaping cell type specific gene expression. Motif enrichment in the epigenetically dynamic regions revealed putative transcription factors that might be responsible for driving pigment cell identity. Through this effort in the relatively uncharacterized iridophores we validate alx4a as a necessary and sufficient transcription factor for iridophore differentiation and present evidence on alx4a's potential regulatory role in guanine synthesis pathway. Overall design: ATAC seq RNA Seq WGBS were generated for 15 somite NCC 24 hpf NCC 4 dpf 5 dpf Melanophore and 4 dpf 5 dpf Iridophore cells from zebrafish.   pubmed:34607603   RNA seq 24hpf NCC rep2 GSM5494235   tissue:Neural crest cells|genotype:TgcrestinA:EGFP|developmental stage:24 hpf|cell type:Neural crest cells RNA seq 24hpf NCC rep2 All libraries were sequenced on Illumina NextSeq 500 platforms. Reads were adapter trimmed with cutadapt. RNA seq reads were aligned to danRer10 genome using STAR. WGBS reads were aligned to danRer10 using bismark with standard parameters. omniATAC seq reads were aligned to danRer10 using bwa mem. Genome build: danRer10 Supplementary files format and content: bigWig bedGraph and text files. Neural crest cells TgcrestinA:EGFP embryos at designated biological time points were dechorionated with Pronase rinsed with egg water to remove the chorion and collected into 1.5ml Eppendorf tubes on ice. 4 dpf 5 dpf mlphaj120 larvae were anesthetized with Tricane for 15 minutes and collected into 50ml conical tubes on ice. Single cells were dissociated from embryos using Gibco TrypLE Express enzyme solution. Neural crest GFP positive cells were sorted and collected on Beckman Couter MoFlo. Melanophore and iridophore were isolated using published protocol developed by the Johnson lab Higdon et al. 2013. Genomic DNA for WGBS was purified from NCCs and pigment cells via phenol chloroform:isoamyl alcohol PCI extraction and ethanol precipitation method. RNA was collected using Trizol following manufacturer's recommendation. Published omniATAC seq protocol was followed to extract materials for ATAC seq. RNA seq libraries were then constructed with TruSeq RNA Library Prep Kit v2 Illumina RS 122 2001 following manufacturer’s instructions. gDNA was bisulfite treated using EZ DNA Methylation Direct kit Zymo D5020 and processed with TruSeq DNA Methylation Kit Illumina 15066014 to generate Illumina compatible WGBS libraries. Published omniATAC seq was followed to generate ATAC seq data.   genotype:TgcrestinA:EGFP|developmental stage:24 hpf|cell type:Neural crest cells GSM5494235 GSM5494235: RNA seq 24hpf NCC rep2; Danio rerio; RNA Seq GSM5494235   1 Single cells were dissociated from embryos using Gibco TrypLE Express enzyme solution. Neural crest GFP positive cells were sorted and collected on Beckman Couter MoFlo. Melanophore and iridophore were isolated using published protocol developed by the Johnson lab Higdon et al. 2013. Genomic DNA for WGBS was purified from NCCs and pigment cells via phenol chloroform:isoamyl alcohol PCI extraction and ethanol precipitation method. RNA was collected using Trizol following manufacturer's recommendation. Published omniATAC seq protocol was followed to extract materials for ATAC seq. RNA seq libraries were then constructed with TruSeq RNA Library Prep Kit v2 Illumina RS 122 2001 following manufacturer's instructions. gDNA was bisulfite treated using EZ DNA Methylation Direct kit Zymo D5020 and processed with TruSeq DNA Methylation Kit Illumina 15066014 to generate Illumina compatible WGBS libraries. Published omniATAC seq was followed to generate ATAC seq data. GEO Accession:GSM5494235 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP330794     RNA_24hpf_GFPpositive_Rep2_R1.fastq.gz RNA_24hpf_GFPpositive_Rep2_R2.fastq.gz fastq fastq 8176577448.0 54585464.0 GSM5494235 r1 0:74.90 1:74.90 A:1881023745;C:2211808195;G:2204838987;T:1878071057;N:835464 74 74     1881023745 2211808195 2204838987 1878071057 835464 SRX11625563 SRS9659654 SRA1268156 GEO Ting Wang Lab, Genetics, Washington University in St. Louis 2 0.95633 0.95564 0.02824 0.02744 0.76846 0.77206 0.50073 0.49727 75 75 B B biological fallback assumption illumina nextseq unknown cdna_unspecified trueseq bulk unknown unknown   United States 2021-08-01 Pharyngula Embryo Brain Nervous System
65479 65479 SRR15321084 SRX11625562 SRS9659653 SRP330794 PRJNA751418 Epigenetic dynamics shaping melanophore and iridophore cell fate in zebrafish GSE181287 Other We charted the global changes in the epigenetic landscape including DNA methylation and chromatin accessibility during neural crest differentiation into melanophores and iridophores in zebrafish to identify epigenetic determinants shaping cell type specific gene expression. Motif enrichment in the epigenetically dynamic regions revealed putative transcription factors that might be responsible for driving pigment cell identity. Through this effort in the relatively uncharacterized iridophores we validate alx4a as a necessary and sufficient transcription factor for iridophore differentiation and present evidence on alx4a's potential regulatory role in guanine synthesis pathway. Overall design: ATAC seq RNA Seq WGBS were generated for 15 somite NCC 24 hpf NCC 4 dpf 5 dpf Melanophore and 4 dpf 5 dpf Iridophore cells from zebrafish.   pubmed:34607603   RNA seq 24hpf NCC rep1 GSM5494234   tissue:Neural crest cells|genotype:TgcrestinA:EGFP|developmental stage:24 hpf|cell type:Neural crest cells RNA seq 24hpf NCC rep1 All libraries were sequenced on Illumina NextSeq 500 platforms. Reads were adapter trimmed with cutadapt. RNA seq reads were aligned to danRer10 genome using STAR. WGBS reads were aligned to danRer10 using bismark with standard parameters. omniATAC seq reads were aligned to danRer10 using bwa mem. Genome build: danRer10 Supplementary files format and content: bigWig bedGraph and text files. Neural crest cells TgcrestinA:EGFP embryos at designated biological time points were dechorionated with Pronase rinsed with egg water to remove the chorion and collected into 1.5ml Eppendorf tubes on ice. 4 dpf 5 dpf mlphaj120 larvae were anesthetized with Tricane for 15 minutes and collected into 50ml conical tubes on ice. Single cells were dissociated from embryos using Gibco TrypLE Express enzyme solution. Neural crest GFP positive cells were sorted and collected on Beckman Couter MoFlo. Melanophore and iridophore were isolated using published protocol developed by the Johnson lab Higdon et al. 2013. Genomic DNA for WGBS was purified from NCCs and pigment cells via phenol chloroform:isoamyl alcohol PCI extraction and ethanol precipitation method. RNA was collected using Trizol following manufacturer's recommendation. Published omniATAC seq protocol was followed to extract materials for ATAC seq. RNA seq libraries were then constructed with TruSeq RNA Library Prep Kit v2 Illumina RS 122 2001 following manufacturer’s instructions. gDNA was bisulfite treated using EZ DNA Methylation Direct kit Zymo D5020 and processed with TruSeq DNA Methylation Kit Illumina 15066014 to generate Illumina compatible WGBS libraries. Published omniATAC seq was followed to generate ATAC seq data.   genotype:TgcrestinA:EGFP|developmental stage:24 hpf|cell type:Neural crest cells GSM5494234 GSM5494234: RNA seq 24hpf NCC rep1; Danio rerio; RNA Seq GSM5494234   1 Single cells were dissociated from embryos using Gibco TrypLE Express enzyme solution. Neural crest GFP positive cells were sorted and collected on Beckman Couter MoFlo. Melanophore and iridophore were isolated using published protocol developed by the Johnson lab Higdon et al. 2013. Genomic DNA for WGBS was purified from NCCs and pigment cells via phenol chloroform:isoamyl alcohol PCI extraction and ethanol precipitation method. RNA was collected using Trizol following manufacturer's recommendation. Published omniATAC seq protocol was followed to extract materials for ATAC seq. RNA seq libraries were then constructed with TruSeq RNA Library Prep Kit v2 Illumina RS 122 2001 following manufacturer's instructions. gDNA was bisulfite treated using EZ DNA Methylation Direct kit Zymo D5020 and processed with TruSeq DNA Methylation Kit Illumina 15066014 to generate Illumina compatible WGBS libraries. Published omniATAC seq was followed to generate ATAC seq data. GEO Accession:GSM5494234 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP330794     RNA_24hpf_GFPpositive_Rep1_R1.fastq.gz RNA_24hpf_GFPpositive_Rep1_R2.fastq.gz fastq fastq 8541069754.0 57018853.0 GSM5494234 r1 0:74.90 1:74.90 A:1946972443;C:2324912704;G:2313298267;T:1955018508;N:867832 74 74     1946972443 2324912704 2313298267 1955018508 867832 SRX11625562 SRS9659653 SRA1268156 GEO Ting Wang Lab, Genetics, Washington University in St. Louis 2 0.95998 0.95963 0.02796 0.02758 0.76499 0.76816 0.48357 0.49514 75 75 B B biological fallback assumption illumina nextseq unknown cdna_unspecified trueseq bulk unknown unknown   United States 2021-08-01 Pharyngula Embryo Brain Nervous System
71455 71455 SRR21631158 SRX17631562 SRS15166365 SRP398129 PRJNA882122 Mutations in cdon and boc affect trunk neural crest cell migration and slow twitch muscle development in zebrafish GSE213728 Transcriptome Analysis Bulk RNA seq of isolated slow twtich muscle and neural crest cells from 24 hpf zebrafish. Overall design: Bulk RNA seq data from FAC sorted slow twitch muscle and neural crest cells isolated from trunks of 24 hpf zebrafish embryos. Trunks of embryos were manually dissected and cells were disassociated using Accumax. Embryos were doubly transgenic for tgsox10:mRFP transgene that labels neural crest cells and tgPACprdm1a:eGFP transgene that labels slow twitch muscle and muscle pioneer cells. Neural crest cells and slow twitch muscle cells were isolated by FACS on a MoFlow XDP100 prepared for stranded Illumina sequencing and sequenced on a NovaSeq600 PE 150bp. Gene expression summaries were produced using featurecounts subread package and DESeq2.       Slow twitch NCC tgsox10:mRFP Sample2 GSM6592892   source name:neural crest cells|tissue:neural crest cells|genotype:wildtype|treatment:n1|geo loc name:missing|collection date:missing Slow twitch NCC tgsox10:mRFP Sample2 Read aligment with STAR counts generated by featurecounts subread. Expression from DESeq2 using normTransform function Supplementary files format and content: tab delim text file Supplementary files format and content: tab delim text file neural crest cells For cyclopamine treated samples embryos were treated with 100uM cyclopamine from 50% epiboloy to 24hpf standard Illumina Kit for stranded RNAseq Embryos reared at 28C until 24hpf. tissue:neural crest cells|genotype:wildtype|treatment:n1 GSM6592892 GSM6592892: Slow twitch NCC tgsox10:mRFP Sample2; Danio rerio; RNA Seq GSM6592892 r1 GSM6592892 1 standard Illumina Kit for stranded RNAseq   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP398129   loader:fastq load.py Sample4_RFP_24hpf_S4_L002_R1_001.fastq.gz Sample4_RFP_24hpf_S4_L002_R2_001.fastq.gz fastq fastq 13884740524.0 45975962.0 GSM6592892 r1 0:151 1:151 A:3031916247;C:2738677707;G:5291000892;T:2821006628;N:2139050 151 151     3031916247 2738677707 5291000892 2821006628 2139050 SRX17631562 SRS15166365 SRA1501497 Lencer Laboratory, Department of Biology, Lafayette College Lencer Laboratory, Department of Biology, Lafayette College 2 0.90321 0.87636 0.09526 0.09316 0.77674 0.77885 0.52923 0.52674 151 151 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified trueseq bulk bulk bulk   United States 2022-09-19 Pharyngula 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");;