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3,113 rows where devstage_curation = "Larval" and tissue_curation_coarse = "Nervous System"

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technology 9

experiment.library_selection 8

tissue_curation 3

experiment.library_strategy 2

experiment.library_source 2

experiment.library_layout 2

tissue_curation_coarse 1

  • Nervous System · 3,113 ✖

experiment.platform 1

devstage_curation_coarse 1

devstage_curation 1

  • Larval · 3,113 ✖
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
101 101 DRR189403 DRX179868 DRS200418 DRP003977 PRJDB4470 Gene expression analysis of the zebrafish brain DRP003977 Other Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.       Telencephalon of adult zebrafrish 30 min post test session of 2 weeks memory test in non trace 2 Way Active Avoidance coditioning 3 SAMD00182246   sample name:CSUS Tel 30 2w memory 3|genotype:wild type|tissue:brain                 Illumina HiSeq 3000 sequencing of SAMD00182246 DRX179868 CSUS Tel 30 2w memory 3 1 SureSelect Strand Specific RNA Library Prep Kit   RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 3000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</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> DRP003977 Illumina HiSeq 3000 sequencing of SAMD00182246       2791119960.0 77531110.0 DRR189403 0:36 A:685050951;C:641519684;G:664655385;T:799677669;N:216271 36       685050951 641519684 664655385 799677669 216271 DRX179868 DRS200418 DRA008865 NIG|National Institute of Genetics (Japan) National Institute of Genetics (Japan) 1 0.89653   0.1773   0.70725   0.49873   36   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Japan 2021-08-08 Larval Larval Brain Nervous System
102 102 DRR189402 DRX179867 DRS200417 DRP003977 PRJDB4470 Gene expression analysis of the zebrafish brain DRP003977 Other Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.       Telencephalon of adult zebrafrish 30 min post test session of 2 weeks memory test in non trace 2 Way Active Avoidance coditioning 2 SAMD00182245   sample name:CSUS Tel 30 2w memory 2|genotype:wild type|tissue:brain                 Illumina HiSeq 3000 sequencing of SAMD00182245 DRX179867 CSUS Tel 30 2w memory 2 1 SureSelect Strand Specific RNA Library Prep Kit   RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 3000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</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> DRP003977 Illumina HiSeq 3000 sequencing of SAMD00182245       1505449224.0 41818034.0 DRR189402 0:36 A:369895057;C:346914787;G:358624651;T:429897489;N:117240 36       369895057 346914787 358624651 429897489 117240 DRX179867 DRS200417 DRA008865 NIG|National Institute of Genetics (Japan) National Institute of Genetics (Japan) 1 0.89514   0.17677   0.7025   0.49571   36   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Japan 2021-08-08 Larval Larval Brain Nervous System
103 103 DRR189401 DRX179866 DRS200416 DRP003977 PRJDB4470 Gene expression analysis of the zebrafish brain DRP003977 Other Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.       Telencephalon of adult zebrafrish 30 min post test session of 2 weeks memory test in non trace 2 Way Active Avoidance coditioning 1 SAMD00182244   sample name:CSUS Tel 30 2w memory 1|genotype:wild type|tissue:brain                 Illumina HiSeq 3000 sequencing of SAMD00182244 DRX179866 CSUS Tel 30 2w memory 1 1 SureSelect Strand Specific RNA Library Prep Kit   RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 3000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</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> DRP003977 Illumina HiSeq 3000 sequencing of SAMD00182244       2088507024.0 58014084.0 DRR189401 0:36 A:516255405;C:478036869;G:496415722;T:597637091;N:161937 36       516255405 478036869 496415722 597637091 161937 DRX179866 DRS200416 DRA008865 NIG|National Institute of Genetics (Japan) National Institute of Genetics (Japan) 1 0.89533   0.18553   0.70981   0.49554   36   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Japan 2021-08-08 Larval Larval Brain Nervous System
156 156 DRR067143 DRX061087 DRS034141 DRP003275 PRJDB4941 Gene expression profiling of granule cells and Purkinje cells in zebrafish cerebellum DRP003275 Other An RNA seq analysis was performed using zebrafish granule cells Purkinje cells IO neurons and glial cells. The transcriptomes were sequenced using Illumina HiSeq with paired end libraries employing the Quartz seq method for low amount total RNA.       Zebrafish RNA seq for Bergmann glial cells using Tg line SAGFFLF251A sample 2 SAMD00057666   sample name:Zebrafish 251A 02|strain:Tg|biomaterial provider:Bioscience and Biotechnology Center Nagoya University|tissue type:cerebellum|cell type:bergmann glial cells|dev stage:14 dpf|replicate:biological replicate 2                 Illumina HiSeq 1500 paired end sequencing of SAMD00057666 DRX061087 1 1 Quartz seq for low amount total RNA   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP003275 Illumina HiSeq 1500 paired end sequencing of SAMD00057666       2040373922.0 10100861.0 DRR067143 0:101 1:101 A:577691972;C:445051245;G:472607289;T:544962357;N:61059 101 101     577691972 445051245 472607289 544962357 61059 DRX061087 DRS034141 DRA004955 RIKEN_CLST_DBFDI|Phyloinformatics Unit RIKEN CLST 2 0.83407 0.83802 0.12612 0.12666 0.73675 0.74079 0.4948 0.49282 101 101 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate quartzseq   Japan 2016-09-19 Larval Larval Brain Nervous System
157 157 DRR067142 DRX061086 DRS034140 DRP003275 PRJDB4941 Gene expression profiling of granule cells and Purkinje cells in zebrafish cerebellum DRP003275 Other An RNA seq analysis was performed using zebrafish granule cells Purkinje cells IO neurons and glial cells. The transcriptomes were sequenced using Illumina HiSeq with paired end libraries employing the Quartz seq method for low amount total RNA.       Zebrafish RNA seq for Bergmann glial cells using Tg line SAGFFLF251A sample 1 SAMD00057665   sample name:Zebrafish 251A 01|strain:Tg|biomaterial provider:Bioscience and Biotechnology Center Nagoya University|tissue type:cerebellum|cell type:bergmann glial cells|dev stage:14 dpf|replicate:biological replicate 1                 Illumina HiSeq 1500 paired end sequencing of SAMD00057665 DRX061086 1 1 Quartz seq for low amount total RNA   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP003275 Illumina HiSeq 1500 paired end sequencing of SAMD00057665       2033951534.0 10069067.0 DRR067142 0:101 1:101 A:589558269;C:431084184;G:460501802;T:552746498;N:60781 101 101     589558269 431084184 460501802 552746498 60781 DRX061086 DRS034140 DRA004955 RIKEN_CLST_DBFDI|Phyloinformatics Unit RIKEN CLST 2 0.8958 0.90339 0.13764 0.1385 0.72563 0.72865 0.49373 0.49916 101 101 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate quartzseq   Japan 2016-09-19 Larval Larval Brain Nervous System
158 158 DRR067141 DRX061085 DRS034139 DRP003275 PRJDB4941 Gene expression profiling of granule cells and Purkinje cells in zebrafish cerebellum DRP003275 Other An RNA seq analysis was performed using zebrafish granule cells Purkinje cells IO neurons and glial cells. The transcriptomes were sequenced using Illumina HiSeq with paired end libraries employing the Quartz seq method for low amount total RNA.       Zebrafish RNA seq for Purkinje cells using Tg line aldoca:GAP Venus sample 3 SAMD00057664   sample name:Zebrafish aldoca 03|strain:Tg|biomaterial provider:Bioscience and Biotechnology Center Nagoya University|tissue type:cerebellum|cell type:purkinje cells|dev stage:14 dpf|replicate:biological replicate 3                 Illumina HiSeq 1500 paired end sequencing of SAMD00057664 DRX061085 1 1 Quartz seq for low amount total RNA   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP003275 Illumina HiSeq 1500 paired end sequencing of SAMD00057664       1931908608.0 9563904.0 DRR067141 0:101 1:101 A:558444394;C:409856521;G:429168864;T:534380258;N:58571 101 101     558444394 409856521 429168864 534380258 58571 DRX061085 DRS034139 DRA004955 RIKEN_CLST_DBFDI|Phyloinformatics Unit RIKEN CLST 2 0.88632 0.89109 0.15695 0.15773 0.75694 0.7599 0.46875 0.49236 101 101 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate quartzseq   Japan 2016-09-19 Larval Larval Brain Nervous System
159 159 DRR067140 DRX061084 DRS034138 DRP003275 PRJDB4941 Gene expression profiling of granule cells and Purkinje cells in zebrafish cerebellum DRP003275 Other An RNA seq analysis was performed using zebrafish granule cells Purkinje cells IO neurons and glial cells. The transcriptomes were sequenced using Illumina HiSeq with paired end libraries employing the Quartz seq method for low amount total RNA.       Zebrafish RNA seq for Purkinje cells using Tg line aldoca:GAP Venus sample 2 SAMD00057663   sample name:Zebrafish aldoca 02|strain:Tg|biomaterial provider:Bioscience and Biotechnology Center Nagoya University|tissue type:cerebellum|cell type:purkinje cells|dev stage:14 dpf|replicate:biological replicate 2                 Illumina HiSeq 1500 paired end sequencing of SAMD00057663 DRX061084 1 1 Quartz seq for low amount total RNA   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP003275 Illumina HiSeq 1500 paired end sequencing of SAMD00057663       1851108406.0 9163903.0 DRR067140 0:101 1:101 A:537339104;C:390802782;G:416335529;T:506575762;N:55229 101 101     537339104 390802782 416335529 506575762 55229 DRX061084 DRS034138 DRA004955 RIKEN_CLST_DBFDI|Phyloinformatics Unit RIKEN CLST 2 0.9055 0.91341 0.1515 0.15333 0.76495 0.76719 0.49219 0.49012 101 101 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate quartzseq   Japan 2016-09-19 Larval Larval Brain Nervous System
160 160 DRR067139 DRX061083 DRS034137 DRP003275 PRJDB4941 Gene expression profiling of granule cells and Purkinje cells in zebrafish cerebellum DRP003275 Other An RNA seq analysis was performed using zebrafish granule cells Purkinje cells IO neurons and glial cells. The transcriptomes were sequenced using Illumina HiSeq with paired end libraries employing the Quartz seq method for low amount total RNA.       Zebrafish RNA seq for Purkinje cells using Tg line aldoca:GAP Venus sample 1 SAMD00057662   sample name:Zebrafish aldoca 01|strain:Tg|biomaterial provider:Bioscience and Biotechnology Center Nagoya University|tissue type:cerebellum|cell type:purkinje cells|dev stage:14 dpf|replicate:biological replicate 1                 Illumina HiSeq 1500 paired end sequencing of SAMD00057662 DRX061083 1 1 Quartz seq for low amount total RNA   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP003275 Illumina HiSeq 1500 paired end sequencing of SAMD00057662       2000078962.0 9901381.0 DRR067139 0:101 1:101 A:583169141;C:420603631;G:446949308;T:549297272;N:59610 101 101     583169141 420603631 446949308 549297272 59610 DRX061083 DRS034137 DRA004955 RIKEN_CLST_DBFDI|Phyloinformatics Unit RIKEN CLST 2 0.9056 0.90932 0.15092 0.15179 0.76173 0.7654 0.49028 0.49604 101 101 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate quartzseq   Japan 2016-09-19 Larval Larval Brain Nervous System
161 161 DRR067138 DRX061082 DRS034136 DRP003275 PRJDB4941 Gene expression profiling of granule cells and Purkinje cells in zebrafish cerebellum DRP003275 Other An RNA seq analysis was performed using zebrafish granule cells Purkinje cells IO neurons and glial cells. The transcriptomes were sequenced using Illumina HiSeq with paired end libraries employing the Quartz seq method for low amount total RNA.       Zebrafish RNA seq for granule cells using Tg line gSA2AzGFF152B sample 2 SAMD00057661   sample name:Zebrafish 152B 02|strain:Tg|biomaterial provider:Bioscience and Biotechnology Center Nagoya University|tissue type:cerebellum|cell type:granule cells|dev stage:14 dpf|replicate:biological replicate 2                 Illumina HiSeq 1500 paired end sequencing of SAMD00057661 DRX061082 1 1 Quartz seq for low amount total RNA   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP003275 Illumina HiSeq 1500 paired end sequencing of SAMD00057661       1997432156.0 9888278.0 DRR067138 0:101 1:101 A:578466824;C:423038930;G:449779231;T:546086391;N:60780 101 101     578466824 423038930 449779231 546086391 60780 DRX061082 DRS034136 DRA004955 RIKEN_CLST_DBFDI|Phyloinformatics Unit RIKEN CLST 2 0.90322 0.91109 0.1463 0.14811 0.75452 0.75633 0.48303 0.48557 101 101 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate quartzseq   Japan 2016-09-19 Larval Larval Brain Nervous System
162 162 DRR067137 DRX061081 DRS034135 DRP003275 PRJDB4941 Gene expression profiling of granule cells and Purkinje cells in zebrafish cerebellum DRP003275 Other An RNA seq analysis was performed using zebrafish granule cells Purkinje cells IO neurons and glial cells. The transcriptomes were sequenced using Illumina HiSeq with paired end libraries employing the Quartz seq method for low amount total RNA.       Zebrafish RNA seq for granule cells using Tg line gSA2AzGFF152B sample 1 SAMD00057660   sample name:Zebrafish 152B 01|strain:Tg|biomaterial provider:Bioscience and Biotechnology Center Nagoya University|tissue type:cerebellum|cell type:granule cells|dev stage:14 dpf|replicate:biological replicate 1                 Illumina HiSeq 1500 paired end sequencing of SAMD00057660 DRX061081 1 1 Quartz seq for low amount total RNA   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP003275 Illumina HiSeq 1500 paired end sequencing of SAMD00057660       1908437218.0 9447709.0 DRR067137 0:101 1:101 A:552150223;C:401993096;G:427236477;T:527000978;N:56444 101 101     552150223 401993096 427236477 527000978 56444 DRX061081 DRS034135 DRA004955 RIKEN_CLST_DBFDI|Phyloinformatics Unit RIKEN CLST 2 0.90474 0.91043 0.17336 0.17401 0.76108 0.76359 0.483 0.48537 101 101 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate quartzseq   Japan 2016-09-19 Larval Larval Brain Nervous System
163 163 DRR067136 DRX061080 DRS034134 DRP003275 PRJDB4941 Gene expression profiling of granule cells and Purkinje cells in zebrafish cerebellum DRP003275 Other An RNA seq analysis was performed using zebrafish granule cells Purkinje cells IO neurons and glial cells. The transcriptomes were sequenced using Illumina HiSeq with paired end libraries employing the Quartz seq method for low amount total RNA.       Zebrafish RNA seq for Inferior olive nuclei using Tg line hspGFFDMC28C sample 3 SAMD00057659   sample name:Zebrafish 28C 03|strain:Tg|biomaterial provider:Bioscience and Biotechnology Center Nagoya University|tissue type:hindbrain|cell type:inferior olive nuclei|dev stage:14 dpf|replicate:biological replicate 3                 Illumina HiSeq 1500 paired end sequencing of SAMD00057659 DRX061080 1 1 Quartz seq for low amount total RNA   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP003275 Illumina HiSeq 1500 paired end sequencing of SAMD00057659       1982971178.0 9816689.0 DRR067136 0:101 1:101 A:504064758;C:488246993;G:520130333;T:470469799;N:59295 101 101     504064758 488246993 520130333 470469799 59295 DRX061080 DRS034134 DRA004955 RIKEN_CLST_DBFDI|Phyloinformatics Unit RIKEN CLST 2 0.53386 0.54375 0.06072 0.06189 0.76351 0.76641 0.4872 0.48857 101 101 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate quartzseq   Japan 2016-09-19 Larval Larval Brain Nervous System
164 164 DRR067135 DRX061079 DRS034133 DRP003275 PRJDB4941 Gene expression profiling of granule cells and Purkinje cells in zebrafish cerebellum DRP003275 Other An RNA seq analysis was performed using zebrafish granule cells Purkinje cells IO neurons and glial cells. The transcriptomes were sequenced using Illumina HiSeq with paired end libraries employing the Quartz seq method for low amount total RNA.       Zebrafish RNA seq for Inferior olive nuclei using Tg line hspGFFDMC28C sample 2 SAMD00057658   sample name:Zebrafish 28C 02|strain:Tg|biomaterial provider:Bioscience and Biotechnology Center Nagoya University|tissue type:hindbrain|cell type:inferior olive nuclei|dev stage:14 dpf|replicate:biological replicate 2                 Illumina HiSeq 1500 paired end sequencing of SAMD00057658 DRX061079 1 1 Quartz seq for low amount total RNA   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP003275 Illumina HiSeq 1500 paired end sequencing of SAMD00057658       1961048320.0 9708160.0 DRR067135 0:101 1:101 A:557469151;C:424691789;G:455244994;T:523583601;N:58785 101 101     557469151 424691789 455244994 523583601 58785 DRX061079 DRS034133 DRA004955 RIKEN_CLST_DBFDI|Phyloinformatics Unit RIKEN CLST 2 0.84854 0.8526 0.10311 0.1042 0.75227 0.75499 0.49321 0.49435 101 101 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate quartzseq   Japan 2016-09-19 Larval Larval Brain Nervous System
165 165 DRR067134 DRX061078 DRS034132 DRP003275 PRJDB4941 Gene expression profiling of granule cells and Purkinje cells in zebrafish cerebellum DRP003275 Other An RNA seq analysis was performed using zebrafish granule cells Purkinje cells IO neurons and glial cells. The transcriptomes were sequenced using Illumina HiSeq with paired end libraries employing the Quartz seq method for low amount total RNA.       Zebrafish RNA seq for Inferior olive nuclei using Tg line hspGFFDMC28C sample 1 SAMD00057657   sample name:Zebrafish 28C 01|strain:Tg|biomaterial provider:Bioscience and Biotechnology Center Nagoya University|tissue type:hindbrain|cell type:inferior olive nuclei|dev stage:14 dpf|replicate:biological replicate 1                 Illumina HiSeq 1500 paired end sequencing of SAMD00057657 DRX061078 1 1 Quartz seq for low amount total RNA   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP003275 Illumina HiSeq 1500 paired end sequencing of SAMD00057657       1931802760.0 9563380.0 DRR067134 0:101 1:101 A:546501397;C:422500710;G:452200521;T:510543489;N:56643 101 101     546501397 422500710 452200521 510543489 56643 DRX061078 DRS034132 DRA004955 RIKEN_CLST_DBFDI|Phyloinformatics Unit RIKEN CLST 2 0.85439 0.85613 0.09867 0.09897 0.76871 0.77082 0.48943 0.48936 101 101 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate quartzseq   Japan 2016-09-19 Larval Larval Brain Nervous System
166 166 DRR067133 DRX061077 DRS034131 DRP003275 PRJDB4941 Gene expression profiling of granule cells and Purkinje cells in zebrafish cerebellum DRP003275 Other An RNA seq analysis was performed using zebrafish granule cells Purkinje cells IO neurons and glial cells. The transcriptomes were sequenced using Illumina HiSeq with paired end libraries employing the Quartz seq method for low amount total RNA.       Zebrafish RNA seq for eurydendroid cells using Tg line hspzGFFgDMC156A sample 2 SAMD00057656   sample name:Zebrafish 156A 02|strain:Tg|biomaterial provider:Bioscience and Biotechnology Center Nagoya University|tissue type:cerebellum|cell type:eurydendroid cells|dev stage:14 dpf|replicate:biological replicate 2                 Illumina HiSeq 1500 paired end sequencing of SAMD00057656 DRX061077 1 1 Quartz seq for low amount total RNA   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP003275 Illumina HiSeq 1500 paired end sequencing of SAMD00057656       2054289096.0 10169748.0 DRR067133 0:101 1:101 A:563764176;C:464768863;G:497506420;T:528187503;N:62134 101 101     563764176 464768863 497506420 528187503 62134 DRX061077 DRS034131 DRA004955 RIKEN_CLST_DBFDI|Phyloinformatics Unit RIKEN CLST 2 0.69311 0.6968 0.12309 0.12389 0.76428 0.76676 0.48379 0.48227 101 101 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate quartzseq   Japan 2016-09-19 Larval Larval Brain Nervous System
167 167 DRR067132 DRX061076 DRS034130 DRP003275 PRJDB4941 Gene expression profiling of granule cells and Purkinje cells in zebrafish cerebellum DRP003275 Other An RNA seq analysis was performed using zebrafish granule cells Purkinje cells IO neurons and glial cells. The transcriptomes were sequenced using Illumina HiSeq with paired end libraries employing the Quartz seq method for low amount total RNA.       Zebrafish RNA seq for eurydendroid cells using Tg line hspzGFFgDMC156A sample 1 SAMD00057655   sample name:Zebrafish 156A 01|strain:Tg|biomaterial provider:Bioscience and Biotechnology Center Nagoya University|tissue type:cerebellum|cell type:eurydendroid cells|dev stage:14 dpf|replicate:biological replicate 1                 Illumina HiSeq 1500 paired end sequencing of SAMD00057655 DRX061076 1 1 Quartz seq for low amount total RNA   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP003275 Illumina HiSeq 1500 paired end sequencing of SAMD00057655       2152665722.0 10656761.0 DRR067132 0:101 1:101 A:585252781;C:495382257;G:522677749;T:549287359;N:65576 101 101     585252781 495382257 522677749 549287359 65576 DRX061076 DRS034130 DRA004955 RIKEN_CLST_DBFDI|Phyloinformatics Unit RIKEN CLST 2 0.67771 0.68253 0.12949 0.1303 0.77216 0.77542 0.4951 0.49452 101 101 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate quartzseq   Japan 2016-09-19 Larval Larval Brain Nervous System
9331 9331 ERR2862354 ERX2868592 ERS2866329 ERP111743 PRJEB29441 Receptor Tyrosine Kinase pathway activation is sufficient to trigger chordoma in zebrafish E-MTAB-7349 Transcriptome Analysis Oncogenic transformation of individual cell fates by developmental signaling cascades and transcription factors triggers diverse cancer types. Chordoma is a rare aggressive tumor arising from transformed notochord remnants. Various potentially oncogenic factors have been found deregulated in chordoma and its metastases yet clear causation remains uncertain. In particular expression of the notochord controlling transcription factor Brachyury is hypothesized as key molecular driver in chordoma formation yet an in vivo model to causally test its oncogenic potential in the notochord is missing. Here we apply a zebrafish model of chordoma onset to identify the notochord transforming potential of tumor implicated candidate genes in vivo. We find that overexpression of human and zebrafish Brachyury including a version with augmented transcriptional activity is insufficient to initiate notochord hyperplasia in vivo. In contrast the repeatedly chordoma implicated receptor tyrosine kinase RTK genes EGFR and KDR/VEGFR2 are sufficient to transform developmental notochord cells akin to direct activation of Ras. Analysis of transcriptome and sub cellular organization from transformed notochords suggests that aberrant activation of RTK/Ras signaling attenuates processes required for the differentiation of notochord cells. Taken together our results provide first in vivo indication for a lack of tumor initiating potential of Brachyury expression in the notochord and suggest activated RTK signaling as potent hyperplasia initiating event in chordoma. ENA FIRST PUBLIC:2018 12 01|ENA LAST UPDATE:2018 10 30   Protocols: 8 dpf wildtype and Tgtwhh:Gal4;TgUAS:EGFP HRASV12 were euthanized with 3% Tricaine methanesulfonate Sigma. Embryos were decapitated and incubated in Tripsin EDTA Sigma for 30 minutes to facilitate tissue dissociation. Notochords were then dissected using tungsten needles and immediately transferred to Trizol LS Ambion. We isolated 30 50 notochords per replicate with a total of 3 replicates per condition 3x wildtype 3x HRASV12. Notochord RNA was extracted following the manufacturer's protocol using Trizol LS. RNA seq libraries were constructed using the Truseq stranded total RNA kit. TUC SAMEA5055152 UZH ENA FIRST PUBLIC:2018 12 01T17:03:21Z|ENA LAST UPDATE:2018 10 30T13:30:13Z|External Id:SAMEA5055152|INSDC center name:UZH|INSDC first public:2018 12 01T17:03:21Z|INSDC last update:2018 10 30T13:30:13Z|INSDC status:public|Submitter Id:E MTAB 7349:TUC|age:8|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:wild type genotype|individual:mixed pool of 30 to 50 embryos|organism part:notochord|sample name:E MTAB 7349:TUC|scientific name:Danio rerio|sex:mixed                 Illumina HiSeq 2500 paired end sequencing; Receptor Tyrosine Kinase pathway activation is sufficient to trigger chordoma in zebrafish E MTAB 7349:TUC p TUC p Receptor Tyrosine Kinase pathway activation is sufficient to trigger chordoma in zebrafish 8 dpf wildtype and Tgtwhh:Gal4;TgUAS:EGFP HRASV12 were euthanized with 3% Tricaine methanesulfonate Sigma. Embryos were decapitated and incubated in Tripsin EDTA Sigma for 30 minutes to facilitate tissue dissociation. Notochords were then dissected using tungsten needles and immediately transferred to Trizol LS Ambion. We isolated 30 50 notochords per replicate with a total of 3 replicates per condition 3x wildtype 3x HRASV12. Notochord RNA was extracted following the manufacturer's protocol using Trizol LS. RNA seq libraries were constructed using the Truseq stranded total RNA kit. Experimental Factor: genotype:wild type genotype RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP111743 Illumina HiSeq 2500 paired end sequencing; Receptor Tyrosine Kinase pathway activation is sufficient to trigger chordoma in zebrafish ENA FIRST PUBLIC:2018 12 01|ENA LAST UPDATE:2018 11 16 AGCGATAG_AGGCTATA__160520_I127_FCH732GBBXX_L8_CDKPEI160513002_1.fq.gz AGCGATAG_AGGCTATA__160520_I127_FCH732GBBXX_L8_CDKPEI160513002_2.fq.gz fastq fastq 12890102400.0 64450512.0 E MTAB 7349:AGCGATAG AGGCTATA 160520 I127 FCH732GBBXX L8 CDKPEI160513002 0:100 1:100 A:3347844573;C:3078635366;G:3118813009;T:3343385073;N:1424379 100 100     3347844573 3078635366 3118813009 3343385073 1424379 ERX2868592 ERS2866329 ERA1640550 European Nucleotide Archive European Nucleotide Archive 2 0.89165 0.8896 0.26768 0.26518 0.75142 0.75459 0.60855 0.6105 100 100 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   Unknown 2018-10-30 Larval Larval Brain Nervous System
9332 9332 ERR2862353 ERX2868591 ERS2866328 ERP111743 PRJEB29441 Receptor Tyrosine Kinase pathway activation is sufficient to trigger chordoma in zebrafish E-MTAB-7349 Transcriptome Analysis Oncogenic transformation of individual cell fates by developmental signaling cascades and transcription factors triggers diverse cancer types. Chordoma is a rare aggressive tumor arising from transformed notochord remnants. Various potentially oncogenic factors have been found deregulated in chordoma and its metastases yet clear causation remains uncertain. In particular expression of the notochord controlling transcription factor Brachyury is hypothesized as key molecular driver in chordoma formation yet an in vivo model to causally test its oncogenic potential in the notochord is missing. Here we apply a zebrafish model of chordoma onset to identify the notochord transforming potential of tumor implicated candidate genes in vivo. We find that overexpression of human and zebrafish Brachyury including a version with augmented transcriptional activity is insufficient to initiate notochord hyperplasia in vivo. In contrast the repeatedly chordoma implicated receptor tyrosine kinase RTK genes EGFR and KDR/VEGFR2 are sufficient to transform developmental notochord cells akin to direct activation of Ras. Analysis of transcriptome and sub cellular organization from transformed notochords suggests that aberrant activation of RTK/Ras signaling attenuates processes required for the differentiation of notochord cells. Taken together our results provide first in vivo indication for a lack of tumor initiating potential of Brachyury expression in the notochord and suggest activated RTK signaling as potent hyperplasia initiating event in chordoma. ENA FIRST PUBLIC:2018 12 01|ENA LAST UPDATE:2018 10 30   Protocols: 8 dpf wildtype and Tgtwhh:Gal4;TgUAS:EGFP HRASV12 were euthanized with 3% Tricaine methanesulfonate Sigma. Embryos were decapitated and incubated in Tripsin EDTA Sigma for 30 minutes to facilitate tissue dissociation. Notochords were then dissected using tungsten needles and immediately transferred to Trizol LS Ambion. We isolated 30 50 notochords per replicate with a total of 3 replicates per condition 3x wildtype 3x HRASV12. Notochord RNA was extracted following the manufacturer's protocol using Trizol LS. RNA seq libraries were constructed using the Truseq stranded total RNA kit. TUB SAMEA5055151 UZH ENA FIRST PUBLIC:2018 12 01T17:03:21Z|ENA LAST UPDATE:2018 10 30T13:30:13Z|External Id:SAMEA5055151|INSDC center name:UZH|INSDC first public:2018 12 01T17:03:21Z|INSDC last update:2018 10 30T13:30:13Z|INSDC status:public|Submitter Id:E MTAB 7349:TUB|age:8|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:wild type genotype|individual:mixed pool of 30 to 50 embryos|organism part:notochord|sample name:E MTAB 7349:TUB|scientific name:Danio rerio|sex:mixed                 Illumina HiSeq 2500 paired end sequencing; Receptor Tyrosine Kinase pathway activation is sufficient to trigger chordoma in zebrafish E MTAB 7349:TUB p TUB p Receptor Tyrosine Kinase pathway activation is sufficient to trigger chordoma in zebrafish 8 dpf wildtype and Tgtwhh:Gal4;TgUAS:EGFP HRASV12 were euthanized with 3% Tricaine methanesulfonate Sigma. Embryos were decapitated and incubated in Tripsin EDTA Sigma for 30 minutes to facilitate tissue dissociation. Notochords were then dissected using tungsten needles and immediately transferred to Trizol LS Ambion. We isolated 30 50 notochords per replicate with a total of 3 replicates per condition 3x wildtype 3x HRASV12. Notochord RNA was extracted following the manufacturer's protocol using Trizol LS. RNA seq libraries were constructed using the Truseq stranded total RNA kit. Experimental Factor: genotype:wild type genotype RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP111743 Illumina HiSeq 2500 paired end sequencing; Receptor Tyrosine Kinase pathway activation is sufficient to trigger chordoma in zebrafish ENA FIRST PUBLIC:2018 12 01|ENA LAST UPDATE:2018 11 16 TCTCGCGC_AGGCTATA__160520_I127_FCH732GBBXX_L8_CDKPEI160513002_2.fq.gz TCTCGCGC_AGGCTATA__160520_I127_FCH732GBBXX_L8_CDKPEI160513002_1.fq.gz fastq fastq 15345882200.0 76729411.0 E MTAB 7349:TCTCGCGC AGGCTATA 160520 I127 FCH732GBBXX L8 CDKPEI160513002 0:100 1:100 A:4257362303;C:3394893224;G:3451042837;T:4240872487;N:1711349 100 100     4257362303 3394893224 3451042837 4240872487 1711349 ERX2868591 ERS2866328 ERA1640550 European Nucleotide Archive European Nucleotide Archive 2 0.86888 0.86735 0.45025 0.44476 0.72036 0.72529 0.56048 0.56274 100 100 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   Unknown 2018-10-30 Larval Larval Brain Nervous System
9333 9333 ERR2862352 ERX2868590 ERS2866327 ERP111743 PRJEB29441 Receptor Tyrosine Kinase pathway activation is sufficient to trigger chordoma in zebrafish E-MTAB-7349 Transcriptome Analysis Oncogenic transformation of individual cell fates by developmental signaling cascades and transcription factors triggers diverse cancer types. Chordoma is a rare aggressive tumor arising from transformed notochord remnants. Various potentially oncogenic factors have been found deregulated in chordoma and its metastases yet clear causation remains uncertain. In particular expression of the notochord controlling transcription factor Brachyury is hypothesized as key molecular driver in chordoma formation yet an in vivo model to causally test its oncogenic potential in the notochord is missing. Here we apply a zebrafish model of chordoma onset to identify the notochord transforming potential of tumor implicated candidate genes in vivo. We find that overexpression of human and zebrafish Brachyury including a version with augmented transcriptional activity is insufficient to initiate notochord hyperplasia in vivo. In contrast the repeatedly chordoma implicated receptor tyrosine kinase RTK genes EGFR and KDR/VEGFR2 are sufficient to transform developmental notochord cells akin to direct activation of Ras. Analysis of transcriptome and sub cellular organization from transformed notochords suggests that aberrant activation of RTK/Ras signaling attenuates processes required for the differentiation of notochord cells. Taken together our results provide first in vivo indication for a lack of tumor initiating potential of Brachyury expression in the notochord and suggest activated RTK signaling as potent hyperplasia initiating event in chordoma. ENA FIRST PUBLIC:2018 12 01|ENA LAST UPDATE:2018 10 30   Protocols: 8 dpf wildtype and Tgtwhh:Gal4;TgUAS:EGFP HRASV12 were euthanized with 3% Tricaine methanesulfonate Sigma. Embryos were decapitated and incubated in Tripsin EDTA Sigma for 30 minutes to facilitate tissue dissociation. Notochords were then dissected using tungsten needles and immediately transferred to Trizol LS Ambion. We isolated 30 50 notochords per replicate with a total of 3 replicates per condition 3x wildtype 3x HRASV12. Notochord RNA was extracted following the manufacturer's protocol using Trizol LS. RNA seq libraries were constructed using the Truseq stranded total RNA kit. TUA SAMEA5055150 UZH ENA FIRST PUBLIC:2018 12 01T17:03:21Z|ENA LAST UPDATE:2018 10 30T13:30:13Z|External Id:SAMEA5055150|INSDC center name:UZH|INSDC first public:2018 12 01T17:03:21Z|INSDC last update:2018 10 30T13:30:13Z|INSDC status:public|Submitter Id:E MTAB 7349:TUA|age:8|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:wild type genotype|individual:mixed pool of 30 to 50 embryos|organism part:notochord|sample name:E MTAB 7349:TUA|scientific name:Danio rerio|sex:mixed                 Illumina HiSeq 2500 paired end sequencing; Receptor Tyrosine Kinase pathway activation is sufficient to trigger chordoma in zebrafish E MTAB 7349:TUA p TUA p Receptor Tyrosine Kinase pathway activation is sufficient to trigger chordoma in zebrafish 8 dpf wildtype and Tgtwhh:Gal4;TgUAS:EGFP HRASV12 were euthanized with 3% Tricaine methanesulfonate Sigma. Embryos were decapitated and incubated in Tripsin EDTA Sigma for 30 minutes to facilitate tissue dissociation. Notochords were then dissected using tungsten needles and immediately transferred to Trizol LS Ambion. We isolated 30 50 notochords per replicate with a total of 3 replicates per condition 3x wildtype 3x HRASV12. Notochord RNA was extracted following the manufacturer's protocol using Trizol LS. RNA seq libraries were constructed using the Truseq stranded total RNA kit. Experimental Factor: genotype:wild type genotype RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP111743 Illumina HiSeq 2500 paired end sequencing; Receptor Tyrosine Kinase pathway activation is sufficient to trigger chordoma in zebrafish ENA FIRST PUBLIC:2018 12 01|ENA LAST UPDATE:2018 11 16 TCCGCGAA_AGGCTATA__160520_I127_FCH732GBBXX_L8_CDKPEI160513002_1.fq.gz TCCGCGAA_AGGCTATA__160520_I127_FCH732GBBXX_L8_CDKPEI160513002_2.fq.gz fastq fastq 11985547000.0 59927735.0 E MTAB 7349:TCCGCGAA AGGCTATA 160520 I127 FCH732GBBXX L8 CDKPEI160513002 0:100 1:100 A:3239652711;C:2732996991;G:2737809176;T:3273773368;N:1314754 100 100     3239652711 2732996991 2737809176 3273773368 1314754 ERX2868590 ERS2866327 ERA1640550 European Nucleotide Archive European Nucleotide Archive 2 0.91524 0.91585 0.32418 0.32053 0.72616 0.72671 0.59362 0.42478 100 100 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   Unknown 2018-10-30 Larval Larval Brain Nervous System
9334 9334 ERR2862351 ERX2868589 ERS2866326 ERP111743 PRJEB29441 Receptor Tyrosine Kinase pathway activation is sufficient to trigger chordoma in zebrafish E-MTAB-7349 Transcriptome Analysis Oncogenic transformation of individual cell fates by developmental signaling cascades and transcription factors triggers diverse cancer types. Chordoma is a rare aggressive tumor arising from transformed notochord remnants. Various potentially oncogenic factors have been found deregulated in chordoma and its metastases yet clear causation remains uncertain. In particular expression of the notochord controlling transcription factor Brachyury is hypothesized as key molecular driver in chordoma formation yet an in vivo model to causally test its oncogenic potential in the notochord is missing. Here we apply a zebrafish model of chordoma onset to identify the notochord transforming potential of tumor implicated candidate genes in vivo. We find that overexpression of human and zebrafish Brachyury including a version with augmented transcriptional activity is insufficient to initiate notochord hyperplasia in vivo. In contrast the repeatedly chordoma implicated receptor tyrosine kinase RTK genes EGFR and KDR/VEGFR2 are sufficient to transform developmental notochord cells akin to direct activation of Ras. Analysis of transcriptome and sub cellular organization from transformed notochords suggests that aberrant activation of RTK/Ras signaling attenuates processes required for the differentiation of notochord cells. Taken together our results provide first in vivo indication for a lack of tumor initiating potential of Brachyury expression in the notochord and suggest activated RTK signaling as potent hyperplasia initiating event in chordoma. ENA FIRST PUBLIC:2018 12 01|ENA LAST UPDATE:2018 10 30   Protocols: 8 dpf wildtype and Tgtwhh:Gal4;TgUAS:EGFP HRASV12 were euthanized with 3% Tricaine methanesulfonate Sigma. Embryos were decapitated and incubated in Tripsin EDTA Sigma for 30 minutes to facilitate tissue dissociation. Notochords were then dissected using tungsten needles and immediately transferred to Trizol LS Ambion. We isolated 30 50 notochords per replicate with a total of 3 replicates per condition 3x wildtype 3x HRASV12. Notochord RNA was extracted following the manufacturer's protocol using Trizol LS. RNA seq libraries were constructed using the Truseq stranded total RNA kit. HRASC SAMEA5055149 UZH ENA FIRST PUBLIC:2018 12 01T17:03:21Z|ENA LAST UPDATE:2018 10 30T13:30:13Z|External Id:SAMEA5055149|INSDC center name:UZH|INSDC first public:2018 12 01T17:03:21Z|INSDC last update:2018 10 30T13:30:13Z|INSDC status:public|Submitter Id:E MTAB 7349:HRASC|age:8|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:Tgtwhh:Gal4;TgUAS:EGFP HRASV12|individual:mixed pool of 30 to 50 embryos|organism part:notochord|sample name:E MTAB 7349:HRASC|scientific name:Danio rerio|sex:mixed                 Illumina HiSeq 2500 paired end sequencing; Receptor Tyrosine Kinase pathway activation is sufficient to trigger chordoma in zebrafish E MTAB 7349:HRASC p HRASC p Receptor Tyrosine Kinase pathway activation is sufficient to trigger chordoma in zebrafish 8 dpf wildtype and Tgtwhh:Gal4;TgUAS:EGFP HRASV12 were euthanized with 3% Tricaine methanesulfonate Sigma. Embryos were decapitated and incubated in Tripsin EDTA Sigma for 30 minutes to facilitate tissue dissociation. Notochords were then dissected using tungsten needles and immediately transferred to Trizol LS Ambion. We isolated 30 50 notochords per replicate with a total of 3 replicates per condition 3x wildtype 3x HRASV12. Notochord RNA was extracted following the manufacturer's protocol using Trizol LS. RNA seq libraries were constructed using the Truseq stranded total RNA kit. Experimental Factor: genotype:Tgtwhh:Gal4;TgUAS:EGFP HRASV12 RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP111743 Illumina HiSeq 2500 paired end sequencing; Receptor Tyrosine Kinase pathway activation is sufficient to trigger chordoma in zebrafish ENA FIRST PUBLIC:2018 12 01|ENA LAST UPDATE:2018 11 16 CGGCTATG_GTCAGTAC__160520_I127_FCH732GBBXX_L8_CDKPEI160513002_1.fq.gz CGGCTATG_GTCAGTAC__160520_I127_FCH732GBBXX_L8_CDKPEI160513002_2.fq.gz fastq fastq 11297151800.0 56485759.0 E MTAB 7349:CGGCTATG GTCAGTAC 160520 I127 FCH732GBBXX L8 CDKPEI160513002 0:100 1:100 A:3202944476;C:2429970659;G:2461948398;T:3201079699;N:1208568 100 100     3202944476 2429970659 2461948398 3201079699 1208568 ERX2868589 ERS2866326 ERA1640550 European Nucleotide Archive European Nucleotide Archive 2 0.89842 0.86269 0.32455 0.30708 0.74245 0.75191 0.7454 0.74185 100 100 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   Unknown 2018-10-30 Larval Larval Brain Nervous System
9335 9335 ERR2862350 ERX2868588 ERS2866325 ERP111743 PRJEB29441 Receptor Tyrosine Kinase pathway activation is sufficient to trigger chordoma in zebrafish E-MTAB-7349 Transcriptome Analysis Oncogenic transformation of individual cell fates by developmental signaling cascades and transcription factors triggers diverse cancer types. Chordoma is a rare aggressive tumor arising from transformed notochord remnants. Various potentially oncogenic factors have been found deregulated in chordoma and its metastases yet clear causation remains uncertain. In particular expression of the notochord controlling transcription factor Brachyury is hypothesized as key molecular driver in chordoma formation yet an in vivo model to causally test its oncogenic potential in the notochord is missing. Here we apply a zebrafish model of chordoma onset to identify the notochord transforming potential of tumor implicated candidate genes in vivo. We find that overexpression of human and zebrafish Brachyury including a version with augmented transcriptional activity is insufficient to initiate notochord hyperplasia in vivo. In contrast the repeatedly chordoma implicated receptor tyrosine kinase RTK genes EGFR and KDR/VEGFR2 are sufficient to transform developmental notochord cells akin to direct activation of Ras. Analysis of transcriptome and sub cellular organization from transformed notochords suggests that aberrant activation of RTK/Ras signaling attenuates processes required for the differentiation of notochord cells. Taken together our results provide first in vivo indication for a lack of tumor initiating potential of Brachyury expression in the notochord and suggest activated RTK signaling as potent hyperplasia initiating event in chordoma. ENA FIRST PUBLIC:2018 12 01|ENA LAST UPDATE:2018 10 30   Protocols: 8 dpf wildtype and Tgtwhh:Gal4;TgUAS:EGFP HRASV12 were euthanized with 3% Tricaine methanesulfonate Sigma. Embryos were decapitated and incubated in Tripsin EDTA Sigma for 30 minutes to facilitate tissue dissociation. Notochords were then dissected using tungsten needles and immediately transferred to Trizol LS Ambion. We isolated 30 50 notochords per replicate with a total of 3 replicates per condition 3x wildtype 3x HRASV12. Notochord RNA was extracted following the manufacturer's protocol using Trizol LS. RNA seq libraries were constructed using the Truseq stranded total RNA kit. HRASB 1A SAMEA5055148 UZH ENA FIRST PUBLIC:2018 12 01T17:03:21Z|ENA LAST UPDATE:2018 10 30T13:30:13Z|External Id:SAMEA5055148|INSDC center name:UZH|INSDC first public:2018 12 01T17:03:21Z|INSDC last update:2018 10 30T13:30:13Z|INSDC status:public|Submitter Id:E MTAB 7349:HRASB 1A|age:8|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:Tgtwhh:Gal4;TgUAS:EGFP HRASV12|individual:mixed pool of 30 to 50 embryos|organism part:notochord|sample name:E MTAB 7349:HRASB 1A|scientific name:Danio rerio|sex:mixed                 Illumina HiSeq 2500 paired end sequencing; Receptor Tyrosine Kinase pathway activation is sufficient to trigger chordoma in zebrafish E MTAB 7349:HRASB 1A p HRASB 1A p Receptor Tyrosine Kinase pathway activation is sufficient to trigger chordoma in zebrafish 8 dpf wildtype and Tgtwhh:Gal4;TgUAS:EGFP HRASV12 were euthanized with 3% Tricaine methanesulfonate Sigma. Embryos were decapitated and incubated in Tripsin EDTA Sigma for 30 minutes to facilitate tissue dissociation. Notochords were then dissected using tungsten needles and immediately transferred to Trizol LS Ambion. We isolated 30 50 notochords per replicate with a total of 3 replicates per condition 3x wildtype 3x HRASV12. Notochord RNA was extracted following the manufacturer's protocol using Trizol LS. RNA seq libraries were constructed using the Truseq stranded total RNA kit. Experimental Factor: genotype:Tgtwhh:Gal4;TgUAS:EGFP HRASV12 RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP111743 Illumina HiSeq 2500 paired end sequencing; Receptor Tyrosine Kinase pathway activation is sufficient to trigger chordoma in zebrafish ENA FIRST PUBLIC:2018 12 01|ENA LAST UPDATE:2018 11 16 TCTCGCGC_GTCAGTAC__160520_I127_FCH732GBBXX_L8_CDKPEI160513002_1.fq.gz TCTCGCGC_GTCAGTAC__160520_I127_FCH732GBBXX_L8_CDKPEI160513002_2.fq.gz fastq fastq 13035635000.0 65178175.0 E MTAB 7349:TCTCGCGC GTCAGTAC 160520 I127 FCH732GBBXX L8 CDKPEI160513002 0:100 1:100 A:3518767071;C:2991842048;G:3005014068;T:3518541297;N:1470516 100 100     3518767071 2991842048 3005014068 3518541297 1470516 ERX2868588 ERS2866325 ERA1640550 European Nucleotide Archive European Nucleotide Archive 2 0.89434 0.89384 0.28234 0.28093 0.7274 0.72813 0.6198 0.62424 100 100 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   Unknown 2018-10-30 Larval Larval Brain Nervous System
9336 9336 ERR2862349 ERX2868587 ERS2866324 ERP111743 PRJEB29441 Receptor Tyrosine Kinase pathway activation is sufficient to trigger chordoma in zebrafish E-MTAB-7349 Transcriptome Analysis Oncogenic transformation of individual cell fates by developmental signaling cascades and transcription factors triggers diverse cancer types. Chordoma is a rare aggressive tumor arising from transformed notochord remnants. Various potentially oncogenic factors have been found deregulated in chordoma and its metastases yet clear causation remains uncertain. In particular expression of the notochord controlling transcription factor Brachyury is hypothesized as key molecular driver in chordoma formation yet an in vivo model to causally test its oncogenic potential in the notochord is missing. Here we apply a zebrafish model of chordoma onset to identify the notochord transforming potential of tumor implicated candidate genes in vivo. We find that overexpression of human and zebrafish Brachyury including a version with augmented transcriptional activity is insufficient to initiate notochord hyperplasia in vivo. In contrast the repeatedly chordoma implicated receptor tyrosine kinase RTK genes EGFR and KDR/VEGFR2 are sufficient to transform developmental notochord cells akin to direct activation of Ras. Analysis of transcriptome and sub cellular organization from transformed notochords suggests that aberrant activation of RTK/Ras signaling attenuates processes required for the differentiation of notochord cells. Taken together our results provide first in vivo indication for a lack of tumor initiating potential of Brachyury expression in the notochord and suggest activated RTK signaling as potent hyperplasia initiating event in chordoma. ENA FIRST PUBLIC:2018 12 01|ENA LAST UPDATE:2018 10 30   Protocols: 8 dpf wildtype and Tgtwhh:Gal4;TgUAS:EGFP HRASV12 were euthanized with 3% Tricaine methanesulfonate Sigma. Embryos were decapitated and incubated in Tripsin EDTA Sigma for 30 minutes to facilitate tissue dissociation. Notochords were then dissected using tungsten needles and immediately transferred to Trizol LS Ambion. We isolated 30 50 notochords per replicate with a total of 3 replicates per condition 3x wildtype 3x HRASV12. Notochord RNA was extracted following the manufacturer's protocol using Trizol LS. RNA seq libraries were constructed using the Truseq stranded total RNA kit. 2A SAMEA5055147 UZH ENA FIRST PUBLIC:2018 12 01T17:03:21Z|ENA LAST UPDATE:2018 10 30T13:30:13Z|External Id:SAMEA5055147|INSDC center name:UZH|INSDC first public:2018 12 01T17:03:21Z|INSDC last update:2018 10 30T13:30:13Z|INSDC status:public|Submitter Id:E MTAB 7349:2A|age:8|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:Tgtwhh:Gal4;TgUAS:EGFP HRASV12|individual:mixed pool of 30 to 50 embryos|organism part:notochord|sample name:E MTAB 7349:2A|scientific name:Danio rerio|sex:mixed                 Illumina HiSeq 2500 paired end sequencing; Receptor Tyrosine Kinase pathway activation is sufficient to trigger chordoma in zebrafish E MTAB 7349:2A p 2A p Receptor Tyrosine Kinase pathway activation is sufficient to trigger chordoma in zebrafish 8 dpf wildtype and Tgtwhh:Gal4;TgUAS:EGFP HRASV12 were euthanized with 3% Tricaine methanesulfonate Sigma. Embryos were decapitated and incubated in Tripsin EDTA Sigma for 30 minutes to facilitate tissue dissociation. Notochords were then dissected using tungsten needles and immediately transferred to Trizol LS Ambion. We isolated 30 50 notochords per replicate with a total of 3 replicates per condition 3x wildtype 3x HRASV12. Notochord RNA was extracted following the manufacturer's protocol using Trizol LS. RNA seq libraries were constructed using the Truseq stranded total RNA kit. Experimental Factor: genotype:Tgtwhh:Gal4;TgUAS:EGFP HRASV12 RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP111743 Illumina HiSeq 2500 paired end sequencing; Receptor Tyrosine Kinase pathway activation is sufficient to trigger chordoma in zebrafish ENA FIRST PUBLIC:2018 12 01|ENA LAST UPDATE:2018 11 16 TCCGCGAA_GTCAGTAC__160520_I127_FCH732GBBXX_L8_CDKPEI160513002_2.fq.gz TCCGCGAA_GTCAGTAC__160520_I127_FCH732GBBXX_L8_CDKPEI160513002_1.fq.gz fastq fastq 11671772800.0 58358864.0 E MTAB 7349:TCCGCGAA GTCAGTAC 160520 I127 FCH732GBBXX L8 CDKPEI160513002 0:100 1:100 A:3164806186;C:2661342106;G:2677258036;T:3167072669;N:1293803 100 100     3164806186 2661342106 2677258036 3167072669 1293803 ERX2868587 ERS2866324 ERA1640550 European Nucleotide Archive European Nucleotide Archive 2 0.89879 0.89878 0.28162 0.28061 0.73212 0.73452 0.59632 0.60115 100 100 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   Unknown 2018-10-30 Larval Larval Brain Nervous System
10176 10176 ERR5858457 ERX5504346 ERS6343450 ERP128749 PRJEB44676 scRNAseq of her4.3+ cells from lesioned and unlesioned zebrafish larvae spinal cord E-MTAB-10390 Transcriptome Analysis To analyse lesion induced gene regulation in progenitor cells at single cell resolution we performed single cell RNAseq on FACS isolated her4.3:GFP progenitor cells from the spinal cord at 24 hours post lesion hpl post spinal injury at 3 dpf dpf compared to age matched uninjured animals. ENA FIRST PUBLIC:2021 05 24|ENA LAST UPDATE:2021 05 24   Protocols: Trunks containing the lesion sites or equivalent site from unlesioned fish are collected and kept in PBS on ice.Incubate the trunks up to 300 in 1 mL of 1X Trypsin EDTA at 37C for 5 7 mins.Stop dissociation by adding FBS to a final concentration of 5%.Centrifuge at 200g for 7 mins.Discard Sups.Resuspend in 500 uL of PBS.Add the cell suspension into a 40 uM cell strainer.Centrifuge at 200g for 7 mins.Resuspend in the buffer for FACS PBS 5% FBS Following cell dissociation and FAC sorting samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines Following cell dissociation and FAC sorting samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines. Naive SAMEA8658904 University Of Edinburgh ENA first public:2021 05 24|ENA last update:2021 05 24|External Id:SAMEA8658904|INSDC center alias:UOE|INSDC center name:University Of Edinburgh|INSDC first public:2021 05 24T00:14:32Z|INSDC last update:2021 05 24T00:14:32Z|INSDC status:public|Submitter Id:E MTAB 10390:Naive|age:4|broker name:ArrayExpress|cell type:ependymo radial glial cell|common name:zebrafish|developmental stage:larval day 4|immunophenotype:Her4.3+ positive|organism part:spinal cord|sample name:E MTAB 10390:Naive|sex:mixed|strain:WIK                 Illumina NovaSeq 6000 paired end sequencing; scRNAseq of her4.3+ cells from lesi1d and unlesi1d zebrafish larvae spinal cord E MTAB 10390:Naive p Naive p scRNAseq of her4.3+ cells from lesioned and unlesioned zebrafish larvae spinal cord Trunks containing the lesion sites or equivalent site from unlesioned fish are collected and kept in PBS on ice.Incubate the trunks up to 300 in 1 mL of 1X Trypsin EDTA at 37C for 5 7 mins.Stop dissociation by adding FBS to a final concentration of 5%.Centrifuge at 200g for 7 mins.Discard Sups.Resuspend in 500 uL of PBS.Add the cell suspension into a 40 uM cell strainer.Centrifuge at 200g for 7 mins.Resuspend in the buffer for FACS PBS 5% FBS Following cell dissociation and FAC sorting samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines Following cell dissociation and FAC sorting samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines. Experimental Factor: injury:n1 RNA-Seq TRANSCRIPTOMIC SINGLE CELL Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   ERP128749 Illumina NovaSeq 6000 paired end sequencing; scRNAseq of her4.3+ cells from lesioned and unlesioned zebrafish larvae spinal cord ENA FIRST PUBLIC:2021 05 24|ENA LAST UPDATE:2021 05 24 Naive.bam bam 44972162730.0 499690697.0 E MTAB 10390:Naive 0:90 A:13658826375;C:8733304343;G:9348137569;T:13228064343;N:3830100 90       13658826375 8733304343 9348137569 13228064343 3830100 ERX5504346 ERS6343450 ERA4142789 University Of Edinburgh|European Nucleotide Archive University Of Edinburgh|European Nucleotide Archive 1 0.89428   0.32693   0.75276   0.5314   90   B   usable mapping rate illumina novaseq_era unknown poly_a unknown sc single_cell_droplet 10x   United Kingdom 2021-05-24 Larval Larval Spinal Cord Nervous System
10177 10177 ERR5858456 ERX5504345 ERS6343449 ERP128749 PRJEB44676 scRNAseq of her4.3+ cells from lesioned and unlesioned zebrafish larvae spinal cord E-MTAB-10390 Transcriptome Analysis To analyse lesion induced gene regulation in progenitor cells at single cell resolution we performed single cell RNAseq on FACS isolated her4.3:GFP progenitor cells from the spinal cord at 24 hours post lesion hpl post spinal injury at 3 dpf dpf compared to age matched uninjured animals. ENA FIRST PUBLIC:2021 05 24|ENA LAST UPDATE:2021 05 24   Protocols: Trunks containing the lesion sites or equivalent site from unlesioned fish are collected and kept in PBS on ice.Incubate the trunks up to 300 in 1 mL of 1X Trypsin EDTA at 37C for 5 7 mins.Stop dissociation by adding FBS to a final concentration of 5%.Centrifuge at 200g for 7 mins.Discard Sups.Resuspend in 500 uL of PBS.Add the cell suspension into a 40 uM cell strainer.Centrifuge at 200g for 7 mins.Resuspend in the buffer for FACS PBS 5% FBS Following cell dissociation and FAC sorting samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines Following cell dissociation and FAC sorting samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines. Lesi1d SAMEA8658903 University Of Edinburgh ENA first public:2021 05 24|ENA last update:2021 05 24|External Id:SAMEA8658903|INSDC center alias:UOE|INSDC center name:University Of Edinburgh|INSDC first public:2021 05 24T00:14:32Z|INSDC last update:2021 05 24T00:14:32Z|INSDC status:public|Submitter Id:E MTAB 10390:Lesi1d|age:4|broker name:ArrayExpress|cell type:ependymo radial glial cell|common name:zebrafish|developmental stage:larval day 4|immunophenotype:Her4.3+ positive|injury:spinal injury lesion|organism part:spinal cord|sample name:E MTAB 10390:Lesi1d|sex:mixed|strain:WIK                 Illumina NovaSeq 6000 paired end sequencing; scRNAseq of her4.3+ cells from lesi1d and unlesi1d zebrafish larvae spinal cord E MTAB 10390:Lesioned p Lesioned p scRNAseq of her4.3+ cells from lesioned and unlesioned zebrafish larvae spinal cord Trunks containing the lesion sites or equivalent site from unlesioned fish are collected and kept in PBS on ice.Incubate the trunks up to 300 in 1 mL of 1X Trypsin EDTA at 37C for 5 7 mins.Stop dissociation by adding FBS to a final concentration of 5%.Centrifuge at 200g for 7 mins.Discard Sups.Resuspend in 500 uL of PBS.Add the cell suspension into a 40 uM cell strainer.Centrifuge at 200g for 7 mins.Resuspend in the buffer for FACS PBS 5% FBS Following cell dissociation and FAC sorting samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines Following cell dissociation and FAC sorting samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines. Experimental Factor: injury:spinal injury lesion RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   ERP128749 Illumina NovaSeq 6000 paired end sequencing; scRNAseq of her4.3+ cells from lesioned and unlesioned zebrafish larvae spinal cord ENA FIRST PUBLIC:2021 05 24|ENA LAST UPDATE:2021 05 24 Lesioned.bam bam 49902588630.0 554473207.0 E MTAB 10390:Lesioned 0:90 A:14713351178;C:10191139050;G:10897887675;T:14095967201;N:4243526 90       14713351178 10191139050 10897887675 14095967201 4243526 ERX5504345 ERS6343449 ERA4142789 University Of Edinburgh|European Nucleotide Archive University Of Edinburgh|European Nucleotide Archive 1 0.91197   0.29137   0.7568   0.56523   90   B   usable mapping rate illumina novaseq_era unknown poly_a unknown sc single_cell_droplet 10x   United Kingdom 2021-05-24 Larval Larval Spinal Cord Nervous System
10407 10407 ERR9077202 ERX8620336 ERS10857224 ERP135966 PRJEB51339 RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae E-MTAB-11505 Transcriptome Analysis Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae. ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21   Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines. Sv2aWT5S8 SAMEA13254181 Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg ENA first public:2022 04 21|ENA last update:2022 04 21|External Id:SAMEA13254181|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC first public:2022 04 21T00:32:07Z|INSDC last update:2022 04 21T00:32:07Z|INSDC status:public|Submitter Id:E MTAB 11505:Sv2aWT5S8|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:sv2a+/+|individual:pool of 10 heads|organism part:head|sample name:E MTAB 11505:Sv2aWT5S8|sex:not available|strain:AB                 NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae E MTAB 11505:Sv2aWT5S8 s Sv2aWT5S8 s RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines. Experimental Factor: genotype:sv2a+/+ RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 500   ERP135966 NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21 sv2aWT5S8L001-1.fastq.gz fastq 652046291.0 8633105.0 E MTAB 11505:sv2aWT5S8L001 0:75.53 1:0 A:159570243;C:156420495;G:154853315;T:181073030;N:129208 75 0     159570243 156420495 154853315 181073030 129208 ERX8620336 ERS10857224 ERA9644804 Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive 1 0.95245   0.1148   0.65756   0.47011   75   B   usable mapping rate illumina nextseq unknown poly_a trueseq bulk unknown unknown   Belgium 2022-04-21 Larval Larval Head Nervous System
10408 10408 ERR9077203 ERX8620336 ERS10857224 ERP135966 PRJEB51339 RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae E-MTAB-11505 Transcriptome Analysis Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae. ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21   Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines. Sv2aWT5S8 SAMEA13254181 Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg ENA first public:2022 04 21|ENA last update:2022 04 21|External Id:SAMEA13254181|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC first public:2022 04 21T00:32:07Z|INSDC last update:2022 04 21T00:32:07Z|INSDC status:public|Submitter Id:E MTAB 11505:Sv2aWT5S8|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:sv2a+/+|individual:pool of 10 heads|organism part:head|sample name:E MTAB 11505:Sv2aWT5S8|sex:not available|strain:AB                 NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae E MTAB 11505:Sv2aWT5S8 s Sv2aWT5S8 s RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines. Experimental Factor: genotype:sv2a+/+ RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 500   ERP135966 NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21 sv2aWT5S8L002-1.fastq.gz fastq 653840525.0 8656886.0 E MTAB 11505:sv2aWT5S8L002 0:75.53 1:0 A:159902458;C:156826842;G:155509070;T:181475104;N:127051 75 0     159902458 156826842 155509070 181475104 127051 ERX8620336 ERS10857224 ERA9644804 Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive 1 0.95226   0.1156   0.65792   0.4667   76   B   usable mapping rate illumina nextseq unknown poly_a trueseq bulk unknown unknown   Belgium 2022-04-21 Larval Larval Head Nervous System
10409 10409 ERR9077204 ERX8620336 ERS10857224 ERP135966 PRJEB51339 RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae E-MTAB-11505 Transcriptome Analysis Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae. ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21   Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines. Sv2aWT5S8 SAMEA13254181 Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg ENA first public:2022 04 21|ENA last update:2022 04 21|External Id:SAMEA13254181|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC first public:2022 04 21T00:32:07Z|INSDC last update:2022 04 21T00:32:07Z|INSDC status:public|Submitter Id:E MTAB 11505:Sv2aWT5S8|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:sv2a+/+|individual:pool of 10 heads|organism part:head|sample name:E MTAB 11505:Sv2aWT5S8|sex:not available|strain:AB                 NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae E MTAB 11505:Sv2aWT5S8 s Sv2aWT5S8 s RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines. Experimental Factor: genotype:sv2a+/+ RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 500   ERP135966 NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21 sv2aWT5S8L003-1.fastq.gz fastq 659584196.0 8732885.0 E MTAB 11505:sv2aWT5S8L003 0:75.53 1:0 A:161257146;C:158299734;G:156793443;T:183128972;N:104901 75 0     161257146 158299734 156793443 183128972 104901 ERX8620336 ERS10857224 ERA9644804 Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive 1 0.95298   0.11485   0.65798   0.46853   76   B   usable mapping rate illumina nextseq unknown poly_a trueseq bulk unknown unknown   Belgium 2022-04-21 Larval Larval Head Nervous System
10410 10410 ERR9077205 ERX8620336 ERS10857224 ERP135966 PRJEB51339 RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae E-MTAB-11505 Transcriptome Analysis Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae. ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21   Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines. Sv2aWT5S8 SAMEA13254181 Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg ENA first public:2022 04 21|ENA last update:2022 04 21|External Id:SAMEA13254181|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC first public:2022 04 21T00:32:07Z|INSDC last update:2022 04 21T00:32:07Z|INSDC status:public|Submitter Id:E MTAB 11505:Sv2aWT5S8|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:sv2a+/+|individual:pool of 10 heads|organism part:head|sample name:E MTAB 11505:Sv2aWT5S8|sex:not available|strain:AB                 NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae E MTAB 11505:Sv2aWT5S8 s Sv2aWT5S8 s RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines. Experimental Factor: genotype:sv2a+/+ RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 500   ERP135966 NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21 sv2aWT5S8L004-1.fastq.gz fastq 666627746.0 8826123.0 E MTAB 11505:sv2aWT5S8L004 0:75.53 1:0 A:162975131;C:159937258;G:158506242;T:185106149;N:102966 75 0     162975131 159937258 158506242 185106149 102966 ERX8620336 ERS10857224 ERA9644804 Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive 1 0.9531   0.11425   0.65736   0.47309   76   B   usable mapping rate illumina nextseq unknown poly_a trueseq bulk unknown unknown   Belgium 2022-04-21 Larval Larval Head Nervous System
10411 10411 ERR9077198 ERX8620335 ERS10857223 ERP135966 PRJEB51339 RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae E-MTAB-11505 Transcriptome Analysis Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae. ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21   Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines. Sv2aWT4S7 SAMEA13254180 Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg ENA first public:2022 04 21|ENA last update:2022 04 21|External Id:SAMEA13254180|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC first public:2022 04 21T00:32:07Z|INSDC last update:2022 04 21T00:32:07Z|INSDC status:public|Submitter Id:E MTAB 11505:Sv2aWT4S7|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:sv2a+/+|individual:pool of 10 heads|organism part:head|sample name:E MTAB 11505:Sv2aWT4S7|sex:not available|strain:AB                 NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae E MTAB 11505:Sv2aWT4S7 s Sv2aWT4S7 s RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines. Experimental Factor: genotype:sv2a+/+ RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 500   ERP135966 NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21 sv2aWT4S7L001-1.fastq.gz fastq 683751258.0 9051795.0 E MTAB 11505:sv2aWT4S7L001 0:75.54 1:0 A:162889923;C:167127644;G:164779384;T:188822907;N:131400 75 0     162889923 167127644 164779384 188822907 131400 ERX8620335 ERS10857223 ERA9644804 Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive 1 0.95739   0.0959   0.6606   0.46826   75   B   usable mapping rate illumina nextseq unknown poly_a trueseq bulk unknown unknown   Belgium 2022-04-21 Larval Larval Head Nervous System
10412 10412 ERR9077199 ERX8620335 ERS10857223 ERP135966 PRJEB51339 RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae E-MTAB-11505 Transcriptome Analysis Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae. ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21   Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines. Sv2aWT4S7 SAMEA13254180 Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg ENA first public:2022 04 21|ENA last update:2022 04 21|External Id:SAMEA13254180|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC first public:2022 04 21T00:32:07Z|INSDC last update:2022 04 21T00:32:07Z|INSDC status:public|Submitter Id:E MTAB 11505:Sv2aWT4S7|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:sv2a+/+|individual:pool of 10 heads|organism part:head|sample name:E MTAB 11505:Sv2aWT4S7|sex:not available|strain:AB                 NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae E MTAB 11505:Sv2aWT4S7 s Sv2aWT4S7 s RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines. Experimental Factor: genotype:sv2a+/+ RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 500   ERP135966 NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21 sv2aWT4S7L002-1.fastq.gz fastq 684187711.0 9057591.0 E MTAB 11505:sv2aWT4S7L002 0:75.54 1:0 A:162923879;C:167246213;G:165071145;T:188818774;N:127700 75 0     162923879 167246213 165071145 188818774 127700 ERX8620335 ERS10857223 ERA9644804 Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive 1 0.95724   0.0959   0.66036   0.47026   76   B   usable mapping rate illumina nextseq unknown poly_a trueseq bulk unknown unknown   Belgium 2022-04-21 Larval Larval Head Nervous System
10413 10413 ERR9077200 ERX8620335 ERS10857223 ERP135966 PRJEB51339 RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae E-MTAB-11505 Transcriptome Analysis Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae. ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21   Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines. Sv2aWT4S7 SAMEA13254180 Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg ENA first public:2022 04 21|ENA last update:2022 04 21|External Id:SAMEA13254180|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC first public:2022 04 21T00:32:07Z|INSDC last update:2022 04 21T00:32:07Z|INSDC status:public|Submitter Id:E MTAB 11505:Sv2aWT4S7|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:sv2a+/+|individual:pool of 10 heads|organism part:head|sample name:E MTAB 11505:Sv2aWT4S7|sex:not available|strain:AB                 NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae E MTAB 11505:Sv2aWT4S7 s Sv2aWT4S7 s RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines. Experimental Factor: genotype:sv2a+/+ RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 500   ERP135966 NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21 sv2aWT4S7L003-1.fastq.gz fastq 692320213.0 9165132.0 E MTAB 11505:sv2aWT4S7L003 0:75.54 1:0 A:164772792;C:169329920;G:166952052;T:191164422;N:101027 75 0     164772792 169329920 166952052 191164422 101027 ERX8620335 ERS10857223 ERA9644804 Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive 1 0.95786   0.09701   0.66131   0.47564   76   B   usable mapping rate illumina nextseq unknown poly_a trueseq bulk unknown unknown   Belgium 2022-04-21 Larval Larval Head Nervous System
10414 10414 ERR9077201 ERX8620335 ERS10857223 ERP135966 PRJEB51339 RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae E-MTAB-11505 Transcriptome Analysis Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae. ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21   Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines. Sv2aWT4S7 SAMEA13254180 Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg ENA first public:2022 04 21|ENA last update:2022 04 21|External Id:SAMEA13254180|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC first public:2022 04 21T00:32:07Z|INSDC last update:2022 04 21T00:32:07Z|INSDC status:public|Submitter Id:E MTAB 11505:Sv2aWT4S7|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:sv2a+/+|individual:pool of 10 heads|organism part:head|sample name:E MTAB 11505:Sv2aWT4S7|sex:not available|strain:AB                 NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae E MTAB 11505:Sv2aWT4S7 s Sv2aWT4S7 s RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines. Experimental Factor: genotype:sv2a+/+ RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 500   ERP135966 NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21 sv2aWT4S7L004-1.fastq.gz fastq 697047881.0 9227702.0 E MTAB 11505:sv2aWT4S7L004 0:75.54 1:0 A:165881728;C:170388393;G:168105900;T:192572068;N:99792 75 0     165881728 170388393 168105900 192572068 99792 ERX8620335 ERS10857223 ERA9644804 Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive 1 0.9584   0.09565   0.66115   0.46967   76   B   usable mapping rate illumina nextseq unknown poly_a trueseq bulk unknown unknown   Belgium 2022-04-21 Larval Larval Head Nervous System
10415 10415 ERR9077194 ERX8620334 ERS10857222 ERP135966 PRJEB51339 RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae E-MTAB-11505 Transcriptome Analysis Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae. ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21   Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines. Sv2aWT3S2 SAMEA13254179 Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg ENA first public:2022 04 21|ENA last update:2022 04 21|External Id:SAMEA13254179|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC first public:2022 04 21T00:32:07Z|INSDC last update:2022 04 21T00:32:07Z|INSDC status:public|Submitter Id:E MTAB 11505:Sv2aWT3S2|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:sv2a+/+|individual:pool of 10 heads|organism part:head|sample name:E MTAB 11505:Sv2aWT3S2|sex:not available|strain:AB                 NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae E MTAB 11505:Sv2aWT3S2 s Sv2aWT3S2 s RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines. Experimental Factor: genotype:sv2a+/+ RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 500   ERP135966 NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21 sv2aWT3S2L001-1.fastq.gz fastq 723508205.0 9579193.0 E MTAB 11505:sv2aWT3S2L001 0:75.53 1:0 A:177832489;C:174193135;G:169978598;T:201360184;N:143799 75 0     177832489 174193135 169978598 201360184 143799 ERX8620334 ERS10857222 ERA9644804 Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive 1 0.95218   0.11732   0.65916   0.47955   71   B   usable mapping rate illumina nextseq unknown poly_a trueseq bulk unknown unknown   Belgium 2022-04-21 Larval Larval Head Nervous System
10416 10416 ERR9077195 ERX8620334 ERS10857222 ERP135966 PRJEB51339 RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae E-MTAB-11505 Transcriptome Analysis Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae. ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21   Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines. Sv2aWT3S2 SAMEA13254179 Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg ENA first public:2022 04 21|ENA last update:2022 04 21|External Id:SAMEA13254179|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC first public:2022 04 21T00:32:07Z|INSDC last update:2022 04 21T00:32:07Z|INSDC status:public|Submitter Id:E MTAB 11505:Sv2aWT3S2|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:sv2a+/+|individual:pool of 10 heads|organism part:head|sample name:E MTAB 11505:Sv2aWT3S2|sex:not available|strain:AB                 NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae E MTAB 11505:Sv2aWT3S2 s Sv2aWT3S2 s RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines. Experimental Factor: genotype:sv2a+/+ RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 500   ERP135966 NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21 sv2aWT3S2L002-1.fastq.gz fastq 726190024.0 9614674.0 E MTAB 11505:sv2aWT3S2L002 0:75.53 1:0 A:178408224;C:174776263;G:170820745;T:202047224;N:137568 75 0     178408224 174776263 170820745 202047224 137568 ERX8620334 ERS10857222 ERA9644804 Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive 1 0.95093   0.11567   0.65865   0.46877   75   B   usable mapping rate illumina nextseq unknown poly_a trueseq bulk unknown unknown   Belgium 2022-04-21 Larval Larval Head Nervous System
10417 10417 ERR9077196 ERX8620334 ERS10857222 ERP135966 PRJEB51339 RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae E-MTAB-11505 Transcriptome Analysis Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae. ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21   Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines. Sv2aWT3S2 SAMEA13254179 Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg ENA first public:2022 04 21|ENA last update:2022 04 21|External Id:SAMEA13254179|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC first public:2022 04 21T00:32:07Z|INSDC last update:2022 04 21T00:32:07Z|INSDC status:public|Submitter Id:E MTAB 11505:Sv2aWT3S2|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:sv2a+/+|individual:pool of 10 heads|organism part:head|sample name:E MTAB 11505:Sv2aWT3S2|sex:not available|strain:AB                 NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae E MTAB 11505:Sv2aWT3S2 s Sv2aWT3S2 s RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines. Experimental Factor: genotype:sv2a+/+ RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 500   ERP135966 NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21 sv2aWT3S2L003-1.fastq.gz fastq 735499955.0 9737845.0 E MTAB 11505:sv2aWT3S2L003 0:75.53 1:0 A:180659962;C:177141362;G:172905323;T:204678308;N:115000 75 0     180659962 177141362 172905323 204678308 115000 ERX8620334 ERS10857222 ERA9644804 Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive 1 0.95233   0.11614   0.65898   0.47114   76   B   usable mapping rate illumina nextseq unknown poly_a trueseq bulk unknown unknown   Belgium 2022-04-21 Larval Larval Head Nervous System
10418 10418 ERR9077197 ERX8620334 ERS10857222 ERP135966 PRJEB51339 RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae E-MTAB-11505 Transcriptome Analysis Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae. ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21   Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines. Sv2aWT3S2 SAMEA13254179 Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg ENA first public:2022 04 21|ENA last update:2022 04 21|External Id:SAMEA13254179|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC first public:2022 04 21T00:32:07Z|INSDC last update:2022 04 21T00:32:07Z|INSDC status:public|Submitter Id:E MTAB 11505:Sv2aWT3S2|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:sv2a+/+|individual:pool of 10 heads|organism part:head|sample name:E MTAB 11505:Sv2aWT3S2|sex:not available|strain:AB                 NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae E MTAB 11505:Sv2aWT3S2 s Sv2aWT3S2 s RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines. Experimental Factor: genotype:sv2a+/+ RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 500   ERP135966 NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21 sv2aWT3S2L004-1.fastq.gz fastq 745285512.0 9867337.0 E MTAB 11505:sv2aWT3S2L004 0:75.53 1:0 A:183067487;C:179408382;G:175250814;T:207445912;N:112917 75 0     183067487 179408382 175250814 207445912 112917 ERX8620334 ERS10857222 ERA9644804 Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive 1 0.95245   0.11655   0.65857   0.47087   76   B   usable mapping rate illumina nextseq unknown poly_a trueseq bulk unknown unknown   Belgium 2022-04-21 Larval Larval Head Nervous System
10419 10419 ERR9077190 ERX8620333 ERS10857221 ERP135966 PRJEB51339 RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae E-MTAB-11505 Transcriptome Analysis Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae. ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21   Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines. Sv2aWT1S1 SAMEA13254178 Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg ENA first public:2022 04 21|ENA last update:2022 04 21|External Id:SAMEA13254178|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC first public:2022 04 21T00:32:07Z|INSDC last update:2022 04 21T00:32:07Z|INSDC status:public|Submitter Id:E MTAB 11505:Sv2aWT1S1|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:sv2a+/+|individual:pool of 10 heads|organism part:head|sample name:E MTAB 11505:Sv2aWT1S1|sex:not available|strain:AB                 NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae E MTAB 11505:Sv2aWT1S1 s Sv2aWT1S1 s RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines. Experimental Factor: genotype:sv2a+/+ RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 500   ERP135966 NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21 sv2aWT1S1L001-1.fastq.gz fastq 647414748.0 8571883.0 E MTAB 11505:sv2aWT1S1L001 0:75.53 1:0 A:154593859;C:160498057;G:153809612;T:178389112;N:124108 75 0     154593859 160498057 153809612 178389112 124108 ERX8620333 ERS10857221 ERA9644804 Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive 1 0.95955   0.08686   0.65955   0.47406   76   B   usable mapping rate illumina nextseq unknown poly_a trueseq bulk unknown unknown   Belgium 2022-04-21 Larval Larval Head Nervous System
10420 10420 ERR9077191 ERX8620333 ERS10857221 ERP135966 PRJEB51339 RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae E-MTAB-11505 Transcriptome Analysis Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae. ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21   Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines. Sv2aWT1S1 SAMEA13254178 Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg ENA first public:2022 04 21|ENA last update:2022 04 21|External Id:SAMEA13254178|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC first public:2022 04 21T00:32:07Z|INSDC last update:2022 04 21T00:32:07Z|INSDC status:public|Submitter Id:E MTAB 11505:Sv2aWT1S1|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:sv2a+/+|individual:pool of 10 heads|organism part:head|sample name:E MTAB 11505:Sv2aWT1S1|sex:not available|strain:AB                 NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae E MTAB 11505:Sv2aWT1S1 s Sv2aWT1S1 s RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines. Experimental Factor: genotype:sv2a+/+ RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 500   ERP135966 NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21 sv2aWT1S1L002-1.fastq.gz fastq 646657758.0 8561861.0 E MTAB 11505:sv2aWT1S1L002 0:75.53 1:0 A:154348044;C:160294625;G:153804048;T:178092212;N:118829 75 0     154348044 160294625 153804048 178092212 118829 ERX8620333 ERS10857221 ERA9644804 Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive 1 0.95942   0.08632   0.65991   0.47539   76   B   usable mapping rate illumina nextseq unknown poly_a trueseq bulk unknown unknown   Belgium 2022-04-21 Larval Larval Head Nervous System
10421 10421 ERR9077192 ERX8620333 ERS10857221 ERP135966 PRJEB51339 RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae E-MTAB-11505 Transcriptome Analysis Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae. ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21   Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines. Sv2aWT1S1 SAMEA13254178 Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg ENA first public:2022 04 21|ENA last update:2022 04 21|External Id:SAMEA13254178|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC first public:2022 04 21T00:32:07Z|INSDC last update:2022 04 21T00:32:07Z|INSDC status:public|Submitter Id:E MTAB 11505:Sv2aWT1S1|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:sv2a+/+|individual:pool of 10 heads|organism part:head|sample name:E MTAB 11505:Sv2aWT1S1|sex:not available|strain:AB                 NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae E MTAB 11505:Sv2aWT1S1 s Sv2aWT1S1 s RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines. Experimental Factor: genotype:sv2a+/+ RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 500   ERP135966 NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21 sv2aWT1S1L003-1.fastq.gz fastq 654781451.0 8669333.0 E MTAB 11505:sv2aWT1S1L003 0:75.53 1:0 A:156252744;C:162396721;G:155681450;T:180352911;N:97625 75 0     156252744 162396721 155681450 180352911 97625 ERX8620333 ERS10857221 ERA9644804 Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive 1 0.95972   0.08498   0.66137   0.47457   75   B   usable mapping rate illumina nextseq unknown poly_a trueseq bulk unknown unknown   Belgium 2022-04-21 Larval Larval Head Nervous System
10422 10422 ERR9077193 ERX8620333 ERS10857221 ERP135966 PRJEB51339 RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae E-MTAB-11505 Transcriptome Analysis Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae. ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21   Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines. Sv2aWT1S1 SAMEA13254178 Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg ENA first public:2022 04 21|ENA last update:2022 04 21|External Id:SAMEA13254178|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC first public:2022 04 21T00:32:07Z|INSDC last update:2022 04 21T00:32:07Z|INSDC status:public|Submitter Id:E MTAB 11505:Sv2aWT1S1|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:sv2a+/+|individual:pool of 10 heads|organism part:head|sample name:E MTAB 11505:Sv2aWT1S1|sex:not available|strain:AB                 NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae E MTAB 11505:Sv2aWT1S1 s Sv2aWT1S1 s RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines. Experimental Factor: genotype:sv2a+/+ RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 500   ERP135966 NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21 sv2aWT1S1L004-1.fastq.gz fastq 659716937.0 8734618.0 E MTAB 11505:sv2aWT1S1L004 0:75.53 1:0 A:157367211;C:163585842;G:156911139;T:181757809;N:94936 75 0     157367211 163585842 156911139 181757809 94936 ERX8620333 ERS10857221 ERA9644804 Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive 1 0.95985   0.08585   0.65857   0.47349   76   B   usable mapping rate illumina nextseq unknown poly_a trueseq bulk unknown unknown   Belgium 2022-04-21 Larval Larval Head Nervous System
10423 10423 ERR9077186 ERX8620332 ERS10857220 ERP135966 PRJEB51339 RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae E-MTAB-11505 Transcriptome Analysis Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae. ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21   Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines. Sv2aHO6S12 SAMEA13254177 Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg ENA first public:2022 04 21|ENA last update:2022 04 21|External Id:SAMEA13254177|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC first public:2022 04 21T00:32:07Z|INSDC last update:2022 04 21T00:32:07Z|INSDC status:public|Submitter Id:E MTAB 11505:Sv2aHO6S12|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:sv2a / |individual:pool of 10 heads|organism part:head|sample name:E MTAB 11505:Sv2aHO6S12|sex:not available|strain:AB                 NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae E MTAB 11505:Sv2aHO6S12 s Sv2aHO6S12 s RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines. Experimental Factor: genotype:sv2a / RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 500   ERP135966 NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21 sv2aHO6S12L001-1.fastq.gz fastq 675018261.0 8937958.0 E MTAB 11505:sv2aHO6S12L001 0:75.52 1:0 A:166564263;C:160539328;G:160003980;T:187773509;N:137181 75 0     166564263 160539328 160003980 187773509 137181 ERX8620332 ERS10857220 ERA9644804 Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive 1 0.94964   0.13009   0.65413   0.47079   76   B   usable mapping rate illumina nextseq unknown poly_a trueseq bulk unknown unknown   Belgium 2022-04-21 Larval Larval Head Nervous System
10424 10424 ERR9077187 ERX8620332 ERS10857220 ERP135966 PRJEB51339 RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae E-MTAB-11505 Transcriptome Analysis Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae. ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21   Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines. Sv2aHO6S12 SAMEA13254177 Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg ENA first public:2022 04 21|ENA last update:2022 04 21|External Id:SAMEA13254177|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC first public:2022 04 21T00:32:07Z|INSDC last update:2022 04 21T00:32:07Z|INSDC status:public|Submitter Id:E MTAB 11505:Sv2aHO6S12|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:sv2a / |individual:pool of 10 heads|organism part:head|sample name:E MTAB 11505:Sv2aHO6S12|sex:not available|strain:AB                 NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae E MTAB 11505:Sv2aHO6S12 s Sv2aHO6S12 s RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines. Experimental Factor: genotype:sv2a / RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 500   ERP135966 NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21 sv2aHO6S12L002-1.fastq.gz fastq 672995667.0 8911161.0 E MTAB 11505:sv2aHO6S12L002 0:75.52 1:0 A:165990319;C:160039398;G:159722501;T:187108781;N:134668 75 0     165990319 160039398 159722501 187108781 134668 ERX8620332 ERS10857220 ERA9644804 Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive 1 0.94837   0.13029   0.65744   0.47959   76   B   usable mapping rate illumina nextseq unknown poly_a trueseq bulk unknown unknown   Belgium 2022-04-21 Larval Larval Head Nervous System
10425 10425 ERR9077188 ERX8620332 ERS10857220 ERP135966 PRJEB51339 RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae E-MTAB-11505 Transcriptome Analysis Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae. ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21   Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines. Sv2aHO6S12 SAMEA13254177 Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg ENA first public:2022 04 21|ENA last update:2022 04 21|External Id:SAMEA13254177|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC first public:2022 04 21T00:32:07Z|INSDC last update:2022 04 21T00:32:07Z|INSDC status:public|Submitter Id:E MTAB 11505:Sv2aHO6S12|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:sv2a / |individual:pool of 10 heads|organism part:head|sample name:E MTAB 11505:Sv2aHO6S12|sex:not available|strain:AB                 NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae E MTAB 11505:Sv2aHO6S12 s Sv2aHO6S12 s RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines. Experimental Factor: genotype:sv2a / RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 500   ERP135966 NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21 sv2aHO6S12L003-1.fastq.gz fastq 683276767.0 9047147.0 E MTAB 11505:sv2aHO6S12L003 0:75.52 1:0 A:168501690;C:162583852;G:162063190;T:190018001;N:110034 75 0     168501690 162583852 162063190 190018001 110034 ERX8620332 ERS10857220 ERA9644804 Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive 1 0.94983   0.13248   0.6565   0.47977   76   B   usable mapping rate illumina nextseq unknown poly_a trueseq bulk unknown unknown   Belgium 2022-04-21 Larval Larval Head Nervous System
10426 10426 ERR9077189 ERX8620332 ERS10857220 ERP135966 PRJEB51339 RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae E-MTAB-11505 Transcriptome Analysis Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae. ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21   Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines. Sv2aHO6S12 SAMEA13254177 Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg ENA first public:2022 04 21|ENA last update:2022 04 21|External Id:SAMEA13254177|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC first public:2022 04 21T00:32:07Z|INSDC last update:2022 04 21T00:32:07Z|INSDC status:public|Submitter Id:E MTAB 11505:Sv2aHO6S12|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:sv2a / |individual:pool of 10 heads|organism part:head|sample name:E MTAB 11505:Sv2aHO6S12|sex:not available|strain:AB                 NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae E MTAB 11505:Sv2aHO6S12 s Sv2aHO6S12 s RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines. Experimental Factor: genotype:sv2a / RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 500   ERP135966 NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21 sv2aHO6S12L004-1.fastq.gz fastq 686469910.0 9089431.0 E MTAB 11505:sv2aHO6S12L004 0:75.52 1:0 A:169287189;C:163276361;G:162844724;T:190954218;N:107418 75 0     169287189 163276361 162844724 190954218 107418 ERX8620332 ERS10857220 ERA9644804 Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive 1 0.95061   0.13029   0.65389   0.48044   76   B   usable mapping rate illumina nextseq unknown poly_a trueseq bulk unknown unknown   Belgium 2022-04-21 Larval Larval Head Nervous System
10427 10427 ERR9077182 ERX8620331 ERS10857219 ERP135966 PRJEB51339 RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae E-MTAB-11505 Transcriptome Analysis Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae. ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21   Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines. Sv2aHO4S10 SAMEA13254176 Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg ENA first public:2022 04 21|ENA last update:2022 04 21|External Id:SAMEA13254176|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC first public:2022 04 21T00:32:07Z|INSDC last update:2022 04 21T00:32:07Z|INSDC status:public|Submitter Id:E MTAB 11505:Sv2aHO4S10|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:sv2a / |individual:pool of 10 heads|organism part:head|sample name:E MTAB 11505:Sv2aHO4S10|sex:not available|strain:AB                 NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae E MTAB 11505:Sv2aHO4S10 s Sv2aHO4S10 s RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines. Experimental Factor: genotype:sv2a / RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 500   ERP135966 NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21 sv2aHO4S10L001-1.fastq.gz fastq 713858966.0 9452474.0 E MTAB 11505:sv2aHO4S10L001 0:75.52 1:0 A:177913695;C:169425317;G:167540012;T:198835532;N:144410 75 0     177913695 169425317 167540012 198835532 144410 ERX8620331 ERS10857219 ERA9644804 Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive 1 0.94848   0.12981   0.6636   0.47772   76   B   usable mapping rate illumina nextseq unknown poly_a trueseq bulk unknown unknown   Belgium 2022-04-21 Larval Larval Head Nervous System
10428 10428 ERR9077183 ERX8620331 ERS10857219 ERP135966 PRJEB51339 RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae E-MTAB-11505 Transcriptome Analysis Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae. ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21   Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines. Sv2aHO4S10 SAMEA13254176 Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg ENA first public:2022 04 21|ENA last update:2022 04 21|External Id:SAMEA13254176|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC first public:2022 04 21T00:32:07Z|INSDC last update:2022 04 21T00:32:07Z|INSDC status:public|Submitter Id:E MTAB 11505:Sv2aHO4S10|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:sv2a / |individual:pool of 10 heads|organism part:head|sample name:E MTAB 11505:Sv2aHO4S10|sex:not available|strain:AB                 NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae E MTAB 11505:Sv2aHO4S10 s Sv2aHO4S10 s RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines. Experimental Factor: genotype:sv2a / RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 500   ERP135966 NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21 sv2aHO4S10L002-1.fastq.gz fastq 717619593.0 9502301.0 E MTAB 11505:sv2aHO4S10L002 0:75.52 1:0 A:178830542;C:170284720;G:168594514;T:199773382;N:136435 75 0     178830542 170284720 168594514 199773382 136435 ERX8620331 ERS10857219 ERA9644804 Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive 1 0.94812   0.12868   0.6645   0.47281   75   B   usable mapping rate illumina nextseq unknown poly_a trueseq bulk unknown unknown   Belgium 2022-04-21 Larval Larval Head Nervous System
10429 10429 ERR9077184 ERX8620331 ERS10857219 ERP135966 PRJEB51339 RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae E-MTAB-11505 Transcriptome Analysis Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae. ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21   Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines. Sv2aHO4S10 SAMEA13254176 Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg ENA first public:2022 04 21|ENA last update:2022 04 21|External Id:SAMEA13254176|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC first public:2022 04 21T00:32:07Z|INSDC last update:2022 04 21T00:32:07Z|INSDC status:public|Submitter Id:E MTAB 11505:Sv2aHO4S10|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:sv2a / |individual:pool of 10 heads|organism part:head|sample name:E MTAB 11505:Sv2aHO4S10|sex:not available|strain:AB                 NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae E MTAB 11505:Sv2aHO4S10 s Sv2aHO4S10 s RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines. Experimental Factor: genotype:sv2a / RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 500   ERP135966 NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21 sv2aHO4S10L003-1.fastq.gz fastq 727263626.0 9629858.0 E MTAB 11505:sv2aHO4S10L003 0:75.52 1:0 A:181201278;C:172619520;G:170780953;T:202550397;N:111478 75 0     181201278 172619520 170780953 202550397 111478 ERX8620331 ERS10857219 ERA9644804 Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive 1 0.94768   0.12827   0.66596   0.47332   76   B   usable mapping rate illumina nextseq unknown poly_a trueseq bulk unknown unknown   Belgium 2022-04-21 Larval Larval Head Nervous System
10430 10430 ERR9077185 ERX8620331 ERS10857219 ERP135966 PRJEB51339 RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae E-MTAB-11505 Transcriptome Analysis Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae. ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21   Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines. Sv2aHO4S10 SAMEA13254176 Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg ENA first public:2022 04 21|ENA last update:2022 04 21|External Id:SAMEA13254176|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC first public:2022 04 21T00:32:07Z|INSDC last update:2022 04 21T00:32:07Z|INSDC status:public|Submitter Id:E MTAB 11505:Sv2aHO4S10|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:sv2a / |individual:pool of 10 heads|organism part:head|sample name:E MTAB 11505:Sv2aHO4S10|sex:not available|strain:AB                 NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae E MTAB 11505:Sv2aHO4S10 s Sv2aHO4S10 s RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines. Experimental Factor: genotype:sv2a / RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 500   ERP135966 NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21 sv2aHO4S10L004-1.fastq.gz fastq 736595278.0 9753337.0 E MTAB 11505:sv2aHO4S10L004 0:75.52 1:0 A:183510872;C:174806534;G:173027794;T:205140640;N:109438 75 0     183510872 174806534 173027794 205140640 109438 ERX8620331 ERS10857219 ERA9644804 Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive 1 0.94925   0.12904   0.66417   0.47297   76   B   usable mapping rate illumina nextseq unknown poly_a trueseq bulk unknown unknown   Belgium 2022-04-21 Larval Larval Head Nervous System
10431 10431 ERR9077178 ERX8620330 ERS10857218 ERP135966 PRJEB51339 RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae E-MTAB-11505 Transcriptome Analysis Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae. ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21   Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines. Sv2aHO3S6 SAMEA13254175 Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg ENA first public:2022 04 21|ENA last update:2022 04 21|External Id:SAMEA13254175|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC first public:2022 04 21T00:32:07Z|INSDC last update:2022 04 21T00:32:07Z|INSDC status:public|Submitter Id:E MTAB 11505:Sv2aHO3S6|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:sv2a / |individual:pool of 10 heads|organism part:head|sample name:E MTAB 11505:Sv2aHO3S6|sex:not available|strain:AB                 NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae E MTAB 11505:Sv2aHO3S6 s Sv2aHO3S6 s RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines. Experimental Factor: genotype:sv2a / RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 500   ERP135966 NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21 sv2aHO3S6L001-1.fastq.gz fastq 710756305.0 9410862.0 E MTAB 11505:sv2aHO3S6L001 0:75.53 1:0 A:175585613;C:170261120;G:166658917;T:198106388;N:144267 75 0     175585613 170261120 166658917 198106388 144267 ERX8620330 ERS10857218 ERA9644804 Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive 1 0.94827   0.14002   0.66785   0.474   75   B   usable mapping rate illumina nextseq unknown poly_a trueseq bulk unknown unknown   Belgium 2022-04-21 Larval Larval Head Nervous System
10432 10432 ERR9077179 ERX8620330 ERS10857218 ERP135966 PRJEB51339 RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae E-MTAB-11505 Transcriptome Analysis Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae. ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21   Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines. Sv2aHO3S6 SAMEA13254175 Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg ENA first public:2022 04 21|ENA last update:2022 04 21|External Id:SAMEA13254175|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC first public:2022 04 21T00:32:07Z|INSDC last update:2022 04 21T00:32:07Z|INSDC status:public|Submitter Id:E MTAB 11505:Sv2aHO3S6|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:sv2a / |individual:pool of 10 heads|organism part:head|sample name:E MTAB 11505:Sv2aHO3S6|sex:not available|strain:AB                 NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae E MTAB 11505:Sv2aHO3S6 s Sv2aHO3S6 s RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines. Experimental Factor: genotype:sv2a / RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 500   ERP135966 NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21 sv2aHO3S6L002-1.fastq.gz fastq 715330324.0 9471415.0 E MTAB 11505:sv2aHO3S6L002 0:75.53 1:0 A:176679775;C:171311031;G:167903237;T:199299483;N:136798 75 0     176679775 171311031 167903237 199299483 136798 ERX8620330 ERS10857218 ERA9644804 Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive 1 0.9469   0.13915   0.67004   0.47654   75   B   usable mapping rate illumina nextseq unknown poly_a trueseq bulk unknown unknown   Belgium 2022-04-21 Larval Larval Head Nervous System
10433 10433 ERR9077180 ERX8620330 ERS10857218 ERP135966 PRJEB51339 RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae E-MTAB-11505 Transcriptome Analysis Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae. ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21   Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines. Sv2aHO3S6 SAMEA13254175 Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg ENA first public:2022 04 21|ENA last update:2022 04 21|External Id:SAMEA13254175|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC first public:2022 04 21T00:32:07Z|INSDC last update:2022 04 21T00:32:07Z|INSDC status:public|Submitter Id:E MTAB 11505:Sv2aHO3S6|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:sv2a / |individual:pool of 10 heads|organism part:head|sample name:E MTAB 11505:Sv2aHO3S6|sex:not available|strain:AB                 NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae E MTAB 11505:Sv2aHO3S6 s Sv2aHO3S6 s RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines. Experimental Factor: genotype:sv2a / RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 500   ERP135966 NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21 sv2aHO3S6L003-1.fastq.gz fastq 722810562.0 9570364.0 E MTAB 11505:sv2aHO3S6L003 0:75.53 1:0 A:178442845;C:173192786;G:169595085;T:201465522;N:114324 75 0     178442845 173192786 169595085 201465522 114324 ERX8620330 ERS10857218 ERA9644804 Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive 1 0.94918   0.13979   0.66902   0.47572   75   B   usable mapping rate illumina nextseq unknown poly_a trueseq bulk unknown unknown   Belgium 2022-04-21 Larval Larval Head Nervous System
10434 10434 ERR9077181 ERX8620330 ERS10857218 ERP135966 PRJEB51339 RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae E-MTAB-11505 Transcriptome Analysis Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae. ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21   Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines. Sv2aHO3S6 SAMEA13254175 Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg ENA first public:2022 04 21|ENA last update:2022 04 21|External Id:SAMEA13254175|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC first public:2022 04 21T00:32:07Z|INSDC last update:2022 04 21T00:32:07Z|INSDC status:public|Submitter Id:E MTAB 11505:Sv2aHO3S6|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:sv2a / |individual:pool of 10 heads|organism part:head|sample name:E MTAB 11505:Sv2aHO3S6|sex:not available|strain:AB                 NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae E MTAB 11505:Sv2aHO3S6 s Sv2aHO3S6 s RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines. Experimental Factor: genotype:sv2a / RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 500   ERP135966 NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21 sv2aHO3S6L004-1.fastq.gz fastq 732990507.0 9705054.0 E MTAB 11505:sv2aHO3S6L004 0:75.53 1:0 A:180951130;C:175567778;G:172037542;T:204323488;N:110569 75 0     180951130 175567778 172037542 204323488 110569 ERX8620330 ERS10857218 ERA9644804 Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive 1 0.94812   0.13893   0.67085   0.47502   75   B   usable mapping rate illumina nextseq unknown poly_a trueseq bulk unknown unknown   Belgium 2022-04-21 Larval Larval Head Nervous System
10435 10435 ERR9077174 ERX8620329 ERS10857217 ERP135966 PRJEB51339 RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae E-MTAB-11505 Transcriptome Analysis Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae. ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21   Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines. Sv2aHET7S9 SAMEA13254174 Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg ENA first public:2022 04 21|ENA last update:2022 04 21|External Id:SAMEA13254174|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC first public:2022 04 21T00:32:07Z|INSDC last update:2022 04 21T00:32:07Z|INSDC status:public|Submitter Id:E MTAB 11505:Sv2aHET7S9|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:sv2a+/ |individual:pool of 10 heads|organism part:head|sample name:E MTAB 11505:Sv2aHET7S9|sex:not available|strain:AB                 NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae E MTAB 11505:Sv2aHET7S9 s Sv2aHET7S9 s RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines. Experimental Factor: genotype:sv2a+/ RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 500   ERP135966 NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21 sv2aHET7S9L001-1.fastq.gz fastq 773209432.0 10238087.0 E MTAB 11505:sv2aHET7S9L001 0:75.52 1:0 A:191962953;C:184699376;G:180774008;T:215620759;N:152336 75 0     191962953 184699376 180774008 215620759 152336 ERX8620329 ERS10857217 ERA9644804 Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive 1 0.95047   0.12485   0.65705   0.4775   76   B   usable mapping rate illumina nextseq unknown poly_a trueseq bulk unknown unknown   Belgium 2022-04-21 Larval Larval Head Nervous System
10436 10436 ERR9077175 ERX8620329 ERS10857217 ERP135966 PRJEB51339 RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae E-MTAB-11505 Transcriptome Analysis Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae. ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21   Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines. Sv2aHET7S9 SAMEA13254174 Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg ENA first public:2022 04 21|ENA last update:2022 04 21|External Id:SAMEA13254174|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC first public:2022 04 21T00:32:07Z|INSDC last update:2022 04 21T00:32:07Z|INSDC status:public|Submitter Id:E MTAB 11505:Sv2aHET7S9|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:sv2a+/ |individual:pool of 10 heads|organism part:head|sample name:E MTAB 11505:Sv2aHET7S9|sex:not available|strain:AB                 NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae E MTAB 11505:Sv2aHET7S9 s Sv2aHET7S9 s RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines. Experimental Factor: genotype:sv2a+/ RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 500   ERP135966 NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21 sv2aHET7S9L002-1.fastq.gz fastq 773106152.0 10236677.0 E MTAB 11505:sv2aHET7S9L002 0:75.52 1:0 A:191812833;C:184676419;G:180997547;T:215473732;N:145621 75 0     191812833 184676419 180997547 215473732 145621 ERX8620329 ERS10857217 ERA9644804 Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive 1 0.95016   0.12464   0.65482   0.47419   76   B   usable mapping rate illumina nextseq unknown poly_a trueseq bulk unknown unknown   Belgium 2022-04-21 Larval Larval Head Nervous System
10437 10437 ERR9077176 ERX8620329 ERS10857217 ERP135966 PRJEB51339 RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae E-MTAB-11505 Transcriptome Analysis Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae. ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21   Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines. Sv2aHET7S9 SAMEA13254174 Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg ENA first public:2022 04 21|ENA last update:2022 04 21|External Id:SAMEA13254174|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC first public:2022 04 21T00:32:07Z|INSDC last update:2022 04 21T00:32:07Z|INSDC status:public|Submitter Id:E MTAB 11505:Sv2aHET7S9|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:sv2a+/ |individual:pool of 10 heads|organism part:head|sample name:E MTAB 11505:Sv2aHET7S9|sex:not available|strain:AB                 NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae E MTAB 11505:Sv2aHET7S9 s Sv2aHET7S9 s RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines. Experimental Factor: genotype:sv2a+/ RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 500   ERP135966 NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21 sv2aHET7S9L003-1.fastq.gz fastq 783061051.0 10368445.0 E MTAB 11505:sv2aHET7S9L003 0:75.52 1:0 A:194289152;C:187108364;G:183177036;T:218370500;N:115999 75 0     194289152 187108364 183177036 218370500 115999 ERX8620329 ERS10857217 ERA9644804 Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive 1 0.95172   0.12488   0.65445   0.48157   76   B   usable mapping rate illumina nextseq unknown poly_a trueseq bulk unknown unknown   Belgium 2022-04-21 Larval Larval Head Nervous System
10438 10438 ERR9077177 ERX8620329 ERS10857217 ERP135966 PRJEB51339 RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae E-MTAB-11505 Transcriptome Analysis Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae. ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21   Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines. Sv2aHET7S9 SAMEA13254174 Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg ENA first public:2022 04 21|ENA last update:2022 04 21|External Id:SAMEA13254174|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC first public:2022 04 21T00:32:07Z|INSDC last update:2022 04 21T00:32:07Z|INSDC status:public|Submitter Id:E MTAB 11505:Sv2aHET7S9|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:sv2a+/ |individual:pool of 10 heads|organism part:head|sample name:E MTAB 11505:Sv2aHET7S9|sex:not available|strain:AB                 NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae E MTAB 11505:Sv2aHET7S9 s Sv2aHET7S9 s RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines. Experimental Factor: genotype:sv2a+/ RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 500   ERP135966 NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21 sv2aHET7S9L004-1.fastq.gz fastq 790150025.0 10462214.0 E MTAB 11505:sv2aHET7S9L004 0:75.52 1:0 A:196056500;C:188746833;G:184927588;T:220305922;N:113182 75 0     196056500 188746833 184927588 220305922 113182 ERX8620329 ERS10857217 ERA9644804 Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive 1 0.95285   0.12478   0.65551   0.4763   76   B   usable mapping rate illumina nextseq unknown poly_a trueseq bulk unknown unknown   Belgium 2022-04-21 Larval Larval Head Nervous System
10439 10439 ERR9077170 ERX8620328 ERS10857216 ERP135966 PRJEB51339 RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae E-MTAB-11505 Transcriptome Analysis Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae. ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21   Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines. Sv2aHET4S5 SAMEA13254173 Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg ENA first public:2022 04 21|ENA last update:2022 04 21|External Id:SAMEA13254173|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC first public:2022 04 21T00:32:07Z|INSDC last update:2022 04 21T00:32:07Z|INSDC status:public|Submitter Id:E MTAB 11505:Sv2aHET4S5|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:sv2a+/ |individual:pool of 10 heads|organism part:head|sample name:E MTAB 11505:Sv2aHET4S5|sex:not available|strain:AB                 NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae E MTAB 11505:Sv2aHET4S5 s Sv2aHET4S5 s RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines. Experimental Factor: genotype:sv2a+/ RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 500   ERP135966 NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21 sv2aHET4S5L001-1.fastq.gz fastq 685650097.0 9076481.0 E MTAB 11505:sv2aHET4S5L001 0:75.54 1:0 A:161812875;C:167870520;G:166985310;T:188850530;N:130862 75 0     161812875 167870520 166985310 188850530 130862 ERX8620328 ERS10857216 ERA9644804 Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive 1 0.95733   0.09974   0.65691   0.47392   76   B   usable mapping rate illumina nextseq unknown poly_a trueseq bulk unknown unknown   Belgium 2022-04-21 Larval Larval Head Nervous System
10440 10440 ERR9077171 ERX8620328 ERS10857216 ERP135966 PRJEB51339 RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae E-MTAB-11505 Transcriptome Analysis Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae. ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21   Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines. Sv2aHET4S5 SAMEA13254173 Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg ENA first public:2022 04 21|ENA last update:2022 04 21|External Id:SAMEA13254173|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC first public:2022 04 21T00:32:07Z|INSDC last update:2022 04 21T00:32:07Z|INSDC status:public|Submitter Id:E MTAB 11505:Sv2aHET4S5|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:sv2a+/ |individual:pool of 10 heads|organism part:head|sample name:E MTAB 11505:Sv2aHET4S5|sex:not available|strain:AB                 NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae E MTAB 11505:Sv2aHET4S5 s Sv2aHET4S5 s RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines. Experimental Factor: genotype:sv2a+/ RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 500   ERP135966 NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21 sv2aHET4S5L002-1.fastq.gz fastq 684402241.0 9059974.0 E MTAB 11505:sv2aHET4S5L002 0:75.54 1:0 A:161493428;C:167520248;G:166882054;T:188383816;N:122695 75 0     161493428 167520248 166882054 188383816 122695 ERX8620328 ERS10857216 ERA9644804 Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive 1 0.95537   0.09915   0.65719   0.48261   76   B   usable mapping rate illumina nextseq unknown poly_a trueseq bulk unknown unknown   Belgium 2022-04-21 Larval Larval Head Nervous System
10441 10441 ERR9077172 ERX8620328 ERS10857216 ERP135966 PRJEB51339 RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae E-MTAB-11505 Transcriptome Analysis Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae. ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21   Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines. Sv2aHET4S5 SAMEA13254173 Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg ENA first public:2022 04 21|ENA last update:2022 04 21|External Id:SAMEA13254173|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC first public:2022 04 21T00:32:07Z|INSDC last update:2022 04 21T00:32:07Z|INSDC status:public|Submitter Id:E MTAB 11505:Sv2aHET4S5|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:sv2a+/ |individual:pool of 10 heads|organism part:head|sample name:E MTAB 11505:Sv2aHET4S5|sex:not available|strain:AB                 NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae E MTAB 11505:Sv2aHET4S5 s Sv2aHET4S5 s RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines. Experimental Factor: genotype:sv2a+/ RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 500   ERP135966 NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21 sv2aHET4S5L003-1.fastq.gz fastq 694099126.0 9188245.0 E MTAB 11505:sv2aHET4S5L003 0:75.54 1:0 A:163727378;C:169989210;G:169143224;T:191137588;N:101726 75 0     163727378 169989210 169143224 191137588 101726 ERX8620328 ERS10857216 ERA9644804 Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive 1 0.95629   0.09861   0.65705   0.47187   75   B   usable mapping rate illumina nextseq unknown poly_a trueseq bulk unknown unknown   Belgium 2022-04-21 Larval Larval Head Nervous System
10442 10442 ERR9077173 ERX8620328 ERS10857216 ERP135966 PRJEB51339 RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae E-MTAB-11505 Transcriptome Analysis Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae. ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21   Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines. Sv2aHET4S5 SAMEA13254173 Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg ENA first public:2022 04 21|ENA last update:2022 04 21|External Id:SAMEA13254173|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC first public:2022 04 21T00:32:07Z|INSDC last update:2022 04 21T00:32:07Z|INSDC status:public|Submitter Id:E MTAB 11505:Sv2aHET4S5|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:sv2a+/ |individual:pool of 10 heads|organism part:head|sample name:E MTAB 11505:Sv2aHET4S5|sex:not available|strain:AB                 NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae E MTAB 11505:Sv2aHET4S5 s Sv2aHET4S5 s RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines. Experimental Factor: genotype:sv2a+/ RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 500   ERP135966 NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21 sv2aHET4S5L004-1.fastq.gz fastq 698753836.0 9249820.0 E MTAB 11505:sv2aHET4S5L004 0:75.54 1:0 A:164809473;C:171057633;G:170349692;T:192441413;N:95625 75 0     164809473 171057633 170349692 192441413 95625 ERX8620328 ERS10857216 ERA9644804 Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive 1 0.95613   0.09885   0.65798   0.47227   76   B   usable mapping rate illumina nextseq unknown poly_a trueseq bulk unknown unknown   Belgium 2022-04-21 Larval Larval Head Nervous System
10443 10443 ERR9077166 ERX8620327 ERS10857215 ERP135966 PRJEB51339 RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae E-MTAB-11505 Transcriptome Analysis Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae. ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21   Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines. Sv2aHET3S4 SAMEA13254172 Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg ENA first public:2022 04 21|ENA last update:2022 04 21|External Id:SAMEA13254172|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC first public:2022 04 21T00:32:07Z|INSDC last update:2022 04 21T00:32:07Z|INSDC status:public|Submitter Id:E MTAB 11505:Sv2aHET3S4|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:sv2a+/ |individual:pool of 10 heads|organism part:head|sample name:E MTAB 11505:Sv2aHET3S4|sex:not available|strain:AB                 NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae E MTAB 11505:Sv2aHET3S4 s Sv2aHET3S4 s RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines. Experimental Factor: genotype:sv2a+/ RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 500   ERP135966 NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21 sv2aHET3S4L001-1.fastq.gz fastq 691298605.0 9151512.0 E MTAB 11505:sv2aHET3S4L001 0:75.54 1:0 A:164743919;C:170752099;G:164763621;T:190912044;N:126922 75 0     164743919 170752099 164763621 190912044 126922 ERX8620327 ERS10857215 ERA9644804 Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive 1 0.95684   0.09604   0.6603   0.47285   76   B   usable mapping rate illumina nextseq unknown poly_a trueseq bulk unknown unknown   Belgium 2022-04-21 Larval Larval Head Nervous System
10444 10444 ERR9077167 ERX8620327 ERS10857215 ERP135966 PRJEB51339 RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae E-MTAB-11505 Transcriptome Analysis Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae. ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21   Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines. Sv2aHET3S4 SAMEA13254172 Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg ENA first public:2022 04 21|ENA last update:2022 04 21|External Id:SAMEA13254172|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC first public:2022 04 21T00:32:07Z|INSDC last update:2022 04 21T00:32:07Z|INSDC status:public|Submitter Id:E MTAB 11505:Sv2aHET3S4|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:sv2a+/ |individual:pool of 10 heads|organism part:head|sample name:E MTAB 11505:Sv2aHET3S4|sex:not available|strain:AB                 NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae E MTAB 11505:Sv2aHET3S4 s Sv2aHET3S4 s RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines. Experimental Factor: genotype:sv2a+/ RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 500   ERP135966 NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21 sv2aHET3S4L002-1.fastq.gz fastq 694080975.0 9188259.0 E MTAB 11505:sv2aHET3S4L002 0:75.54 1:0 A:165336810;C:171397273;G:165632321;T:191591872;N:122699 75 0     165336810 171397273 165632321 191591872 122699 ERX8620327 ERS10857215 ERA9644804 Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive 1 0.95612   0.09694   0.65993   0.46918   76   B   usable mapping rate illumina nextseq unknown poly_a trueseq bulk unknown unknown   Belgium 2022-04-21 Larval Larval Head Nervous System
10445 10445 ERR9077168 ERX8620327 ERS10857215 ERP135966 PRJEB51339 RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae E-MTAB-11505 Transcriptome Analysis Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae. ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21   Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines. Sv2aHET3S4 SAMEA13254172 Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg ENA first public:2022 04 21|ENA last update:2022 04 21|External Id:SAMEA13254172|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC first public:2022 04 21T00:32:07Z|INSDC last update:2022 04 21T00:32:07Z|INSDC status:public|Submitter Id:E MTAB 11505:Sv2aHET3S4|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:sv2a+/ |individual:pool of 10 heads|organism part:head|sample name:E MTAB 11505:Sv2aHET3S4|sex:not available|strain:AB                 NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae E MTAB 11505:Sv2aHET3S4 s Sv2aHET3S4 s RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines. Experimental Factor: genotype:sv2a+/ RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 500   ERP135966 NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21 sv2aHET3S4L003-1.fastq.gz fastq 703689889.0 9315387.0 E MTAB 11505:sv2aHET3S4L003 0:75.54 1:0 A:167575230;C:173881977;G:167845574;T:194289403;N:97705 75 0     167575230 173881977 167845574 194289403 97705 ERX8620327 ERS10857215 ERA9644804 Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive 1 0.9577   0.09608   0.66042   0.47022   74   B   usable mapping rate illumina nextseq unknown poly_a trueseq bulk unknown unknown   Belgium 2022-04-21 Larval Larval Head Nervous System
10446 10446 ERR9077169 ERX8620327 ERS10857215 ERP135966 PRJEB51339 RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae E-MTAB-11505 Transcriptome Analysis Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae. ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21   Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines. Sv2aHET3S4 SAMEA13254172 Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg ENA first public:2022 04 21|ENA last update:2022 04 21|External Id:SAMEA13254172|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC first public:2022 04 21T00:32:07Z|INSDC last update:2022 04 21T00:32:07Z|INSDC status:public|Submitter Id:E MTAB 11505:Sv2aHET3S4|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:sv2a+/ |individual:pool of 10 heads|organism part:head|sample name:E MTAB 11505:Sv2aHET3S4|sex:not available|strain:AB                 NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae E MTAB 11505:Sv2aHET3S4 s Sv2aHET3S4 s RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines. Experimental Factor: genotype:sv2a+/ RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 500   ERP135966 NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21 sv2aHET3S4L004-1.fastq.gz fastq 712116538.0 9426961.0 E MTAB 11505:sv2aHET3S4L004 0:75.54 1:0 A:169598596;C:175885948;G:169866534;T:196669400;N:96060 75 0     169598596 175885948 169866534 196669400 96060 ERX8620327 ERS10857215 ERA9644804 Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive 1 0.95734   0.09716   0.66054   0.47257   75   B   usable mapping rate illumina nextseq unknown poly_a trueseq bulk unknown unknown   Belgium 2022-04-21 Larval Larval Head Nervous System
10447 10447 ERR9077162 ERX8620326 ERS10857214 ERP135966 PRJEB51339 RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae E-MTAB-11505 Transcriptome Analysis Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae. ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21   Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines. Sv2aHET2S3 SAMEA13254171 Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg ENA first public:2022 04 21|ENA last update:2022 04 21|External Id:SAMEA13254171|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC first public:2022 04 21T00:32:07Z|INSDC last update:2022 04 21T00:32:07Z|INSDC status:public|Submitter Id:E MTAB 11505:Sv2aHET2S3|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:sv2a+/ |individual:pool of 10 heads|organism part:head|sample name:E MTAB 11505:Sv2aHET2S3|sex:not available|strain:AB                 NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae E MTAB 11505:Sv2aHET2S3 s Sv2aHET2S3 s RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines. Experimental Factor: genotype:sv2a+/ RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 500   ERP135966 NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21 sv2aHET2S3L001-1.fastq.gz fastq 733440522.0 9709422.0 E MTAB 11505:sv2aHET2S3L001 0:75.54 1:0 A:173670000;C:181175353;G:175392793;T:203059256;N:143120 75 0     173670000 181175353 175392793 203059256 143120 ERX8620326 ERS10857214 ERA9644804 Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive 1 0.95885   0.08758   0.65393   0.47249   76   B   usable mapping rate illumina nextseq unknown poly_a trueseq bulk unknown unknown   Belgium 2022-04-21 Larval Larval Head Nervous System
10448 10448 ERR9077163 ERX8620326 ERS10857214 ERP135966 PRJEB51339 RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae E-MTAB-11505 Transcriptome Analysis Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae. ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21   Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines. Sv2aHET2S3 SAMEA13254171 Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg ENA first public:2022 04 21|ENA last update:2022 04 21|External Id:SAMEA13254171|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC first public:2022 04 21T00:32:07Z|INSDC last update:2022 04 21T00:32:07Z|INSDC status:public|Submitter Id:E MTAB 11505:Sv2aHET2S3|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:sv2a+/ |individual:pool of 10 heads|organism part:head|sample name:E MTAB 11505:Sv2aHET2S3|sex:not available|strain:AB                 NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae E MTAB 11505:Sv2aHET2S3 s Sv2aHET2S3 s RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines. Experimental Factor: genotype:sv2a+/ RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 500   ERP135966 NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21 sv2aHET2S3L002-1.fastq.gz fastq 732121929.0 9691967.0 E MTAB 11505:sv2aHET2S3L002 0:75.54 1:0 A:173332091;C:180805738;G:175271736;T:202574727;N:137637 75 0     173332091 180805738 175271736 202574727 137637 ERX8620326 ERS10857214 ERA9644804 Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive 1 0.95775   0.08879   0.6564   0.4718   76   B   usable mapping rate illumina nextseq unknown poly_a trueseq bulk unknown unknown   Belgium 2022-04-21 Larval Larval Head Nervous System
10449 10449 ERR9077164 ERX8620326 ERS10857214 ERP135966 PRJEB51339 RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae E-MTAB-11505 Transcriptome Analysis Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae. ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21   Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines. Sv2aHET2S3 SAMEA13254171 Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg ENA first public:2022 04 21|ENA last update:2022 04 21|External Id:SAMEA13254171|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC first public:2022 04 21T00:32:07Z|INSDC last update:2022 04 21T00:32:07Z|INSDC status:public|Submitter Id:E MTAB 11505:Sv2aHET2S3|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:sv2a+/ |individual:pool of 10 heads|organism part:head|sample name:E MTAB 11505:Sv2aHET2S3|sex:not available|strain:AB                 NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae E MTAB 11505:Sv2aHET2S3 s Sv2aHET2S3 s RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines. Experimental Factor: genotype:sv2a+/ RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 500   ERP135966 NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21 sv2aHET2S3L003-1.fastq.gz fastq 743488189.0 9842286.0 E MTAB 11505:sv2aHET2S3L003 0:75.54 1:0 A:175979238;C:183726319;G:177933958;T:205735955;N:112719 75 0     175979238 183726319 177933958 205735955 112719 ERX8620326 ERS10857214 ERA9644804 Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive 1 0.9593   0.08716   0.65437   0.46976   75   B   usable mapping rate illumina nextseq unknown poly_a trueseq bulk unknown unknown   Belgium 2022-04-21 Larval Larval Head Nervous System
10450 10450 ERR9077165 ERX8620326 ERS10857214 ERP135966 PRJEB51339 RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae E-MTAB-11505 Transcriptome Analysis Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae. ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21   Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines. Sv2aHET2S3 SAMEA13254171 Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg ENA first public:2022 04 21|ENA last update:2022 04 21|External Id:SAMEA13254171|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC first public:2022 04 21T00:32:07Z|INSDC last update:2022 04 21T00:32:07Z|INSDC status:public|Submitter Id:E MTAB 11505:Sv2aHET2S3|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:sv2a+/ |individual:pool of 10 heads|organism part:head|sample name:E MTAB 11505:Sv2aHET2S3|sex:not available|strain:AB                 NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae E MTAB 11505:Sv2aHET2S3 s Sv2aHET2S3 s RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines. Experimental Factor: genotype:sv2a+/ RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA NextSeq 500   ERP135966 NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21 sv2aHET2S3L004-1.fastq.gz fastq 747723481.0 9898304.0 E MTAB 11505:sv2aHET2S3L004 0:75.54 1:0 A:176935451;C:184684782;G:179046040;T:206946124;N:111084 75 0     176935451 184684782 179046040 206946124 111084 ERX8620326 ERS10857214 ERA9644804 Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive 1 0.95934   0.08676   0.65533   0.47523   75   B   usable mapping rate illumina nextseq unknown poly_a trueseq bulk unknown unknown   Belgium 2022-04-21 Larval Larval Head Nervous System
11025 11025 ERR9787516 ERX9334792 ERS12088364 ERP137937 PRJEB53153 RNA seq of depdc5 / tsc2 / depdc5 / x tsc2 / and wildtype zebrafish larvae E-MTAB-11776 Transcriptome Analysis Transcriptome analysis of the heads of 5 dpf epdc5 / tsc2 / depdc5 / x tsc2 / and wildtype zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae. ENA FIRST PUBLIC:2022 09 12|ENA LAST UPDATE:2022 09 12   Protocols: 5 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled in quadruplicate per genotype. otal RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. Illumina TruSeq Stranded mRNA Seq sample preparation kit was used to prepare the mRNA sequencing library according to the manufacturer guidelines. Sample 9 SAMEA14460887 Laboratory for Molecular Biodiscovery, KU Leuven ENA FIRST PUBLIC:2022 09 12|ENA LAST UPDATE:2022 09 12|External Id:SAMEA14460887|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven|INSDC first public:2022 09 12T12:19:24Z|INSDC last update:2022 09 12T12:19:24Z|INSDC status:public|Submitter Id:E MTAB 11776:Sample 9|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:tsc2 / |individual:pool of 10 larvae|isolate:not applicable|organism part:head|sample name:E MTAB 11776:Sample 9|scientific name:Danio rerio|sex:non available|strain:AB                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of depdc5 / tsc2 / depdc5 / x tsc2 / and wildtype zebrafish larvae E MTAB 11776:Sample 9 p Sample 9 p RNA seq of depdc5 / tsc2 / depdc5 / x tsc2 / and wildtype zebrafish larvae 5 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled in quadruplicate per genotype. otal RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. Illumina TruSeq Stranded mRNA Seq sample preparation kit was used to prepare the mRNA sequencing library according to the manufacturer guidelines. Experimental Factor: genotype:tsc2 / RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP137937 Illumina NovaSeq 6000 paired end sequencing; RNA seq of depdc5 / tsc2 / depdc5 / x tsc2 / and wildtype zebrafish larvae ENA FIRST PUBLIC:2022 09 12|ENA LAST UPDATE:2022 09 12 TSCHOM1_1.fastq.gz TSCHOM1_2.fastq.gz fastq fastq 6360351174.0 31486887.0 E MTAB 11776:TSCHOM1 0:101 1:101 A:1750731340;C:1410426576;G:1460021447;T:1739131898;N:39913 101 101     1750731340 1410426576 1460021447 1739131898 39913 ERX9334792 ERS12088364 ERA14756702 Laboratory for Molecular Biodiscovery, KU Leuven|European Nucleotide Archive Laboratory for Molecular Biodiscovery, KU Leuven|European Nucleotide Archive 2 0.93517 0.92417 0.15551 0.15199 0.67736 0.6786 0.48763 0.48988 101 101 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   Belgium 2022-09-12 Larval Larval Head Nervous System
11026 11026 ERR9787515 ERX9334791 ERS12088363 ERP137937 PRJEB53153 RNA seq of depdc5 / tsc2 / depdc5 / x tsc2 / and wildtype zebrafish larvae E-MTAB-11776 Transcriptome Analysis Transcriptome analysis of the heads of 5 dpf epdc5 / tsc2 / depdc5 / x tsc2 / and wildtype zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae. ENA FIRST PUBLIC:2022 09 12|ENA LAST UPDATE:2022 09 12   Protocols: 5 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled in quadruplicate per genotype. otal RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. Illumina TruSeq Stranded mRNA Seq sample preparation kit was used to prepare the mRNA sequencing library according to the manufacturer guidelines. Sample 8 SAMEA14460886 Laboratory for Molecular Biodiscovery, KU Leuven ENA FIRST PUBLIC:2022 09 12|ENA LAST UPDATE:2022 09 12|External Id:SAMEA14460886|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven|INSDC first public:2022 09 12T12:19:24Z|INSDC last update:2022 09 12T12:19:24Z|INSDC status:public|Submitter Id:E MTAB 11776:Sample 8|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:depdc5 / |individual:pool of 10 larvae|isolate:not applicable|organism part:head|sample name:E MTAB 11776:Sample 8|scientific name:Danio rerio|sex:non available|strain:AB                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of depdc5 / tsc2 / depdc5 / x tsc2 / and wildtype zebrafish larvae E MTAB 11776:Sample 8 p Sample 8 p RNA seq of depdc5 / tsc2 / depdc5 / x tsc2 / and wildtype zebrafish larvae 5 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled in quadruplicate per genotype. otal RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. Illumina TruSeq Stranded mRNA Seq sample preparation kit was used to prepare the mRNA sequencing library according to the manufacturer guidelines. Experimental Factor: genotype:depdc5 / RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP137937 Illumina NovaSeq 6000 paired end sequencing; RNA seq of depdc5 / tsc2 / depdc5 / x tsc2 / and wildtype zebrafish larvae ENA FIRST PUBLIC:2022 09 12|ENA LAST UPDATE:2022 09 12 DEPHOM4_1.fastq.gz DEPHOM4_2.fastq.gz fastq fastq 6195443828.0 30670514.0 E MTAB 11776:DEPHOM4 0:101 1:101 A:1524344281;C:1573560980;G:1585093004;T:1512406843;N:38720 101 101     1524344281 1573560980 1585093004 1512406843 38720 ERX9334791 ERS12088363 ERA14756702 Laboratory for Molecular Biodiscovery, KU Leuven|European Nucleotide Archive Laboratory for Molecular Biodiscovery, KU Leuven|European Nucleotide Archive 2 0.95088 0.9542 0.17631 0.17203 0.71121 0.70981 0.56015 0.57999 101 101 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   Belgium 2022-09-12 Larval Larval Head Nervous System
11027 11027 ERR9787514 ERX9334790 ERS12088362 ERP137937 PRJEB53153 RNA seq of depdc5 / tsc2 / depdc5 / x tsc2 / and wildtype zebrafish larvae E-MTAB-11776 Transcriptome Analysis Transcriptome analysis of the heads of 5 dpf epdc5 / tsc2 / depdc5 / x tsc2 / and wildtype zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae. ENA FIRST PUBLIC:2022 09 12|ENA LAST UPDATE:2022 09 12   Protocols: 5 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled in quadruplicate per genotype. otal RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. Illumina TruSeq Stranded mRNA Seq sample preparation kit was used to prepare the mRNA sequencing library according to the manufacturer guidelines. Sample 7 SAMEA14460885 Laboratory for Molecular Biodiscovery, KU Leuven ENA FIRST PUBLIC:2022 09 12|ENA LAST UPDATE:2022 09 12|External Id:SAMEA14460885|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven|INSDC first public:2022 09 12T12:19:23Z|INSDC last update:2022 09 12T12:19:23Z|INSDC status:public|Submitter Id:E MTAB 11776:Sample 7|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:depdc5 / |individual:pool of 10 larvae|isolate:not applicable|organism part:head|sample name:E MTAB 11776:Sample 7|scientific name:Danio rerio|sex:non available|strain:AB                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of depdc5 / tsc2 / depdc5 / x tsc2 / and wildtype zebrafish larvae E MTAB 11776:Sample 7 p Sample 7 p RNA seq of depdc5 / tsc2 / depdc5 / x tsc2 / and wildtype zebrafish larvae 5 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled in quadruplicate per genotype. otal RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. Illumina TruSeq Stranded mRNA Seq sample preparation kit was used to prepare the mRNA sequencing library according to the manufacturer guidelines. Experimental Factor: genotype:depdc5 / RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP137937 Illumina NovaSeq 6000 paired end sequencing; RNA seq of depdc5 / tsc2 / depdc5 / x tsc2 / and wildtype zebrafish larvae ENA FIRST PUBLIC:2022 09 12|ENA LAST UPDATE:2022 09 12 DEPHOM7_1.fastq.gz DEPHOM7_2.fastq.gz fastq fastq 6201660378.0 30701289.0 E MTAB 11776:DEPHOM7 0:101 1:101 A:1699906420;C:1382805098;G:1427335171;T:1691574092;N:39597 101 101     1699906420 1382805098 1427335171 1691574092 39597 ERX9334790 ERS12088362 ERA14756702 Laboratory for Molecular Biodiscovery, KU Leuven|European Nucleotide Archive Laboratory for Molecular Biodiscovery, KU Leuven|European Nucleotide Archive 2 0.92781 0.92603 0.15556 0.15416 0.67965 0.67963 0.48209 0.48229 101 101 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   Belgium 2022-09-12 Larval Larval Head Nervous System
11028 11028 ERR9787513 ERX9334789 ERS12088361 ERP137937 PRJEB53153 RNA seq of depdc5 / tsc2 / depdc5 / x tsc2 / and wildtype zebrafish larvae E-MTAB-11776 Transcriptome Analysis Transcriptome analysis of the heads of 5 dpf epdc5 / tsc2 / depdc5 / x tsc2 / and wildtype zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae. ENA FIRST PUBLIC:2022 09 12|ENA LAST UPDATE:2022 09 12   Protocols: 5 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled in quadruplicate per genotype. otal RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. Illumina TruSeq Stranded mRNA Seq sample preparation kit was used to prepare the mRNA sequencing library according to the manufacturer guidelines. Sample 6 SAMEA14460884 Laboratory for Molecular Biodiscovery, KU Leuven ENA FIRST PUBLIC:2022 09 12|ENA LAST UPDATE:2022 09 12|External Id:SAMEA14460884|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven|INSDC first public:2022 09 12T12:19:23Z|INSDC last update:2022 09 12T12:19:23Z|INSDC status:public|Submitter Id:E MTAB 11776:Sample 6|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:depdc5 / |individual:pool of 10 larvae|isolate:not applicable|organism part:head|sample name:E MTAB 11776:Sample 6|scientific name:Danio rerio|sex:non available|strain:AB                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of depdc5 / tsc2 / depdc5 / x tsc2 / and wildtype zebrafish larvae E MTAB 11776:Sample 6 p Sample 6 p RNA seq of depdc5 / tsc2 / depdc5 / x tsc2 / and wildtype zebrafish larvae 5 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled in quadruplicate per genotype. otal RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. Illumina TruSeq Stranded mRNA Seq sample preparation kit was used to prepare the mRNA sequencing library according to the manufacturer guidelines. Experimental Factor: genotype:depdc5 / RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP137937 Illumina NovaSeq 6000 paired end sequencing; RNA seq of depdc5 / tsc2 / depdc5 / x tsc2 / and wildtype zebrafish larvae ENA FIRST PUBLIC:2022 09 12|ENA LAST UPDATE:2022 09 12 DEPHOM6_1.fastq.gz DEPHOM6_2.fastq.gz fastq fastq 6255857382.0 30969591.0 E MTAB 11776:DEPHOM6 0:101 1:101 A:1722554517;C:1398134491;G:1424183345;T:1710945949;N:39080 101 101     1722554517 1398134491 1424183345 1710945949 39080 ERX9334789 ERS12088361 ERA14756702 Laboratory for Molecular Biodiscovery, KU Leuven|European Nucleotide Archive Laboratory for Molecular Biodiscovery, KU Leuven|European Nucleotide Archive 2 0.93476 0.93206 0.16121 0.1592 0.67882 0.67898 0.48043 0.47851 101 101 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   Belgium 2022-09-12 Larval Larval Head Nervous System
11029 11029 ERR9787512 ERX9334788 ERS12088360 ERP137937 PRJEB53153 RNA seq of depdc5 / tsc2 / depdc5 / x tsc2 / and wildtype zebrafish larvae E-MTAB-11776 Transcriptome Analysis Transcriptome analysis of the heads of 5 dpf epdc5 / tsc2 / depdc5 / x tsc2 / and wildtype zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae. ENA FIRST PUBLIC:2022 09 12|ENA LAST UPDATE:2022 09 12   Protocols: 5 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled in quadruplicate per genotype. otal RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. Illumina TruSeq Stranded mRNA Seq sample preparation kit was used to prepare the mRNA sequencing library according to the manufacturer guidelines. Sample 5 SAMEA14460883 Laboratory for Molecular Biodiscovery, KU Leuven ENA FIRST PUBLIC:2022 09 12|ENA LAST UPDATE:2022 09 12|External Id:SAMEA14460883|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven|INSDC first public:2022 09 12T12:19:23Z|INSDC last update:2022 09 12T12:19:23Z|INSDC status:public|Submitter Id:E MTAB 11776:Sample 5|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:depdc5 / |individual:pool of 10 larvae|isolate:not applicable|organism part:head|sample name:E MTAB 11776:Sample 5|scientific name:Danio rerio|sex:non available|strain:AB                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of depdc5 / tsc2 / depdc5 / x tsc2 / and wildtype zebrafish larvae E MTAB 11776:Sample 5 p Sample 5 p RNA seq of depdc5 / tsc2 / depdc5 / x tsc2 / and wildtype zebrafish larvae 5 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled in quadruplicate per genotype. otal RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. Illumina TruSeq Stranded mRNA Seq sample preparation kit was used to prepare the mRNA sequencing library according to the manufacturer guidelines. Experimental Factor: genotype:depdc5 / RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP137937 Illumina NovaSeq 6000 paired end sequencing; RNA seq of depdc5 / tsc2 / depdc5 / x tsc2 / and wildtype zebrafish larvae ENA FIRST PUBLIC:2022 09 12|ENA LAST UPDATE:2022 09 12 DEPHOM1_1.fastq.gz DEPHOM1_2.fastq.gz fastq fastq 6340417006.0 31388203.0 E MTAB 11776:DEPHOM1 0:101 1:101 A:1738622221;C:1420060351;G:1455477148;T:1726216833;N:40453 101 101     1738622221 1420060351 1455477148 1726216833 40453 ERX9334788 ERS12088360 ERA14756702 Laboratory for Molecular Biodiscovery, KU Leuven|European Nucleotide Archive Laboratory for Molecular Biodiscovery, KU Leuven|European Nucleotide Archive 2 0.93634 0.93167 0.15036 0.14813 0.67809 0.67813 0.47978 0.47851 101 101 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   Belgium 2022-09-12 Larval Larval Head Nervous System
11030 11030 ERR9787511 ERX9334787 ERS12088359 ERP137937 PRJEB53153 RNA seq of depdc5 / tsc2 / depdc5 / x tsc2 / and wildtype zebrafish larvae E-MTAB-11776 Transcriptome Analysis Transcriptome analysis of the heads of 5 dpf epdc5 / tsc2 / depdc5 / x tsc2 / and wildtype zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae. ENA FIRST PUBLIC:2022 09 12|ENA LAST UPDATE:2022 09 12   Protocols: 5 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled in quadruplicate per genotype. otal RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. Illumina TruSeq Stranded mRNA Seq sample preparation kit was used to prepare the mRNA sequencing library according to the manufacturer guidelines. Sample 4 SAMEA14460882 Laboratory for Molecular Biodiscovery, KU Leuven ENA FIRST PUBLIC:2022 09 12|ENA LAST UPDATE:2022 09 12|External Id:SAMEA14460882|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven|INSDC first public:2022 09 12T12:19:23Z|INSDC last update:2022 09 12T12:19:23Z|INSDC status:public|Submitter Id:E MTAB 11776:Sample 4|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:depdc5 / x tsc2 / |individual:pool of 10 larvae|isolate:not applicable|organism part:head|sample name:E MTAB 11776:Sample 4|scientific name:Danio rerio|sex:non available|strain:AB                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of depdc5 / tsc2 / depdc5 / x tsc2 / and wildtype zebrafish larvae E MTAB 11776:Sample 4 p Sample 4 p RNA seq of depdc5 / tsc2 / depdc5 / x tsc2 / and wildtype zebrafish larvae 5 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled in quadruplicate per genotype. otal RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. Illumina TruSeq Stranded mRNA Seq sample preparation kit was used to prepare the mRNA sequencing library according to the manufacturer guidelines. Experimental Factor: genotype:depdc5 / x tsc2 / RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP137937 Illumina NovaSeq 6000 paired end sequencing; RNA seq of depdc5 / tsc2 / depdc5 / x tsc2 / and wildtype zebrafish larvae ENA FIRST PUBLIC:2022 09 12|ENA LAST UPDATE:2022 09 12 2XHOM7_1.fastq.gz 2XHOM7_2.fastq.gz fastq fastq 6291880446.0 31147923.0 E MTAB 11776:2XHOM7 0:101 1:101 A:1712784902;C:1424143534;G:1452943449;T:1701969086;N:39475 101 101     1712784902 1424143534 1452943449 1701969086 39475 ERX9334787 ERS12088359 ERA14756702 Laboratory for Molecular Biodiscovery, KU Leuven|European Nucleotide Archive Laboratory for Molecular Biodiscovery, KU Leuven|European Nucleotide Archive 2 0.93869 0.93511 0.15405 0.15042 0.67377 0.67351 0.50599 0.50683 101 101 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   Belgium 2022-09-12 Larval Larval Head Nervous System
11031 11031 ERR9787510 ERX9334786 ERS12088358 ERP137937 PRJEB53153 RNA seq of depdc5 / tsc2 / depdc5 / x tsc2 / and wildtype zebrafish larvae E-MTAB-11776 Transcriptome Analysis Transcriptome analysis of the heads of 5 dpf epdc5 / tsc2 / depdc5 / x tsc2 / and wildtype zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae. ENA FIRST PUBLIC:2022 09 12|ENA LAST UPDATE:2022 09 12   Protocols: 5 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled in quadruplicate per genotype. otal RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. Illumina TruSeq Stranded mRNA Seq sample preparation kit was used to prepare the mRNA sequencing library according to the manufacturer guidelines. Sample 3 SAMEA14460881 Laboratory for Molecular Biodiscovery, KU Leuven ENA FIRST PUBLIC:2022 09 12|ENA LAST UPDATE:2022 09 12|External Id:SAMEA14460881|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven|INSDC first public:2022 09 12T12:19:23Z|INSDC last update:2022 09 12T12:19:23Z|INSDC status:public|Submitter Id:E MTAB 11776:Sample 3|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:depdc5 / x tsc2 / |individual:pool of 10 larvae|isolate:not applicable|organism part:head|sample name:E MTAB 11776:Sample 3|scientific name:Danio rerio|sex:non available|strain:AB                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of depdc5 / tsc2 / depdc5 / x tsc2 / and wildtype zebrafish larvae E MTAB 11776:Sample 3 p Sample 3 p RNA seq of depdc5 / tsc2 / depdc5 / x tsc2 / and wildtype zebrafish larvae 5 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled in quadruplicate per genotype. otal RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. Illumina TruSeq Stranded mRNA Seq sample preparation kit was used to prepare the mRNA sequencing library according to the manufacturer guidelines. Experimental Factor: genotype:depdc5 / x tsc2 / RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP137937 Illumina NovaSeq 6000 paired end sequencing; RNA seq of depdc5 / tsc2 / depdc5 / x tsc2 / and wildtype zebrafish larvae ENA FIRST PUBLIC:2022 09 12|ENA LAST UPDATE:2022 09 12 2XHOM6_1.fastq.gz 2XHOM6_2.fastq.gz fastq fastq 6214327596.0 30763998.0 E MTAB 11776:2XHOM6 0:101 1:101 A:1705019759;C:1384064144;G:1432455427;T:1692749964;N:38302 101 101     1705019759 1384064144 1432455427 1692749964 38302 ERX9334786 ERS12088358 ERA14756702 Laboratory for Molecular Biodiscovery, KU Leuven|European Nucleotide Archive Laboratory for Molecular Biodiscovery, KU Leuven|European Nucleotide Archive 2 0.93591 0.92636 0.14492 0.14145 0.67489 0.67491 0.47753 0.49286 101 101 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   Belgium 2022-09-12 Larval Larval Head Nervous System
11032 11032 ERR9787509 ERX9334785 ERS12088357 ERP137937 PRJEB53153 RNA seq of depdc5 / tsc2 / depdc5 / x tsc2 / and wildtype zebrafish larvae E-MTAB-11776 Transcriptome Analysis Transcriptome analysis of the heads of 5 dpf epdc5 / tsc2 / depdc5 / x tsc2 / and wildtype zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae. ENA FIRST PUBLIC:2022 09 12|ENA LAST UPDATE:2022 09 12   Protocols: 5 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled in quadruplicate per genotype. otal RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. Illumina TruSeq Stranded mRNA Seq sample preparation kit was used to prepare the mRNA sequencing library according to the manufacturer guidelines. Sample 2 SAMEA14460880 Laboratory for Molecular Biodiscovery, KU Leuven ENA FIRST PUBLIC:2022 09 12|ENA LAST UPDATE:2022 09 12|External Id:SAMEA14460880|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven|INSDC first public:2022 09 12T12:19:23Z|INSDC last update:2022 09 12T12:19:23Z|INSDC status:public|Submitter Id:E MTAB 11776:Sample 2|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:depdc5 / x tsc2 / |individual:pool of 10 larvae|isolate:not applicable|organism part:head|sample name:E MTAB 11776:Sample 2|scientific name:Danio rerio|sex:non available|strain:AB                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of depdc5 / tsc2 / depdc5 / x tsc2 / and wildtype zebrafish larvae E MTAB 11776:Sample 2 p Sample 2 p RNA seq of depdc5 / tsc2 / depdc5 / x tsc2 / and wildtype zebrafish larvae 5 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled in quadruplicate per genotype. otal RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. Illumina TruSeq Stranded mRNA Seq sample preparation kit was used to prepare the mRNA sequencing library according to the manufacturer guidelines. Experimental Factor: genotype:depdc5 / x tsc2 / RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP137937 Illumina NovaSeq 6000 paired end sequencing; RNA seq of depdc5 / tsc2 / depdc5 / x tsc2 / and wildtype zebrafish larvae ENA FIRST PUBLIC:2022 09 12|ENA LAST UPDATE:2022 09 12 2XHOM4_1.fastq.gz 2XHOM4_2.fastq.gz fastq fastq 6301691990.0 31196495.0 E MTAB 11776:2XHOM4 0:101 1:101 A:1698118705;C:1442276237;G:1473988715;T:1687268823;N:39510 101 101     1698118705 1442276237 1473988715 1687268823 39510 ERX9334785 ERS12088357 ERA14756702 Laboratory for Molecular Biodiscovery, KU Leuven|European Nucleotide Archive Laboratory for Molecular Biodiscovery, KU Leuven|European Nucleotide Archive 2 0.94255 0.93839 0.13232 0.13007 0.67326 0.67294 0.49084 0.49291 101 101 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   Belgium 2022-09-12 Larval Larval Head Nervous System
11033 11033 ERR9787508 ERX9334784 ERS12088356 ERP137937 PRJEB53153 RNA seq of depdc5 / tsc2 / depdc5 / x tsc2 / and wildtype zebrafish larvae E-MTAB-11776 Transcriptome Analysis Transcriptome analysis of the heads of 5 dpf epdc5 / tsc2 / depdc5 / x tsc2 / and wildtype zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae. ENA FIRST PUBLIC:2022 09 12|ENA LAST UPDATE:2022 09 12   Protocols: 5 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled in quadruplicate per genotype. otal RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. Illumina TruSeq Stranded mRNA Seq sample preparation kit was used to prepare the mRNA sequencing library according to the manufacturer guidelines. Sample 16 SAMEA14460879 Laboratory for Molecular Biodiscovery, KU Leuven ENA FIRST PUBLIC:2022 09 12|ENA LAST UPDATE:2022 09 12|External Id:SAMEA14460879|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven|INSDC first public:2022 09 12T12:19:23Z|INSDC last update:2022 09 12T12:19:23Z|INSDC status:public|Submitter Id:E MTAB 11776:Sample 16|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:wild type genotype|individual:pool of 10 larvae|isolate:not applicable|organism part:head|sample name:E MTAB 11776:Sample 16|scientific name:Danio rerio|sex:non available|strain:AB                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of depdc5 / tsc2 / depdc5 / x tsc2 / and wildtype zebrafish larvae E MTAB 11776:Sample 16 p Sample 16 p RNA seq of depdc5 / tsc2 / depdc5 / x tsc2 / and wildtype zebrafish larvae 5 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled in quadruplicate per genotype. otal RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. Illumina TruSeq Stranded mRNA Seq sample preparation kit was used to prepare the mRNA sequencing library according to the manufacturer guidelines. Experimental Factor: genotype:wild type genotype RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP137937 Illumina NovaSeq 6000 paired end sequencing; RNA seq of depdc5 / tsc2 / depdc5 / x tsc2 / and wildtype zebrafish larvae ENA FIRST PUBLIC:2022 09 12|ENA LAST UPDATE:2022 09 12 WT7_1.fastq.gz WT7_2.fastq.gz fastq fastq 6206666746.0 30726073.0 E MTAB 11776:WT7 0:101 1:101 A:1705689174;C:1387290312;G:1420249657;T:1693397929;N:39674 101 101     1705689174 1387290312 1420249657 1693397929 39674 ERX9334784 ERS12088356 ERA14756702 Laboratory for Molecular Biodiscovery, KU Leuven|European Nucleotide Archive Laboratory for Molecular Biodiscovery, KU Leuven|European Nucleotide Archive 2 0.93493 0.92964 0.15803 0.1554 0.67405 0.67501 0.47988 0.46768 101 101 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   Belgium 2022-09-12 Larval Larval Head Nervous System
11034 11034 ERR9787507 ERX9334783 ERS12088355 ERP137937 PRJEB53153 RNA seq of depdc5 / tsc2 / depdc5 / x tsc2 / and wildtype zebrafish larvae E-MTAB-11776 Transcriptome Analysis Transcriptome analysis of the heads of 5 dpf epdc5 / tsc2 / depdc5 / x tsc2 / and wildtype zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae. ENA FIRST PUBLIC:2022 09 12|ENA LAST UPDATE:2022 09 12   Protocols: 5 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled in quadruplicate per genotype. otal RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. Illumina TruSeq Stranded mRNA Seq sample preparation kit was used to prepare the mRNA sequencing library according to the manufacturer guidelines. Sample 15 SAMEA14460878 Laboratory for Molecular Biodiscovery, KU Leuven ENA FIRST PUBLIC:2022 09 12|ENA LAST UPDATE:2022 09 12|External Id:SAMEA14460878|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven|INSDC first public:2022 09 12T12:19:23Z|INSDC last update:2022 09 12T12:19:23Z|INSDC status:public|Submitter Id:E MTAB 11776:Sample 15|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:wild type genotype|individual:pool of 10 larvae|isolate:not applicable|organism part:head|sample name:E MTAB 11776:Sample 15|scientific name:Danio rerio|sex:non available|strain:AB                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of depdc5 / tsc2 / depdc5 / x tsc2 / and wildtype zebrafish larvae E MTAB 11776:Sample 15 p Sample 15 p RNA seq of depdc5 / tsc2 / depdc5 / x tsc2 / and wildtype zebrafish larvae 5 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled in quadruplicate per genotype. otal RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. Illumina TruSeq Stranded mRNA Seq sample preparation kit was used to prepare the mRNA sequencing library according to the manufacturer guidelines. Experimental Factor: genotype:wild type genotype RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP137937 Illumina NovaSeq 6000 paired end sequencing; RNA seq of depdc5 / tsc2 / depdc5 / x tsc2 / and wildtype zebrafish larvae ENA FIRST PUBLIC:2022 09 12|ENA LAST UPDATE:2022 09 12 WT6_1.fastq.gz WT6_2.fastq.gz fastq fastq 6360740630.0 31488815.0 E MTAB 11776:WT6 0:101 1:101 A:1735195643;C:1436805269;G:1469558083;T:1719141699;N:39936 101 101     1735195643 1436805269 1469558083 1719141699 39936 ERX9334783 ERS12088355 ERA14756702 Laboratory for Molecular Biodiscovery, KU Leuven|European Nucleotide Archive Laboratory for Molecular Biodiscovery, KU Leuven|European Nucleotide Archive 2 0.93629 0.93343 0.15169 0.1501 0.67572 0.67517 0.47499 0.47879 101 101 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   Belgium 2022-09-12 Larval Larval Head Nervous System
11035 11035 ERR9787506 ERX9334782 ERS12088354 ERP137937 PRJEB53153 RNA seq of depdc5 / tsc2 / depdc5 / x tsc2 / and wildtype zebrafish larvae E-MTAB-11776 Transcriptome Analysis Transcriptome analysis of the heads of 5 dpf epdc5 / tsc2 / depdc5 / x tsc2 / and wildtype zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae. ENA FIRST PUBLIC:2022 09 12|ENA LAST UPDATE:2022 09 12   Protocols: 5 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled in quadruplicate per genotype. otal RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. Illumina TruSeq Stranded mRNA Seq sample preparation kit was used to prepare the mRNA sequencing library according to the manufacturer guidelines. Sample 14 SAMEA14460877 Laboratory for Molecular Biodiscovery, KU Leuven ENA FIRST PUBLIC:2022 09 12|ENA LAST UPDATE:2022 09 12|External Id:SAMEA14460877|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven|INSDC first public:2022 09 12T12:19:23Z|INSDC last update:2022 09 12T12:19:23Z|INSDC status:public|Submitter Id:E MTAB 11776:Sample 14|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:wild type genotype|individual:pool of 10 larvae|isolate:not applicable|organism part:head|sample name:E MTAB 11776:Sample 14|scientific name:Danio rerio|sex:non available|strain:AB                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of depdc5 / tsc2 / depdc5 / x tsc2 / and wildtype zebrafish larvae E MTAB 11776:Sample 14 p Sample 14 p RNA seq of depdc5 / tsc2 / depdc5 / x tsc2 / and wildtype zebrafish larvae 5 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled in quadruplicate per genotype. otal RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. Illumina TruSeq Stranded mRNA Seq sample preparation kit was used to prepare the mRNA sequencing library according to the manufacturer guidelines. Experimental Factor: genotype:wild type genotype RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP137937 Illumina NovaSeq 6000 paired end sequencing; RNA seq of depdc5 / tsc2 / depdc5 / x tsc2 / and wildtype zebrafish larvae ENA FIRST PUBLIC:2022 09 12|ENA LAST UPDATE:2022 09 12 WT4_1.fastq.gz WT4_2.fastq.gz fastq fastq 6227472342.0 30829071.0 E MTAB 11776:WT4 0:101 1:101 A:1668352581;C:1434152947;G:1468645621;T:1656281986;N:39207 101 101     1668352581 1434152947 1468645621 1656281986 39207 ERX9334782 ERS12088354 ERA14756702 Laboratory for Molecular Biodiscovery, KU Leuven|European Nucleotide Archive Laboratory for Molecular Biodiscovery, KU Leuven|European Nucleotide Archive 2 0.94261 0.93675 0.15334 0.15049 0.67927 0.67872 0.48762 0.49138 101 101 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   Belgium 2022-09-12 Larval Larval Head Nervous System
11036 11036 ERR9787505 ERX9334781 ERS12088353 ERP137937 PRJEB53153 RNA seq of depdc5 / tsc2 / depdc5 / x tsc2 / and wildtype zebrafish larvae E-MTAB-11776 Transcriptome Analysis Transcriptome analysis of the heads of 5 dpf epdc5 / tsc2 / depdc5 / x tsc2 / and wildtype zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae. ENA FIRST PUBLIC:2022 09 12|ENA LAST UPDATE:2022 09 12   Protocols: 5 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled in quadruplicate per genotype. otal RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. Illumina TruSeq Stranded mRNA Seq sample preparation kit was used to prepare the mRNA sequencing library according to the manufacturer guidelines. Sample 13 SAMEA14460876 Laboratory for Molecular Biodiscovery, KU Leuven ENA FIRST PUBLIC:2022 09 12|ENA LAST UPDATE:2022 09 12|External Id:SAMEA14460876|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven|INSDC first public:2022 09 12T12:19:23Z|INSDC last update:2022 09 12T12:19:23Z|INSDC status:public|Submitter Id:E MTAB 11776:Sample 13|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:wild type genotype|individual:pool of 10 larvae|isolate:not applicable|organism part:head|sample name:E MTAB 11776:Sample 13|scientific name:Danio rerio|sex:non available|strain:AB                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of depdc5 / tsc2 / depdc5 / x tsc2 / and wildtype zebrafish larvae E MTAB 11776:Sample 13 p Sample 13 p RNA seq of depdc5 / tsc2 / depdc5 / x tsc2 / and wildtype zebrafish larvae 5 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled in quadruplicate per genotype. otal RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. Illumina TruSeq Stranded mRNA Seq sample preparation kit was used to prepare the mRNA sequencing library according to the manufacturer guidelines. Experimental Factor: genotype:wild type genotype RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP137937 Illumina NovaSeq 6000 paired end sequencing; RNA seq of depdc5 / tsc2 / depdc5 / x tsc2 / and wildtype zebrafish larvae ENA FIRST PUBLIC:2022 09 12|ENA LAST UPDATE:2022 09 12 WT1_1.fastq.gz WT1_2.fastq.gz fastq fastq 6332757570.0 31350285.0 E MTAB 11776:WT1 0:101 1:101 A:1726838066;C:1431452165;G:1460746594;T:1713681043;N:39702 101 101     1726838066 1431452165 1460746594 1713681043 39702 ERX9334781 ERS12088353 ERA14756702 Laboratory for Molecular Biodiscovery, KU Leuven|European Nucleotide Archive Laboratory for Molecular Biodiscovery, KU Leuven|European Nucleotide Archive 2 0.92422 0.93556 0.14884 0.14926 0.67694 0.67564 0.48223 0.48884 101 101 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   Belgium 2022-09-12 Larval Larval Head Nervous System
11037 11037 ERR9787504 ERX9334780 ERS12088352 ERP137937 PRJEB53153 RNA seq of depdc5 / tsc2 / depdc5 / x tsc2 / and wildtype zebrafish larvae E-MTAB-11776 Transcriptome Analysis Transcriptome analysis of the heads of 5 dpf epdc5 / tsc2 / depdc5 / x tsc2 / and wildtype zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae. ENA FIRST PUBLIC:2022 09 12|ENA LAST UPDATE:2022 09 12   Protocols: 5 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled in quadruplicate per genotype. otal RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. Illumina TruSeq Stranded mRNA Seq sample preparation kit was used to prepare the mRNA sequencing library according to the manufacturer guidelines. Sample 12 SAMEA14460875 Laboratory for Molecular Biodiscovery, KU Leuven ENA FIRST PUBLIC:2022 09 12|ENA LAST UPDATE:2022 09 12|External Id:SAMEA14460875|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven|INSDC first public:2022 09 12T12:19:23Z|INSDC last update:2022 09 12T12:19:23Z|INSDC status:public|Submitter Id:E MTAB 11776:Sample 12|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:tsc2 / |individual:pool of 10 larvae|isolate:not applicable|organism part:head|sample name:E MTAB 11776:Sample 12|scientific name:Danio rerio|sex:non available|strain:AB                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of depdc5 / tsc2 / depdc5 / x tsc2 / and wildtype zebrafish larvae E MTAB 11776:Sample 12 p Sample 12 p RNA seq of depdc5 / tsc2 / depdc5 / x tsc2 / and wildtype zebrafish larvae 5 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled in quadruplicate per genotype. otal RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. Illumina TruSeq Stranded mRNA Seq sample preparation kit was used to prepare the mRNA sequencing library according to the manufacturer guidelines. Experimental Factor: genotype:tsc2 / RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP137937 Illumina NovaSeq 6000 paired end sequencing; RNA seq of depdc5 / tsc2 / depdc5 / x tsc2 / and wildtype zebrafish larvae ENA FIRST PUBLIC:2022 09 12|ENA LAST UPDATE:2022 09 12 TSCHOM7_1.fastq.gz TSCHOM7_2.fastq.gz fastq fastq 6216990360.0 30777180.0 E MTAB 11776:TSCHOM7 0:101 1:101 A:1710256020;C:1390027205;G:1419250792;T:1697417099;N:39244 101 101     1710256020 1390027205 1419250792 1697417099 39244 ERX9334780 ERS12088352 ERA14756702 Laboratory for Molecular Biodiscovery, KU Leuven|European Nucleotide Archive Laboratory for Molecular Biodiscovery, KU Leuven|European Nucleotide Archive 2 0.93162 0.92801 0.15191 0.14943 0.67789 0.67951 0.47915 0.47762 101 101 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   Belgium 2022-09-12 Larval Larval Head Nervous System
11038 11038 ERR9787503 ERX9334779 ERS12088351 ERP137937 PRJEB53153 RNA seq of depdc5 / tsc2 / depdc5 / x tsc2 / and wildtype zebrafish larvae E-MTAB-11776 Transcriptome Analysis Transcriptome analysis of the heads of 5 dpf epdc5 / tsc2 / depdc5 / x tsc2 / and wildtype zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae. ENA FIRST PUBLIC:2022 09 12|ENA LAST UPDATE:2022 09 12   Protocols: 5 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled in quadruplicate per genotype. otal RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. Illumina TruSeq Stranded mRNA Seq sample preparation kit was used to prepare the mRNA sequencing library according to the manufacturer guidelines. Sample 11 SAMEA14460874 Laboratory for Molecular Biodiscovery, KU Leuven ENA FIRST PUBLIC:2022 09 12|ENA LAST UPDATE:2022 09 12|External Id:SAMEA14460874|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven|INSDC first public:2022 09 12T12:19:23Z|INSDC last update:2022 09 12T12:19:23Z|INSDC status:public|Submitter Id:E MTAB 11776:Sample 11|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:tsc2 / |individual:pool of 10 larvae|isolate:not applicable|organism part:head|sample name:E MTAB 11776:Sample 11|scientific name:Danio rerio|sex:non available|strain:AB                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of depdc5 / tsc2 / depdc5 / x tsc2 / and wildtype zebrafish larvae E MTAB 11776:Sample 11 p Sample 11 p RNA seq of depdc5 / tsc2 / depdc5 / x tsc2 / and wildtype zebrafish larvae 5 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled in quadruplicate per genotype. otal RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. Illumina TruSeq Stranded mRNA Seq sample preparation kit was used to prepare the mRNA sequencing library according to the manufacturer guidelines. Experimental Factor: genotype:tsc2 / RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP137937 Illumina NovaSeq 6000 paired end sequencing; RNA seq of depdc5 / tsc2 / depdc5 / x tsc2 / and wildtype zebrafish larvae ENA FIRST PUBLIC:2022 09 12|ENA LAST UPDATE:2022 09 12 TSCHOM6_1.fastq.gz TSCHOM6_2.fastq.gz fastq fastq 6199081848.0 30688524.0 E MTAB 11776:TSCHOM6 0:101 1:101 A:1705859045;C:1387530558;G:1415224718;T:1690428701;N:38826 101 101     1705859045 1387530558 1415224718 1690428701 38826 ERX9334779 ERS12088351 ERA14756702 Laboratory for Molecular Biodiscovery, KU Leuven|European Nucleotide Archive Laboratory for Molecular Biodiscovery, KU Leuven|European Nucleotide Archive 2 0.93583 0.93349 0.15923 0.15664 0.67976 0.67986 0.48632 0.48376 101 101 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   Belgium 2022-09-12 Larval Larval Head Nervous System
11039 11039 ERR9787502 ERX9334778 ERS12088350 ERP137937 PRJEB53153 RNA seq of depdc5 / tsc2 / depdc5 / x tsc2 / and wildtype zebrafish larvae E-MTAB-11776 Transcriptome Analysis Transcriptome analysis of the heads of 5 dpf epdc5 / tsc2 / depdc5 / x tsc2 / and wildtype zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae. ENA FIRST PUBLIC:2022 09 12|ENA LAST UPDATE:2022 09 12   Protocols: 5 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled in quadruplicate per genotype. otal RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. Illumina TruSeq Stranded mRNA Seq sample preparation kit was used to prepare the mRNA sequencing library according to the manufacturer guidelines. Sample 10 SAMEA14460873 Laboratory for Molecular Biodiscovery, KU Leuven ENA FIRST PUBLIC:2022 09 12|ENA LAST UPDATE:2022 09 12|External Id:SAMEA14460873|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven|INSDC first public:2022 09 12T12:19:23Z|INSDC last update:2022 09 12T12:19:23Z|INSDC status:public|Submitter Id:E MTAB 11776:Sample 10|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:tsc2 / |individual:pool of 10 larvae|isolate:not applicable|organism part:head|sample name:E MTAB 11776:Sample 10|scientific name:Danio rerio|sex:non available|strain:AB                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of depdc5 / tsc2 / depdc5 / x tsc2 / and wildtype zebrafish larvae E MTAB 11776:Sample 10 p Sample 10 p RNA seq of depdc5 / tsc2 / depdc5 / x tsc2 / and wildtype zebrafish larvae 5 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled in quadruplicate per genotype. otal RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. Illumina TruSeq Stranded mRNA Seq sample preparation kit was used to prepare the mRNA sequencing library according to the manufacturer guidelines. Experimental Factor: genotype:tsc2 / RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP137937 Illumina NovaSeq 6000 paired end sequencing; RNA seq of depdc5 / tsc2 / depdc5 / x tsc2 / and wildtype zebrafish larvae ENA FIRST PUBLIC:2022 09 12|ENA LAST UPDATE:2022 09 12 TSCHOM4_1.fastq.gz TSCHOM4_2.fastq.gz fastq fastq 6287836204.0 31127902.0 E MTAB 11776:TSCHOM4 0:101 1:101 A:1673762523;C:1453880149;G:1493343671;T:1666809849;N:40012 101 101     1673762523 1453880149 1493343671 1666809849 40012 ERX9334778 ERS12088350 ERA14756702 Laboratory for Molecular Biodiscovery, KU Leuven|European Nucleotide Archive Laboratory for Molecular Biodiscovery, KU Leuven|European Nucleotide Archive 2 0.94269 0.9375 0.14166 0.13979 0.67476 0.67722 0.4927 0.49365 101 101 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   Belgium 2022-09-12 Larval Larval Head Nervous System
11040 11040 ERR9787501 ERX9334777 ERS12088349 ERP137937 PRJEB53153 RNA seq of depdc5 / tsc2 / depdc5 / x tsc2 / and wildtype zebrafish larvae E-MTAB-11776 Transcriptome Analysis Transcriptome analysis of the heads of 5 dpf epdc5 / tsc2 / depdc5 / x tsc2 / and wildtype zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae. ENA FIRST PUBLIC:2022 09 12|ENA LAST UPDATE:2022 09 12   Protocols: 5 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled in quadruplicate per genotype. otal RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. Illumina TruSeq Stranded mRNA Seq sample preparation kit was used to prepare the mRNA sequencing library according to the manufacturer guidelines. Sample 1 SAMEA14460872 Laboratory for Molecular Biodiscovery, KU Leuven ENA FIRST PUBLIC:2022 09 12|ENA LAST UPDATE:2022 09 12|External Id:SAMEA14460872|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven|INSDC first public:2022 09 12T12:19:23Z|INSDC last update:2022 09 12T12:19:23Z|INSDC status:public|Submitter Id:E MTAB 11776:Sample 1|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:depdc5 / x tsc2 / |individual:pool of 10 larvae|isolate:not applicable|organism part:head|sample name:E MTAB 11776:Sample 1|scientific name:Danio rerio|sex:non available|strain:AB                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of depdc5 / tsc2 / depdc5 / x tsc2 / and wildtype zebrafish larvae E MTAB 11776:Sample 1 p Sample 1 p RNA seq of depdc5 / tsc2 / depdc5 / x tsc2 / and wildtype zebrafish larvae 5 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled in quadruplicate per genotype. otal RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. Illumina TruSeq Stranded mRNA Seq sample preparation kit was used to prepare the mRNA sequencing library according to the manufacturer guidelines. Experimental Factor: genotype:depdc5 / x tsc2 / RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP137937 Illumina NovaSeq 6000 paired end sequencing; RNA seq of depdc5 / tsc2 / depdc5 / x tsc2 / and wildtype zebrafish larvae ENA FIRST PUBLIC:2022 09 12|ENA LAST UPDATE:2022 09 12 2XHOM1_1.fastq.gz 2XHOM1_2.fastq.gz fastq fastq 6232605768.0 30854484.0 E MTAB 11776:2XHOM1 0:101 1:101 A:1725401812;C:1384507160;G:1410306583;T:1712351429;N:38784 101 101     1725401812 1384507160 1410306583 1712351429 38784 ERX9334777 ERS12088349 ERA14756702 Laboratory for Molecular Biodiscovery, KU Leuven|European Nucleotide Archive Laboratory for Molecular Biodiscovery, KU Leuven|European Nucleotide Archive 2 0.93594 0.93262 0.15282 0.14977 0.67503 0.67373 0.49522 0.49759 101 101 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   Belgium 2022-09-12 Larval Larval Head Nervous System
11047 11047 ERR10476807 ERX9997150 ERS13672475 ERP138527 PRJEB53713 Time course whole brain transcriptome and methylome profiles of early life high GC exposed zebrafish f79d57b2-1e93-4ca0-8fda-fd881a2a0c1e Other Whole brain transcriptome mRNA profiles of zebrafish which exposed to elavated glucocorticoid GC optogenetically at 6 13 120 dpf dpf and post predatory stress looming dots stress at xxx dpf. All subjective adults at 120 dpf were female. Tubingen strain was used as wildtype control and brains from transgenic line Tgstar:bPAC 2A tdTomatouoe300 +/ and / were sequenced on Illumina NovaSeq6000 by TRON gGmbH Mainz Germany. Paired end TruSeq Stranded mRNA libraries Illumina CA USA were constructed and over 20M of 50 bp reads/sample were sequenced. Oxford Nanopore sequencing was used for DNA methylation identification. These data were generated for the study by Choi et al. 2024. https://www.biorxiv.org/content/10.1101/2023.02.13.528363v4 ENA FIRST PUBLIC:2024 02 06|ENA LAST UPDATE:2024 02 06   star:bPAC+/ whole brain pooled 15 brains star:bPAC+/ whole brain day6 SAMEA111562619 Living Systems Institute, University of Exeter INSDC center name:Living Systems Institute University of Exeter|Submitter Id:star pos d6 1|collection date:2019 12|common name:zebrafish|dev stage:6 dpf|geographic location country and/or sea:Germany|sample name:star pos d6 1|scientific name:Danio rerio|sex:N/A|strain:Tübingen|tissue type:brain                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 09 11 2022 11:52:59:183 283033 Sample 0256 076 FR NSP TR1 SL1 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   ERP138527 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 02 06|ENA LAST UPDATE:2024 02 06 0256_076_FR_NSP_TR1_SL1_S7_L001_R1_001-pooled.fastq.gz 0256_076_FR_NSP_TR1_SL1_S7_L001_R2_001-pooled.fastq.gz fastq fastq 2974117224.0 29158012.0 ena RUN TAB 09 11 2022 11:52:59:183 283034 0:51 1:51 A:816102587;C:662715848;G:672777315;T:822487687;N:33787 51 51     816102587 662715848 672777315 822487687 33787 ERX9997150 ERS13672475 ERA18581410 living systems institute, university of exeter|European Nucleotide Archive living systems institute, university of exeter|European Nucleotide Archive                       B B biological fallback assumption illumina novaseq_era full_length poly_a trueseq bulk unknown unknown   United Kingdom 2024-02-06 Larval Larval Brain Nervous System
11050 11050 ERR10476814 ERX9997157 ERS13672482 ERP138527 PRJEB53713 Time course whole brain transcriptome and methylome profiles of early life high GC exposed zebrafish f79d57b2-1e93-4ca0-8fda-fd881a2a0c1e Other Whole brain transcriptome mRNA profiles of zebrafish which exposed to elavated glucocorticoid GC optogenetically at 6 13 120 dpf dpf and post predatory stress looming dots stress at xxx dpf. All subjective adults at 120 dpf were female. Tubingen strain was used as wildtype control and brains from transgenic line Tgstar:bPAC 2A tdTomatouoe300 +/ and / were sequenced on Illumina NovaSeq6000 by TRON gGmbH Mainz Germany. Paired end TruSeq Stranded mRNA libraries Illumina CA USA were constructed and over 20M of 50 bp reads/sample were sequenced. Oxford Nanopore sequencing was used for DNA methylation identification. These data were generated for the study by Choi et al. 2024. https://www.biorxiv.org/content/10.1101/2023.02.13.528363v4 ENA FIRST PUBLIC:2024 02 06|ENA LAST UPDATE:2024 02 06   star:bPAC+/ whole brain pooled 15 brains star:bPAC+/ whole brain day13 SAMEA111562626 Living Systems Institute, University of Exeter INSDC center name:Living Systems Institute University of Exeter|Submitter Id:star pos d13 3|collection date:2019 12|common name:zebrafish|dev stage:13 dpf|geographic location country and/or sea:Germany|sample name:star pos d13 3|scientific name:Danio rerio|sex:N/A|strain:Tübingen|tissue type:brain                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 09 11 2022 11:52:59:186 283047 Sample 0256 083 FR NSP TR2 SL1 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   ERP138527 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 02 06|ENA LAST UPDATE:2024 02 06 0256_083_FR_NSP_TR2_SL1_S14_L001_R1_001-pooled.fastq.gz 0256_083_FR_NSP_TR2_SL1_S14_L001_R2_001-pooled.fastq.gz fastq fastq 5492667156.0 53849678.0 ena RUN TAB 09 11 2022 11:52:59:186 283048 0:51 1:51 A:1546610275;C:1178241230;G:1195797489;T:1571955787;N:62375 51 51     1546610275 1178241230 1195797489 1571955787 62375 ERX9997157 ERS13672482 ERA18581410 living systems institute, university of exeter|European Nucleotide Archive living systems institute, university of exeter|European Nucleotide Archive                       B B biological fallback assumption illumina novaseq_era full_length poly_a trueseq bulk unknown unknown   United Kingdom 2024-02-06 Larval Larval Brain Nervous System
11051 11051 ERR10476829 ERX9997172 ERS13672497 ERP138527 PRJEB53713 Time course whole brain transcriptome and methylome profiles of early life high GC exposed zebrafish f79d57b2-1e93-4ca0-8fda-fd881a2a0c1e Other Whole brain transcriptome mRNA profiles of zebrafish which exposed to elavated glucocorticoid GC optogenetically at 6 13 120 dpf dpf and post predatory stress looming dots stress at xxx dpf. All subjective adults at 120 dpf were female. Tubingen strain was used as wildtype control and brains from transgenic line Tgstar:bPAC 2A tdTomatouoe300 +/ and / were sequenced on Illumina NovaSeq6000 by TRON gGmbH Mainz Germany. Paired end TruSeq Stranded mRNA libraries Illumina CA USA were constructed and over 20M of 50 bp reads/sample were sequenced. Oxford Nanopore sequencing was used for DNA methylation identification. These data were generated for the study by Choi et al. 2024. https://www.biorxiv.org/content/10.1101/2023.02.13.528363v4 ENA FIRST PUBLIC:2024 02 06|ENA LAST UPDATE:2024 02 06   star:bPAC / whole brain pooled 15 brains star:bPAC / whole brain day6 SAMEA111562641 Living Systems Institute, University of Exeter INSDC center name:Living Systems Institute University of Exeter|Submitter Id:star neg d6 3|collection date:2019 12|common name:zebrafish|dev stage:6 dpf|geographic location country and/or sea:Germany|sample name:star neg d6 3|scientific name:Danio rerio|sex:N/A|strain:Tübingen|tissue type:brain                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 09 11 2022 11:52:59:192 283077 Sample 0256 103 FR NSP TR1 SL1 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   ERP138527 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 02 06|ENA LAST UPDATE:2024 02 06 0256_103_FR_NSP_TR1_SL1_S32_L001_R1_001-pooled.fastq.gz 0256_103_FR_NSP_TR1_SL1_S32_L001_R2_001-pooled.fastq.gz fastq fastq 3120070248.0 30588924.0 ena RUN TAB 09 11 2022 11:52:59:193 283078 0:51 1:51 A:846274026;C:707353227;G:707836608;T:858570820;N:35567 51 51     846274026 707353227 707836608 858570820 35567 ERX9997172 ERS13672497 ERA18581410 living systems institute, university of exeter|European Nucleotide Archive living systems institute, university of exeter|European Nucleotide Archive                       B B biological fallback assumption illumina novaseq_era full_length poly_a trueseq bulk unknown unknown   United Kingdom 2024-02-06 Larval Larval Brain Nervous System
11053 11053 ERR10476796 ERX9997139 ERS13672464 ERP138527 PRJEB53713 Time course whole brain transcriptome and methylome profiles of early life high GC exposed zebrafish f79d57b2-1e93-4ca0-8fda-fd881a2a0c1e Other Whole brain transcriptome mRNA profiles of zebrafish which exposed to elavated glucocorticoid GC optogenetically at 6 13 120 dpf dpf and post predatory stress looming dots stress at xxx dpf. All subjective adults at 120 dpf were female. Tubingen strain was used as wildtype control and brains from transgenic line Tgstar:bPAC 2A tdTomatouoe300 +/ and / were sequenced on Illumina NovaSeq6000 by TRON gGmbH Mainz Germany. Paired end TruSeq Stranded mRNA libraries Illumina CA USA were constructed and over 20M of 50 bp reads/sample were sequenced. Oxford Nanopore sequencing was used for DNA methylation identification. These data were generated for the study by Choi et al. 2024. https://www.biorxiv.org/content/10.1101/2023.02.13.528363v4 ENA FIRST PUBLIC:2024 02 06|ENA LAST UPDATE:2024 02 06   wildtype whole brain pooled 15 brains wildtype whole brain day13 SAMEA111562608 Living Systems Institute, University of Exeter INSDC center name:Living Systems Institute University of Exeter|Submitter Id:tu wt d13 5|collection date:2019 12|common name:zebrafish|dev stage:13 dpf|geographic location country and/or sea:Germany|sample name:tu wt d13 5|scientific name:Danio rerio|sex:N/A|strain:Tübingen|tissue type:brain                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 09 11 2022 11:52:59:178 283011 Sample 0256 010 FR NSP TR1 SL1 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   ERP138527 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 02 06|ENA LAST UPDATE:2024 02 06 0256_010_FR_NSP_TR1_SL1_S21_L001_R1_001-pooled.fastq.gz 0256_010_FR_NSP_TR1_SL1_S21_L001_R2_001-pooled.fastq.gz fastq fastq 2969687772.0 29114586.0 ena RUN TAB 09 11 2022 11:52:59:179 283012 0:51 1:51 A:762435544;C:713336460;G:731717998;T:762096042;N:101728 51 51     762435544 713336460 731717998 762096042 101728 ERX9997139 ERS13672464 ERA18581410 living systems institute, university of exeter|European Nucleotide Archive living systems institute, university of exeter|European Nucleotide Archive                       B B biological fallback assumption illumina novaseq_era full_length poly_a trueseq bulk unknown unknown   United Kingdom 2024-02-06 Larval Larval Brain Nervous System
11055 11055 ERR10476836 ERX9997179 ERS13672504 ERP138527 PRJEB53713 Time course whole brain transcriptome and methylome profiles of early life high GC exposed zebrafish f79d57b2-1e93-4ca0-8fda-fd881a2a0c1e Other Whole brain transcriptome mRNA profiles of zebrafish which exposed to elavated glucocorticoid GC optogenetically at 6 13 120 dpf dpf and post predatory stress looming dots stress at xxx dpf. All subjective adults at 120 dpf were female. Tubingen strain was used as wildtype control and brains from transgenic line Tgstar:bPAC 2A tdTomatouoe300 +/ and / were sequenced on Illumina NovaSeq6000 by TRON gGmbH Mainz Germany. Paired end TruSeq Stranded mRNA libraries Illumina CA USA were constructed and over 20M of 50 bp reads/sample were sequenced. Oxford Nanopore sequencing was used for DNA methylation identification. These data were generated for the study by Choi et al. 2024. https://www.biorxiv.org/content/10.1101/2023.02.13.528363v4 ENA FIRST PUBLIC:2024 02 06|ENA LAST UPDATE:2024 02 06   star:bPAC / whole brain pooled 15 brains star:bPAC / whole brain day13 SAMEA111562648 Living Systems Institute, University of Exeter INSDC center name:Living Systems Institute University of Exeter|Submitter Id:star neg d13 5|collection date:2019 12|common name:zebrafish|dev stage:13 dpf|geographic location country and/or sea:Germany|sample name:star neg d13 5|scientific name:Danio rerio|sex:N/A|strain:Tübingen|tissue type:brain                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 09 11 2022 11:52:59:195 283091 Sample 0256 110 FR NSP TR2 SL1 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   ERP138527 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 02 06|ENA LAST UPDATE:2024 02 06 0256_110_FR_NSP_TR2_SL1_S39_L001_R1_001-pooled.fastq.gz 0256_110_FR_NSP_TR2_SL1_S39_L001_R2_001-pooled.fastq.gz fastq fastq 2758547160.0 27044580.0 ena RUN TAB 09 11 2022 11:52:59:196 283092 0:51 1:51 A:732517446;C:640766914;G:643632251;T:741598802;N:31747 51 51     732517446 640766914 643632251 741598802 31747 ERX9997179 ERS13672504 ERA18581410 living systems institute, university of exeter|European Nucleotide Archive living systems institute, university of exeter|European Nucleotide Archive                       B B biological fallback assumption illumina novaseq_era full_length poly_a trueseq bulk unknown unknown   United Kingdom 2024-02-06 Larval Larval Brain Nervous System
11056 11056 ERR10476808 ERX9997151 ERS13672476 ERP138527 PRJEB53713 Time course whole brain transcriptome and methylome profiles of early life high GC exposed zebrafish f79d57b2-1e93-4ca0-8fda-fd881a2a0c1e Other Whole brain transcriptome mRNA profiles of zebrafish which exposed to elavated glucocorticoid GC optogenetically at 6 13 120 dpf dpf and post predatory stress looming dots stress at xxx dpf. All subjective adults at 120 dpf were female. Tubingen strain was used as wildtype control and brains from transgenic line Tgstar:bPAC 2A tdTomatouoe300 +/ and / were sequenced on Illumina NovaSeq6000 by TRON gGmbH Mainz Germany. Paired end TruSeq Stranded mRNA libraries Illumina CA USA were constructed and over 20M of 50 bp reads/sample were sequenced. Oxford Nanopore sequencing was used for DNA methylation identification. These data were generated for the study by Choi et al. 2024. https://www.biorxiv.org/content/10.1101/2023.02.13.528363v4 ENA FIRST PUBLIC:2024 02 06|ENA LAST UPDATE:2024 02 06   star:bPAC+/ whole brain pooled 15 brains star:bPAC+/ whole brain day6 SAMEA111562620 Living Systems Institute, University of Exeter INSDC center name:Living Systems Institute University of Exeter|Submitter Id:star pos d6 2|collection date:2019 12|common name:zebrafish|dev stage:6 dpf|geographic location country and/or sea:Germany|sample name:star pos d6 2|scientific name:Danio rerio|sex:N/A|strain:Tübingen|tissue type:brain                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 09 11 2022 11:52:59:184 283035 Sample 0256 077 FR NSP TR1 SL1 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   ERP138527 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 02 06|ENA LAST UPDATE:2024 02 06 0256_077_FR_NSP_TR1_SL1_S8_L001_R1_001-pooled.fastq.gz 0256_077_FR_NSP_TR1_SL1_S8_L001_R2_001-pooled.fastq.gz fastq fastq 3595088328.0 35245964.0 ena RUN TAB 09 11 2022 11:52:59:184 283036 0:51 1:51 A:985480827;C:803117311;G:811895458;T:994553698;N:41034 51 51     985480827 803117311 811895458 994553698 41034 ERX9997151 ERS13672476 ERA18581410 living systems institute, university of exeter|European Nucleotide Archive living systems institute, university of exeter|European Nucleotide Archive                       B B biological fallback assumption illumina novaseq_era full_length poly_a trueseq bulk unknown unknown   United Kingdom 2024-02-06 Larval Larval Brain Nervous System
11058 11058 ERR10476827 ERX9997170 ERS13672495 ERP138527 PRJEB53713 Time course whole brain transcriptome and methylome profiles of early life high GC exposed zebrafish f79d57b2-1e93-4ca0-8fda-fd881a2a0c1e Other Whole brain transcriptome mRNA profiles of zebrafish which exposed to elavated glucocorticoid GC optogenetically at 6 13 120 dpf dpf and post predatory stress looming dots stress at xxx dpf. All subjective adults at 120 dpf were female. Tubingen strain was used as wildtype control and brains from transgenic line Tgstar:bPAC 2A tdTomatouoe300 +/ and / were sequenced on Illumina NovaSeq6000 by TRON gGmbH Mainz Germany. Paired end TruSeq Stranded mRNA libraries Illumina CA USA were constructed and over 20M of 50 bp reads/sample were sequenced. Oxford Nanopore sequencing was used for DNA methylation identification. These data were generated for the study by Choi et al. 2024. https://www.biorxiv.org/content/10.1101/2023.02.13.528363v4 ENA FIRST PUBLIC:2024 02 06|ENA LAST UPDATE:2024 02 06   star:bPAC / whole brain pooled 15 brains star:bPAC / whole brain day6 SAMEA111562639 Living Systems Institute, University of Exeter INSDC center name:Living Systems Institute University of Exeter|Submitter Id:star neg d6 1|collection date:2019 12|common name:zebrafish|dev stage:6 dpf|geographic location country and/or sea:Germany|sample name:star neg d6 1|scientific name:Danio rerio|sex:N/A|strain:Tübingen|tissue type:brain                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 09 11 2022 11:52:59:192 283073 Sample 0256 101 FR NSP TR1 SL1 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   ERP138527 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 02 06|ENA LAST UPDATE:2024 02 06 0256_101_FR_NSP_TR1_SL1_S30_L001_R1_001-pooled.fastq.gz 0256_101_FR_NSP_TR1_SL1_S30_L001_R2_001-pooled.fastq.gz fastq fastq 3504125952.0 34354176.0 ena RUN TAB 09 11 2022 11:52:59:192 283074 0:51 1:51 A:947138693;C:797358353;G:798903844;T:960685108;N:39954 51 51     947138693 797358353 798903844 960685108 39954 ERX9997170 ERS13672495 ERA18581410 living systems institute, university of exeter|European Nucleotide Archive living systems institute, university of exeter|European Nucleotide Archive                       B B biological fallback assumption illumina novaseq_era full_length poly_a trueseq bulk unknown unknown   United Kingdom 2024-02-06 Larval Larval Brain Nervous System
11060 11060 ERR10476794 ERX9997137 ERS13672462 ERP138527 PRJEB53713 Time course whole brain transcriptome and methylome profiles of early life high GC exposed zebrafish f79d57b2-1e93-4ca0-8fda-fd881a2a0c1e Other Whole brain transcriptome mRNA profiles of zebrafish which exposed to elavated glucocorticoid GC optogenetically at 6 13 120 dpf dpf and post predatory stress looming dots stress at xxx dpf. All subjective adults at 120 dpf were female. Tubingen strain was used as wildtype control and brains from transgenic line Tgstar:bPAC 2A tdTomatouoe300 +/ and / were sequenced on Illumina NovaSeq6000 by TRON gGmbH Mainz Germany. Paired end TruSeq Stranded mRNA libraries Illumina CA USA were constructed and over 20M of 50 bp reads/sample were sequenced. Oxford Nanopore sequencing was used for DNA methylation identification. These data were generated for the study by Choi et al. 2024. https://www.biorxiv.org/content/10.1101/2023.02.13.528363v4 ENA FIRST PUBLIC:2024 02 06|ENA LAST UPDATE:2024 02 06   wildtype whole brain pooled 15 brains wildtype whole brain day13 SAMEA111562606 Living Systems Institute, University of Exeter INSDC center name:Living Systems Institute University of Exeter|Submitter Id:tu wt d13 3|collection date:2019 12|common name:zebrafish|dev stage:13 dpf|geographic location country and/or sea:Germany|sample name:tu wt d13 3|scientific name:Danio rerio|sex:N/A|strain:Tübingen|tissue type:brain                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 09 11 2022 11:52:59:178 283007 Sample 0256 008 FR NSP TR1 SL1 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   ERP138527 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 02 06|ENA LAST UPDATE:2024 02 06 0256_008_FR_NSP_TR1_SL1_S1_L001_R1_001-pooled.fastq.gz 0256_008_FR_NSP_TR1_SL1_S1_L001_R2_001-pooled.fastq.gz fastq fastq 2659023618.0 26068859.0 ena RUN TAB 09 11 2022 11:52:59:178 283008 0:51 1:51 A:670947753;C:637136773;G:677570266;T:673338670;N:30156 51 51     670947753 637136773 677570266 673338670 30156 ERX9997137 ERS13672462 ERA18581410 living systems institute, university of exeter|European Nucleotide Archive living systems institute, university of exeter|European Nucleotide Archive                       B B biological fallback assumption illumina novaseq_era full_length poly_a trueseq bulk unknown unknown   United Kingdom 2024-02-06 Larval Larval Brain Nervous System
11061 11061 ERR10476833 ERX9997176 ERS13672501 ERP138527 PRJEB53713 Time course whole brain transcriptome and methylome profiles of early life high GC exposed zebrafish f79d57b2-1e93-4ca0-8fda-fd881a2a0c1e Other Whole brain transcriptome mRNA profiles of zebrafish which exposed to elavated glucocorticoid GC optogenetically at 6 13 120 dpf dpf and post predatory stress looming dots stress at xxx dpf. All subjective adults at 120 dpf were female. Tubingen strain was used as wildtype control and brains from transgenic line Tgstar:bPAC 2A tdTomatouoe300 +/ and / were sequenced on Illumina NovaSeq6000 by TRON gGmbH Mainz Germany. Paired end TruSeq Stranded mRNA libraries Illumina CA USA were constructed and over 20M of 50 bp reads/sample were sequenced. Oxford Nanopore sequencing was used for DNA methylation identification. These data were generated for the study by Choi et al. 2024. https://www.biorxiv.org/content/10.1101/2023.02.13.528363v4 ENA FIRST PUBLIC:2024 02 06|ENA LAST UPDATE:2024 02 06   star:bPAC / whole brain pooled 15 brains star:bPAC / whole brain day13 SAMEA111562645 Living Systems Institute, University of Exeter INSDC center name:Living Systems Institute University of Exeter|Submitter Id:star neg d13 2|collection date:2019 12|common name:zebrafish|dev stage:13 dpf|geographic location country and/or sea:Germany|sample name:star neg d13 2|scientific name:Danio rerio|sex:N/A|strain:Tübingen|tissue type:brain                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 09 11 2022 11:52:59:194 283085 Sample 0256 107 FR NSP TR2 SL1 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   ERP138527 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 02 06|ENA LAST UPDATE:2024 02 06 0256_107_FR_NSP_TR2_SL1_S36_L001_R1_001-pooled.fastq.gz 0256_107_FR_NSP_TR2_SL1_S36_L001_R2_001-pooled.fastq.gz fastq fastq 3282322362.0 32179631.0 ena RUN TAB 09 11 2022 11:52:59:194 283086 0:51 1:51 A:898607442;C:734331926;G:739939203;T:909406172;N:37619 51 51     898607442 734331926 739939203 909406172 37619 ERX9997176 ERS13672501 ERA18581410 living systems institute, university of exeter|European Nucleotide Archive living systems institute, university of exeter|European Nucleotide Archive                       B B biological fallback assumption illumina novaseq_era full_length poly_a trueseq bulk unknown unknown   United Kingdom 2024-02-06 Larval Larval Brain Nervous System
11063 11063 ERR10476828 ERX9997171 ERS13672496 ERP138527 PRJEB53713 Time course whole brain transcriptome and methylome profiles of early life high GC exposed zebrafish f79d57b2-1e93-4ca0-8fda-fd881a2a0c1e Other Whole brain transcriptome mRNA profiles of zebrafish which exposed to elavated glucocorticoid GC optogenetically at 6 13 120 dpf dpf and post predatory stress looming dots stress at xxx dpf. All subjective adults at 120 dpf were female. Tubingen strain was used as wildtype control and brains from transgenic line Tgstar:bPAC 2A tdTomatouoe300 +/ and / were sequenced on Illumina NovaSeq6000 by TRON gGmbH Mainz Germany. Paired end TruSeq Stranded mRNA libraries Illumina CA USA were constructed and over 20M of 50 bp reads/sample were sequenced. Oxford Nanopore sequencing was used for DNA methylation identification. These data were generated for the study by Choi et al. 2024. https://www.biorxiv.org/content/10.1101/2023.02.13.528363v4 ENA FIRST PUBLIC:2024 02 06|ENA LAST UPDATE:2024 02 06   star:bPAC / whole brain pooled 15 brains star:bPAC / whole brain day6 SAMEA111562640 Living Systems Institute, University of Exeter INSDC center name:Living Systems Institute University of Exeter|Submitter Id:star neg d6 2|collection date:2019 12|common name:zebrafish|dev stage:6 dpf|geographic location country and/or sea:Germany|sample name:star neg d6 2|scientific name:Danio rerio|sex:N/A|strain:Tübingen|tissue type:brain                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 09 11 2022 11:52:59:192 283075 Sample 0256 102 FR NSP TR1 SL1 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   ERP138527 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 02 06|ENA LAST UPDATE:2024 02 06 0256_102_FR_NSP_TR1_SL1_S31_L001_R1_001-pooled.fastq.gz 0256_102_FR_NSP_TR1_SL1_S31_L001_R2_001-pooled.fastq.gz fastq fastq 3969901404.0 38920602.0 ena RUN TAB 09 11 2022 11:52:59:192 283076 0:51 1:51 A:1079447747;C:894502841;G:908706945;T:1087198510;N:45361 51 51     1079447747 894502841 908706945 1087198510 45361 ERX9997171 ERS13672496 ERA18581410 living systems institute, university of exeter|European Nucleotide Archive living systems institute, university of exeter|European Nucleotide Archive                       B B biological fallback assumption illumina novaseq_era full_length poly_a trueseq bulk unknown unknown   United Kingdom 2024-02-06 Larval Larval Brain Nervous System
11068 11068 ERR10476790 ERX9997133 ERS13672458 ERP138527 PRJEB53713 Time course whole brain transcriptome and methylome profiles of early life high GC exposed zebrafish f79d57b2-1e93-4ca0-8fda-fd881a2a0c1e Other Whole brain transcriptome mRNA profiles of zebrafish which exposed to elavated glucocorticoid GC optogenetically at 6 13 120 dpf dpf and post predatory stress looming dots stress at xxx dpf. All subjective adults at 120 dpf were female. Tubingen strain was used as wildtype control and brains from transgenic line Tgstar:bPAC 2A tdTomatouoe300 +/ and / were sequenced on Illumina NovaSeq6000 by TRON gGmbH Mainz Germany. Paired end TruSeq Stranded mRNA libraries Illumina CA USA were constructed and over 20M of 50 bp reads/sample were sequenced. Oxford Nanopore sequencing was used for DNA methylation identification. These data were generated for the study by Choi et al. 2024. https://www.biorxiv.org/content/10.1101/2023.02.13.528363v4 ENA FIRST PUBLIC:2024 02 06|ENA LAST UPDATE:2024 02 06   wildtype whole brain pooled 15 brains wildtype whole brain day6 SAMEA111562602 Living Systems Institute, University of Exeter INSDC center name:Living Systems Institute University of Exeter|Submitter Id:tu wt d6 4|collection date:2019 12|common name:zebrafish|dev stage:6 dpf|geographic location country and/or sea:Germany|sample name:tu wt d6 4|scientific name:Danio rerio|sex:N/A|strain:Tübingen|tissue type:brain                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 09 11 2022 11:52:59:176 282999 Sample 0256 004 FR NSP TR1 SL1 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   ERP138527 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 02 06|ENA LAST UPDATE:2024 02 06 0256_004_FR_NSP_TR1_SL1_S16_L001_R1_001-pooled.fastq.gz 0256_004_FR_NSP_TR1_SL1_S16_L001_R2_001-pooled.fastq.gz fastq fastq 2693489520.0 26406760.0 ena RUN TAB 09 11 2022 11:52:59:176 283000 0:51 1:51 A:701762127;C:639663261;G:643729664;T:708242984;N:91484 51 51     701762127 639663261 643729664 708242984 91484 ERX9997133 ERS13672458 ERA18581410 living systems institute, university of exeter|European Nucleotide Archive living systems institute, university of exeter|European Nucleotide Archive                       B B biological fallback assumption illumina novaseq_era full_length poly_a trueseq bulk unknown unknown   United Kingdom 2024-02-06 Larval Larval Brain Nervous System
11070 11070 ERR10476791 ERX9997134 ERS13672459 ERP138527 PRJEB53713 Time course whole brain transcriptome and methylome profiles of early life high GC exposed zebrafish f79d57b2-1e93-4ca0-8fda-fd881a2a0c1e Other Whole brain transcriptome mRNA profiles of zebrafish which exposed to elavated glucocorticoid GC optogenetically at 6 13 120 dpf dpf and post predatory stress looming dots stress at xxx dpf. All subjective adults at 120 dpf were female. Tubingen strain was used as wildtype control and brains from transgenic line Tgstar:bPAC 2A tdTomatouoe300 +/ and / were sequenced on Illumina NovaSeq6000 by TRON gGmbH Mainz Germany. Paired end TruSeq Stranded mRNA libraries Illumina CA USA were constructed and over 20M of 50 bp reads/sample were sequenced. Oxford Nanopore sequencing was used for DNA methylation identification. These data were generated for the study by Choi et al. 2024. https://www.biorxiv.org/content/10.1101/2023.02.13.528363v4 ENA FIRST PUBLIC:2024 02 06|ENA LAST UPDATE:2024 02 06   wildtype whole brain pooled 15 brains wildtype whole brain day6 SAMEA111562603 Living Systems Institute, University of Exeter INSDC center name:Living Systems Institute University of Exeter|Submitter Id:tu wt d6 5|collection date:2019 12|common name:zebrafish|dev stage:6 dpf|geographic location country and/or sea:Germany|sample name:tu wt d6 5|scientific name:Danio rerio|sex:N/A|strain:Tübingen|tissue type:brain                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 09 11 2022 11:52:59:176 283001 Sample 0256 005 FR NSP TR1 SL1 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   ERP138527 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 02 06|ENA LAST UPDATE:2024 02 06 0256_005_FR_NSP_TR1_SL1_S17_L001_R1_001-pooled.fastq.gz 0256_005_FR_NSP_TR1_SL1_S17_L001_R2_001-pooled.fastq.gz fastq fastq 2904430620.0 28474810.0 ena RUN TAB 09 11 2022 11:52:59:176 283002 0:51 1:51 A:777892611;C:666758312;G:672026589;T:787654140;N:98968 51 51     777892611 666758312 672026589 787654140 98968 ERX9997134 ERS13672459 ERA18581410 living systems institute, university of exeter|European Nucleotide Archive living systems institute, university of exeter|European Nucleotide Archive                       B B biological fallback assumption illumina novaseq_era full_length poly_a trueseq bulk unknown unknown   United Kingdom 2024-02-06 Larval Larval Brain Nervous System
11074 11074 ERR10476788 ERX9997131 ERS13672456 ERP138527 PRJEB53713 Time course whole brain transcriptome and methylome profiles of early life high GC exposed zebrafish f79d57b2-1e93-4ca0-8fda-fd881a2a0c1e Other Whole brain transcriptome mRNA profiles of zebrafish which exposed to elavated glucocorticoid GC optogenetically at 6 13 120 dpf dpf and post predatory stress looming dots stress at xxx dpf. All subjective adults at 120 dpf were female. Tubingen strain was used as wildtype control and brains from transgenic line Tgstar:bPAC 2A tdTomatouoe300 +/ and / were sequenced on Illumina NovaSeq6000 by TRON gGmbH Mainz Germany. Paired end TruSeq Stranded mRNA libraries Illumina CA USA were constructed and over 20M of 50 bp reads/sample were sequenced. Oxford Nanopore sequencing was used for DNA methylation identification. These data were generated for the study by Choi et al. 2024. https://www.biorxiv.org/content/10.1101/2023.02.13.528363v4 ENA FIRST PUBLIC:2024 02 06|ENA LAST UPDATE:2024 02 06   wildtype whole brain pooled 15 brains wildtype whole brain day6 SAMEA111562600 Living Systems Institute, University of Exeter INSDC center name:Living Systems Institute University of Exeter|Submitter Id:tu wt d6 2|collection date:2019 12|common name:zebrafish|dev stage:6 dpf|geographic location country and/or sea:Germany|sample name:tu wt d6 2|scientific name:Danio rerio|sex:N/A|strain:Tübingen|tissue type:brain                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 09 11 2022 11:52:59:175 282995 Sample 0256 002 FR NSP TR1 SL1 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   ERP138527 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 02 06|ENA LAST UPDATE:2024 02 06 0256_002_FR_NSP_TR1_SL1_S14_L001_R1_001-pooled.fastq.gz 0256_002_FR_NSP_TR1_SL1_S14_L001_R2_001-pooled.fastq.gz fastq fastq 2385303456.0 23385328.0 ena RUN TAB 09 11 2022 11:52:59:175 282996 0:51 1:51 A:620601269;C:567608030;G:568555174;T:628457831;N:81152 51 51     620601269 567608030 568555174 628457831 81152 ERX9997131 ERS13672456 ERA18581410 living systems institute, university of exeter|European Nucleotide Archive living systems institute, university of exeter|European Nucleotide Archive                       B B biological fallback assumption illumina novaseq_era full_length poly_a trueseq bulk unknown unknown   United Kingdom 2024-02-06 Larval Larval Brain Nervous System
11077 11077 ERR10476816 ERX9997159 ERS13672484 ERP138527 PRJEB53713 Time course whole brain transcriptome and methylome profiles of early life high GC exposed zebrafish f79d57b2-1e93-4ca0-8fda-fd881a2a0c1e Other Whole brain transcriptome mRNA profiles of zebrafish which exposed to elavated glucocorticoid GC optogenetically at 6 13 120 dpf dpf and post predatory stress looming dots stress at xxx dpf. All subjective adults at 120 dpf were female. Tubingen strain was used as wildtype control and brains from transgenic line Tgstar:bPAC 2A tdTomatouoe300 +/ and / were sequenced on Illumina NovaSeq6000 by TRON gGmbH Mainz Germany. Paired end TruSeq Stranded mRNA libraries Illumina CA USA were constructed and over 20M of 50 bp reads/sample were sequenced. Oxford Nanopore sequencing was used for DNA methylation identification. These data were generated for the study by Choi et al. 2024. https://www.biorxiv.org/content/10.1101/2023.02.13.528363v4 ENA FIRST PUBLIC:2024 02 06|ENA LAST UPDATE:2024 02 06   star:bPAC+/ whole brain pooled 15 brains star:bPAC+/ whole brain day13 SAMEA111562628 Living Systems Institute, University of Exeter INSDC center name:Living Systems Institute University of Exeter|Submitter Id:star pos d13 5|collection date:2019 12|common name:zebrafish|dev stage:13 dpf|geographic location country and/or sea:Germany|sample name:star pos d13 5|scientific name:Danio rerio|sex:N/A|strain:Tübingen|tissue type:brain                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 09 11 2022 11:52:59:187 283051 Sample 0256 085 FR NSP TRP SL1 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   ERP138527 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 02 06|ENA LAST UPDATE:2024 02 06 0256_085_FR_NSP_TRP_SL1_S16_L001_R1_001-pooled.fastq.gz 0256_085_FR_NSP_TRP_SL1_S16_L001_R2_001-pooled.fastq.gz fastq fastq 3264856596.0 32008398.0 ena RUN TAB 09 11 2022 11:52:59:187 283052 0:51 1:51 A:908889213;C:708892816;G:727180747;T:919857088;N:36732 51 51     908889213 708892816 727180747 919857088 36732 ERX9997159 ERS13672484 ERA18581410 living systems institute, university of exeter|European Nucleotide Archive living systems institute, university of exeter|European Nucleotide Archive                       B B biological fallback assumption illumina novaseq_era full_length poly_a trueseq bulk unknown unknown   United Kingdom 2024-02-06 Larval Larval Brain Nervous System
11078 11078 ERR10476813 ERX9997156 ERS13672481 ERP138527 PRJEB53713 Time course whole brain transcriptome and methylome profiles of early life high GC exposed zebrafish f79d57b2-1e93-4ca0-8fda-fd881a2a0c1e Other Whole brain transcriptome mRNA profiles of zebrafish which exposed to elavated glucocorticoid GC optogenetically at 6 13 120 dpf dpf and post predatory stress looming dots stress at xxx dpf. All subjective adults at 120 dpf were female. Tubingen strain was used as wildtype control and brains from transgenic line Tgstar:bPAC 2A tdTomatouoe300 +/ and / were sequenced on Illumina NovaSeq6000 by TRON gGmbH Mainz Germany. Paired end TruSeq Stranded mRNA libraries Illumina CA USA were constructed and over 20M of 50 bp reads/sample were sequenced. Oxford Nanopore sequencing was used for DNA methylation identification. These data were generated for the study by Choi et al. 2024. https://www.biorxiv.org/content/10.1101/2023.02.13.528363v4 ENA FIRST PUBLIC:2024 02 06|ENA LAST UPDATE:2024 02 06   star:bPAC+/ whole brain pooled 15 brains star:bPAC+/ whole brain day13 SAMEA111562625 Living Systems Institute, University of Exeter INSDC center name:Living Systems Institute University of Exeter|Submitter Id:star pos d13 2|collection date:2019 12|common name:zebrafish|dev stage:13 dpf|geographic location country and/or sea:Germany|sample name:star pos d13 2|scientific name:Danio rerio|sex:N/A|strain:Tübingen|tissue type:brain                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 09 11 2022 11:52:59:186 283045 Sample 0256 082 FR NSP TR2 SL1 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   ERP138527 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 02 06|ENA LAST UPDATE:2024 02 06 0256_082_FR_NSP_TR2_SL1_S13_L001_R1_001-pooled.fastq.gz 0256_082_FR_NSP_TR2_SL1_S13_L001_R2_001-pooled.fastq.gz fastq fastq 3037654248.0 29780924.0 ena RUN TAB 09 11 2022 11:52:59:186 283046 0:51 1:51 A:859112641;C:645943863;G:660257800;T:872305592;N:34352 51 51     859112641 645943863 660257800 872305592 34352 ERX9997156 ERS13672481 ERA18581410 living systems institute, university of exeter|European Nucleotide Archive living systems institute, university of exeter|European Nucleotide Archive                       B B biological fallback assumption illumina novaseq_era full_length poly_a trueseq bulk unknown unknown   United Kingdom 2024-02-06 Larval Larval Brain Nervous System
11079 11079 ERR10476832 ERX9997175 ERS13672500 ERP138527 PRJEB53713 Time course whole brain transcriptome and methylome profiles of early life high GC exposed zebrafish f79d57b2-1e93-4ca0-8fda-fd881a2a0c1e Other Whole brain transcriptome mRNA profiles of zebrafish which exposed to elavated glucocorticoid GC optogenetically at 6 13 120 dpf dpf and post predatory stress looming dots stress at xxx dpf. All subjective adults at 120 dpf were female. Tubingen strain was used as wildtype control and brains from transgenic line Tgstar:bPAC 2A tdTomatouoe300 +/ and / were sequenced on Illumina NovaSeq6000 by TRON gGmbH Mainz Germany. Paired end TruSeq Stranded mRNA libraries Illumina CA USA were constructed and over 20M of 50 bp reads/sample were sequenced. Oxford Nanopore sequencing was used for DNA methylation identification. These data were generated for the study by Choi et al. 2024. https://www.biorxiv.org/content/10.1101/2023.02.13.528363v4 ENA FIRST PUBLIC:2024 02 06|ENA LAST UPDATE:2024 02 06   star:bPAC / whole brain pooled 15 brains star:bPAC / whole brain day13 SAMEA111562644 Living Systems Institute, University of Exeter INSDC center name:Living Systems Institute University of Exeter|Submitter Id:star neg d13 1|collection date:2019 12|common name:zebrafish|dev stage:13 dpf|geographic location country and/or sea:Germany|sample name:star neg d13 1|scientific name:Danio rerio|sex:N/A|strain:Tübingen|tissue type:brain                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 09 11 2022 11:52:59:194 283083 Sample 0256 106 FR NSP TR1 SL1 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   ERP138527 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 02 06|ENA LAST UPDATE:2024 02 06 0256_106_FR_NSP_TR1_SL1_S35_L001_R1_001-pooled.fastq.gz 0256_106_FR_NSP_TR1_SL1_S35_L001_R2_001-pooled.fastq.gz fastq fastq 2761703040.0 27075520.0 ena RUN TAB 09 11 2022 11:52:59:194 283084 0:51 1:51 A:761065450;C:610246142;G:622228689;T:768131440;N:31319 51 51     761065450 610246142 622228689 768131440 31319 ERX9997175 ERS13672500 ERA18581410 living systems institute, university of exeter|European Nucleotide Archive living systems institute, university of exeter|European Nucleotide Archive                       B B biological fallback assumption illumina novaseq_era full_length poly_a trueseq bulk unknown unknown   United Kingdom 2024-02-06 Larval Larval Brain Nervous System
11080 11080 ERR10476810 ERX9997153 ERS13672478 ERP138527 PRJEB53713 Time course whole brain transcriptome and methylome profiles of early life high GC exposed zebrafish f79d57b2-1e93-4ca0-8fda-fd881a2a0c1e Other Whole brain transcriptome mRNA profiles of zebrafish which exposed to elavated glucocorticoid GC optogenetically at 6 13 120 dpf dpf and post predatory stress looming dots stress at xxx dpf. All subjective adults at 120 dpf were female. Tubingen strain was used as wildtype control and brains from transgenic line Tgstar:bPAC 2A tdTomatouoe300 +/ and / were sequenced on Illumina NovaSeq6000 by TRON gGmbH Mainz Germany. Paired end TruSeq Stranded mRNA libraries Illumina CA USA were constructed and over 20M of 50 bp reads/sample were sequenced. Oxford Nanopore sequencing was used for DNA methylation identification. These data were generated for the study by Choi et al. 2024. https://www.biorxiv.org/content/10.1101/2023.02.13.528363v4 ENA FIRST PUBLIC:2024 02 06|ENA LAST UPDATE:2024 02 06   star:bPAC+/ whole brain pooled 15 brains star:bPAC+/ whole brain day6 SAMEA111562622 Living Systems Institute, University of Exeter INSDC center name:Living Systems Institute University of Exeter|Submitter Id:star pos d6 4|collection date:2019 12|common name:zebrafish|dev stage:6 dpf|geographic location country and/or sea:Germany|sample name:star pos d6 4|scientific name:Danio rerio|sex:N/A|strain:Tübingen|tissue type:brain                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 09 11 2022 11:52:59:184 283039 Sample 0256 079 FR NSP TR1 SL1 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   ERP138527 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2024 02 06|ENA LAST UPDATE:2024 02 06 0256_079_FR_NSP_TR1_SL1_S10_L001_R1_001-pooled.fastq.gz 0256_079_FR_NSP_TR1_SL1_S10_L001_R2_001-pooled.fastq.gz fastq fastq 2745379674.0 26915487.0 ena RUN TAB 09 11 2022 11:52:59:185 283040 0:51 1:51 A:762974242;C:602287296;G:611894421;T:768192503;N:31212 51 51     762974242 602287296 611894421 768192503 31212 ERX9997153 ERS13672478 ERA18581410 living systems institute, university of exeter|European Nucleotide Archive living systems institute, university of exeter|European Nucleotide Archive                       B B biological fallback assumption illumina novaseq_era full_length poly_a trueseq bulk unknown unknown   United Kingdom 2024-02-06 Larval Larval 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");;