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624 rows where experiment.library_selection = "RANDOM", experiment.platform = "ILLUMINA" and technology = "unknown"

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tissue_curation >10

devstage_curation >10

devstage_curation_coarse 6

experiment.library_strategy 4

experiment.library_source 2

experiment.library_layout 2

technology 1

  • unknown · 624 ✖

experiment.platform 1

  • ILLUMINA · 624 ✖

experiment.library_selection 1

  • RANDOM · 624 ✖
Link rowid ▼ run.accession experiment.accession sample.accession study.accession bioproject study.title study.alias study.type study.abstract study.attributes study.PMIDs sample.description sample.title sample.alias sample.centername sample.attributes GEOsample.title GEOsample.dataprocessing GEOsample.source GEOsample.treatmentprotocol GEOsample.extractprotocol GEOsample.growthprotocol GEOsample.characteristics GEOsample.accession experiment.title experiment.alias experiment.library_name experiment.design_description experiment.library_construction_protocol experiment.attributes experiment.library_strategy experiment.library_source experiment.library_selection experiment.library_layout experiment.platform experiment.instrument_model experiment.spot_descriptor experiment.study_ref run.title run.attributes run.filename run.semantic_name run.total_bases run.total_spots run.alias run.read_lengths run.base_counts run.r1_length run.r2_length run.r3_length run.r4_length run.Acount run.Ccount run.Gcount run.Tcount run.Ncount run.experiment run.pool_member submission.accession submission.srasource submission.bioprojectsource seqdetective.n_mates seqdetective.mapping_rate.mate1 seqdetective.mapping_rate.mate2 seqdetective.nofeature_rate.mate1 seqdetective.nofeature_rate.mate2 seqdetective.sparsity.mate1 seqdetective.sparsity.mate2 seqdetective.pos_strand_rate.mate1 seqdetective.pos_strand_rate.mate2 seqdetective.readlen.mate1 seqdetective.readlen.mate2 seqdetective.judgement.mate1 seqdetective.judgement.mate2 seqdetective.judgement.reason platform_family instrument_generation read_bias selection_class prep_kit sc_or_bulk tech_class technology tech_variant submission.bioprojectsource.country earliest_date devstage_curation devstage_curation_coarse tissue_curation tissue_curation_coarse
32 32 DRR408242 DRX393848 DRS407006 DRP012035 PRJDB14274 Zebrafish Gut RNA seq. DRP012035 Transcriptome Analysis A project to find differential expressed genes between larval and adult zebrafish gut. We dissected guts of wild type AB line and prepared three duplicates for each of larval and adult gut. Libraries for NGS are prepared using illumina TruSeq standard mRNA sample prep kit.     zebrafish wild type AB adult gut replicate 3 zebrafish adult gut replicate 3 SAMD00529462   sample name:zebrafish adult gut replicate 3|biological replicate:adult 3|strain:AB                 Illumina HiSeq 1500 sequencing of SAMD00529462 DRX393848 AR019 gut 6 adult 1 1   RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 1500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>126</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP012035 Illumina HiSeq 1500 sequencing of SAMD00529462       3546347364.0 28145614.0 DRR408242 0:126 1:0 A:919466631;C:829424335;G:818581155;T:978810217;N:65026 126 0     919466631 829424335 818581155 978810217 65026 DRX393848 DRS407006 DRA014885 NIBB|NIBB core research facilities, National Institute for Basic Biology University of Hyogo                       B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   Japan 2024-09-20 Adult Adult Gut Digestive System
33 33 DRR408241 DRX393847 DRS407005 DRP012035 PRJDB14274 Zebrafish Gut RNA seq. DRP012035 Transcriptome Analysis A project to find differential expressed genes between larval and adult zebrafish gut. We dissected guts of wild type AB line and prepared three duplicates for each of larval and adult gut. Libraries for NGS are prepared using illumina TruSeq standard mRNA sample prep kit.     zebrafish wild type AB adult gut replicate 2 zebrafish adult gut replicate 2 SAMD00529461   sample name:zebrafish adult gut replicate 2|biological replicate:adult 2|strain:AB                 Illumina HiSeq 1500 sequencing of SAMD00529461 DRX393847 AR006 gut 4 adult 1 1   RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 1500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>126</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP012035 Illumina HiSeq 1500 sequencing of SAMD00529461       3671973648.0 29142648.0 DRR408241 0:126 1:0 A:942167543;C:859431290;G:852661772;T:1017643011;N:70032 126 0     942167543 859431290 852661772 1017643011 70032 DRX393847 DRS407005 DRA014885 NIBB|NIBB core research facilities, National Institute for Basic Biology University of Hyogo                       B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   Japan 2024-09-20 Adult Adult Gut Digestive System
34 34 DRR408240 DRX393846 DRS407004 DRP012035 PRJDB14274 Zebrafish Gut RNA seq. DRP012035 Transcriptome Analysis A project to find differential expressed genes between larval and adult zebrafish gut. We dissected guts of wild type AB line and prepared three duplicates for each of larval and adult gut. Libraries for NGS are prepared using illumina TruSeq standard mRNA sample prep kit.     zebrafish wild type AB adult gut replicate 1 zebrafish adult gut replicate 1 SAMD00529460   sample name:zebrafish adult gut replicate 1|biological replicate:adult 1|strain:AB                 Illumina HiSeq 1500 sequencing of SAMD00529460 DRX393846 AR004 gut 2 adult 1 1   RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 1500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>126</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP012035 Illumina HiSeq 1500 sequencing of SAMD00529460       3480523704.0 27623204.0 DRR408240 0:126 1:0 A:898051986;C:827557593;G:816541244;T:938307607;N:65274 126 0     898051986 827557593 816541244 938307607 65274 DRX393846 DRS407004 DRA014885 NIBB|NIBB core research facilities, National Institute for Basic Biology University of Hyogo                       B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   Japan 2024-09-20 Adult Adult Gut Digestive System
35 35 DRR408239 DRX393845 DRS407003 DRP012035 PRJDB14274 Zebrafish Gut RNA seq. DRP012035 Transcriptome Analysis A project to find differential expressed genes between larval and adult zebrafish gut. We dissected guts of wild type AB line and prepared three duplicates for each of larval and adult gut. Libraries for NGS are prepared using illumina TruSeq standard mRNA sample prep kit.     zebrafish wild type AB larval gut replicate 3 zebrafish larval gut replicate 3 SAMD00529459   sample name:zebrafish larval gut replicate 3|biological replicate:larval 3|strain:AB                 Illumina HiSeq 1500 sequencing of SAMD00529459 DRX393845 AR012 gut 5 5 dpf 6 dpf larvae 1 1   RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 1500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>126</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP012035 Illumina HiSeq 1500 sequencing of SAMD00529459       3463982046.0 27491921.0 DRR408239 0:126 1:0 A:842552557;C:849757648;G:837664725;T:933942026;N:65090 126 0     842552557 849757648 837664725 933942026 65090 DRX393845 DRS407003 DRA014885 NIBB|NIBB core research facilities, National Institute for Basic Biology University of Hyogo                       B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   Japan 2024-09-20 Larval Larval Gut Digestive System
36 36 DRR408238 DRX393844 DRS407002 DRP012035 PRJDB14274 Zebrafish Gut RNA seq. DRP012035 Transcriptome Analysis A project to find differential expressed genes between larval and adult zebrafish gut. We dissected guts of wild type AB line and prepared three duplicates for each of larval and adult gut. Libraries for NGS are prepared using illumina TruSeq standard mRNA sample prep kit.     zebrafish wild type AB larval gut replicate 2 zebrafish larval gut replicate 2 SAMD00529458   sample name:zebrafish larval gut replicate 2|biological replicate:larval 2|strain:AB                 Illumina HiSeq 1500 sequencing of SAMD00529458 DRX393844 AR005 gut 3 5 dpf 6 dpf larvae 1 1   RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 1500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>126</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP012035 Illumina HiSeq 1500 sequencing of SAMD00529458       3782320416.0 30018416.0 DRR408238 0:126 1:0 A:930337206;C:920645770;G:906559955;T:1024704277;N:73208 126 0     930337206 920645770 906559955 1024704277 73208 DRX393844 DRS407002 DRA014885 NIBB|NIBB core research facilities, National Institute for Basic Biology University of Hyogo                       B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   Japan 2024-09-20 Larval Larval Gut Digestive System
37 37 DRR408237 DRX393843 DRS407001 DRP012035 PRJDB14274 Zebrafish Gut RNA seq. DRP012035 Transcriptome Analysis A project to find differential expressed genes between larval and adult zebrafish gut. We dissected guts of wild type AB line and prepared three duplicates for each of larval and adult gut. Libraries for NGS are prepared using illumina TruSeq standard mRNA sample prep kit.     zebrafish wild type AB larval gut replicate 1 zebrafish larval gut replicate 1 SAMD00529457   sample name:zebrafish larval gut replicate 1|biological replicate:larval 1|strain:AB                 Illumina HiSeq 1500 sequencing of SAMD00529457 DRX393843 AR002 gut 1 5 dpf 6 dpf larvae 1 1   RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 1500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>126</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP012035 Illumina HiSeq 1500 sequencing of SAMD00529457       3606885828.0 28626078.0 DRR408237 0:126 1:0 A:879148446;C:885673723;G:870330963;T:971663212;N:69484 126 0     879148446 885673723 870330963 971663212 69484 DRX393843 DRS407001 DRA014885 NIBB|NIBB core research facilities, National Institute for Basic Biology University of Hyogo                       B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   Japan 2024-09-20 Larval Larval Gut Digestive System
38 38 DRR408248 DRX393854 DRS407179 DRP012042 PRJDB14275 Zebrafish EN/ENCDC RNA seq DRP012042 Transcriptome Analysis A project to find differential expressed genes between enteric neurons ENs and enteric neural crest derived cells ENCDCs in larval zebrafish gut. We dissected guts of transgenic line TgSAGFFLF217B; uas:gfp for ENs and Tgsox10:cre; EF1alpha:loxP gfp loxP dsred for ENCDCs and isolated GFP+ ENs and dsRed+ ENCDCs. Three duplicates for each of ENs and ENCDCs are prepared. Libraries for NGS are prepared using SMART Seq V4 Ultra Low Input RNA Kit.     zebrafish 5 day DsRed positive enteric neural crest derived cells replicate 3 zebrafish ENCDC replicate 3 SAMD00529468   sample name:zebrafish ENCDC replicate 3|biological replicate:enteric neural crest derived cells 3|strain:Tgsox10:cre; EF3alpha:loxP gfp loxP dsred                 NextSeq 550 paired end sequencing of SAMD00529468 DRX393854 190326ENvsNC N706 5day;NeuralCrestDerivedCell;rep3 1 1   RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA NextSeq 550 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>160</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>81</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP012042 NextSeq 550 paired end sequencing of SAMD00529468       3803721121.0 24526633.0 DRR408248 0:77.54 1:77.54 A:999106107;C:897663781;G:921501114;T:979486853;N:5963266 77 77     999106107 897663781 921501114 979486853 5963266 DRX393854 DRS407179 DRA014886 NIBB|NIBB core research facilities, National Institute for Basic Biology University of Hyogo                       B B biological fallback assumption illumina nextseq unknown random_priming unknown bulk unknown unknown   Japan 2024-09-22 Undetermined Larval Brain Nervous System
39 39 DRR408247 DRX393853 DRS407178 DRP012042 PRJDB14275 Zebrafish EN/ENCDC RNA seq DRP012042 Transcriptome Analysis A project to find differential expressed genes between enteric neurons ENs and enteric neural crest derived cells ENCDCs in larval zebrafish gut. We dissected guts of transgenic line TgSAGFFLF217B; uas:gfp for ENs and Tgsox10:cre; EF1alpha:loxP gfp loxP dsred for ENCDCs and isolated GFP+ ENs and dsRed+ ENCDCs. Three duplicates for each of ENs and ENCDCs are prepared. Libraries for NGS are prepared using SMART Seq V4 Ultra Low Input RNA Kit.     zebrafish 5 day DsRed positive enteric neural crest derived cells replicate 2 zebrafish ENCDC replicate 2 SAMD00529467   sample name:zebrafish ENCDC replicate 2|biological replicate:enteric neural crest derived cells 2|strain:Tgsox10:cre; EF2alpha:loxP gfp loxP dsred                 NextSeq 550 paired end sequencing of SAMD00529467 DRX393853 190326ENvsNC N705 5day;NeuralCrestDerivedCell;rep2 1 1   RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA NextSeq 550 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>160</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>81</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP012042 NextSeq 550 paired end sequencing of SAMD00529467       3436798274.0 22156202.0 DRR408247 0:77.56 1:77.56 A:900848174;C:812031426;G:832960423;T:885671203;N:5287048 77 77     900848174 812031426 832960423 885671203 5287048 DRX393853 DRS407178 DRA014886 NIBB|NIBB core research facilities, National Institute for Basic Biology University of Hyogo                       B B biological fallback assumption illumina nextseq unknown random_priming unknown bulk unknown unknown   Japan 2024-09-22 Undetermined Larval Brain Nervous System
40 40 DRR408246 DRX393852 DRS407177 DRP012042 PRJDB14275 Zebrafish EN/ENCDC RNA seq DRP012042 Transcriptome Analysis A project to find differential expressed genes between enteric neurons ENs and enteric neural crest derived cells ENCDCs in larval zebrafish gut. We dissected guts of transgenic line TgSAGFFLF217B; uas:gfp for ENs and Tgsox10:cre; EF1alpha:loxP gfp loxP dsred for ENCDCs and isolated GFP+ ENs and dsRed+ ENCDCs. Three duplicates for each of ENs and ENCDCs are prepared. Libraries for NGS are prepared using SMART Seq V4 Ultra Low Input RNA Kit.     zebrafish 5 day DsRed positive enteric neural crest derived cells replicate 1 zebrafish ENCDC replicate 1 SAMD00529466   sample name:zebrafish ENCDC replicate 1|biological replicate:enteric neural crest derived cells 1|strain:Tgsox10:cre; EF1alpha:loxP gfp loxP dsred                 NextSeq 550 paired end sequencing of SAMD00529466 DRX393852 190326ENvsNC N704 5day;NeuralCrestDerivedCell;rep1 1 1   RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA NextSeq 550 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>160</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>81</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP012042 NextSeq 550 paired end sequencing of SAMD00529466       3582073512.0 23135170.0 DRR408246 0:77.41 1:77.42 A:943152815;C:841972211;G:863627245;T:927361159;N:5960082 77 77     943152815 841972211 863627245 927361159 5960082 DRX393852 DRS407177 DRA014886 NIBB|NIBB core research facilities, National Institute for Basic Biology University of Hyogo                       B B biological fallback assumption illumina nextseq unknown random_priming unknown bulk unknown unknown   Japan 2024-09-22 Undetermined Larval Brain Nervous System
41 41 DRR408245 DRX393851 DRS407176 DRP012042 PRJDB14275 Zebrafish EN/ENCDC RNA seq DRP012042 Transcriptome Analysis A project to find differential expressed genes between enteric neurons ENs and enteric neural crest derived cells ENCDCs in larval zebrafish gut. We dissected guts of transgenic line TgSAGFFLF217B; uas:gfp for ENs and Tgsox10:cre; EF1alpha:loxP gfp loxP dsred for ENCDCs and isolated GFP+ ENs and dsRed+ ENCDCs. Three duplicates for each of ENs and ENCDCs are prepared. Libraries for NGS are prepared using SMART Seq V4 Ultra Low Input RNA Kit.     zebrafish 5 day GFP positive enteric neurons replicate 3 zebrafish EN replicate 3 SAMD00529465   sample name:zebrafish EN replicate 3|biological replicate:eneteric neurons 3|strain:TgSAGFFLF219B; uas:gfp                 NextSeq 550 paired end sequencing of SAMD00529465 DRX393851 190326ENvsNC N703 5day;EntericNeuron;rep3 1 1   RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA NextSeq 550 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>160</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>81</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP012042 NextSeq 550 paired end sequencing of SAMD00529465       3729799291.0 23985772.0 DRR408245 0:77.75 1:77.75 A:978752781;C:879988139;G:903976580;T:962122970;N:4958821 77 77     978752781 879988139 903976580 962122970 4958821 DRX393851 DRS407176 DRA014886 NIBB|NIBB core research facilities, National Institute for Basic Biology University of Hyogo                       B B biological fallback assumption illumina nextseq unknown random_priming unknown bulk unknown unknown   Japan 2024-09-22 Undetermined Larval Undetermined Undetermined
42 42 DRR408244 DRX393850 DRS407175 DRP012042 PRJDB14275 Zebrafish EN/ENCDC RNA seq DRP012042 Transcriptome Analysis A project to find differential expressed genes between enteric neurons ENs and enteric neural crest derived cells ENCDCs in larval zebrafish gut. We dissected guts of transgenic line TgSAGFFLF217B; uas:gfp for ENs and Tgsox10:cre; EF1alpha:loxP gfp loxP dsred for ENCDCs and isolated GFP+ ENs and dsRed+ ENCDCs. Three duplicates for each of ENs and ENCDCs are prepared. Libraries for NGS are prepared using SMART Seq V4 Ultra Low Input RNA Kit.     zebrafish 5 day GFP positive enteric neurons replicate 2 zebrafish EN replicate 2 SAMD00529464   sample name:zebrafish EN replicate 2|biological replicate:eneteric neurons 2|strain:TgSAGFFLF218B; uas:gfp                 NextSeq 550 paired end sequencing of SAMD00529464 DRX393850 190326ENvsNC N702 5day;EntericNeuron;rep2 1 1   RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA NextSeq 550 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>160</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>81</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP012042 NextSeq 550 paired end sequencing of SAMD00529464       3315994810.0 21477755.0 DRR408244 0:77.19 1:77.20 A:873970427;C:778042505;G:798459853;T:859611841;N:5910184 77 77     873970427 778042505 798459853 859611841 5910184 DRX393850 DRS407175 DRA014886 NIBB|NIBB core research facilities, National Institute for Basic Biology University of Hyogo                       B B biological fallback assumption illumina nextseq unknown random_priming unknown bulk unknown unknown   Japan 2024-09-22 Undetermined Larval Undetermined Undetermined
43 43 DRR408243 DRX393849 DRS407174 DRP012042 PRJDB14275 Zebrafish EN/ENCDC RNA seq DRP012042 Transcriptome Analysis A project to find differential expressed genes between enteric neurons ENs and enteric neural crest derived cells ENCDCs in larval zebrafish gut. We dissected guts of transgenic line TgSAGFFLF217B; uas:gfp for ENs and Tgsox10:cre; EF1alpha:loxP gfp loxP dsred for ENCDCs and isolated GFP+ ENs and dsRed+ ENCDCs. Three duplicates for each of ENs and ENCDCs are prepared. Libraries for NGS are prepared using SMART Seq V4 Ultra Low Input RNA Kit.     zebrafish 5 day GFP positive enteric neurons replicate 1 zebrafish EN replicate 1 SAMD00529463   sample name:zebrafish EN replicate 1|biological replicate:eneteric neurons 1|strain:TgSAGFFLF217B; uas:gfp                 NextSeq 550 paired end sequencing of SAMD00529463 DRX393849 190326ENvsNC N701 5day;EntericNeuron;rep1 1 1   RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA NextSeq 550 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>160</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>81</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP012042 NextSeq 550 paired end sequencing of SAMD00529463       2999501518.0 19455440.0 DRR408243 0:77.08 1:77.09 A:788053541;C:705895776;G:724185148;T:775760738;N:5606315 77 77     788053541 705895776 724185148 775760738 5606315 DRX393849 DRS407174 DRA014886 NIBB|NIBB core research facilities, National Institute for Basic Biology University of Hyogo                       B B biological fallback assumption illumina nextseq unknown random_priming unknown bulk unknown unknown   Japan 2024-09-22 Undetermined Larval Undetermined Undetermined
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
9367 9367 ERR145653 ERX121572 ERS151242 ERP001552 PRJEB3112 The effects of temperature on gene expression in zebrafish E-MTAB-1155 Transcriptome Analysis Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.     Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction. WW3 F M pooled fish SAMEA1487368 Genepool AdultAcclimationTemperature:27 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T16:01:13Z|External Id:SAMEA1487368|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T16:01:13Z|INSDC status:public|Submitter Id:E MTAB 1155:WW3 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:27 degree C|sample name:E MTAB 1155:WW3 F M pooled fish|scientific name:Danio rerio|sex:mixed sex                 The effects of temperature on gene expression in zebrafish E MTAB 1155:WW3 B seq WW3 pooled extract The effects of temperature on gene expression in zebrafish Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations. Experimental Factor: EmbryonicTemperature:27 degree C|Experimental Factor: AdultAcclimationTemperature:27 degree C RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</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>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP001552 Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16 WW3_B_1.fq.gz WW3_B_2.fq.gz fastq fastq 4347695086.0 21523243.0 E MTAB 1155:WW3 B 0:101 1:101 A:1074237454;C:1092333862;G:1102729864;T:1065390007;N:13003899 101 101     1074237454 1092333862 1102729864 1065390007 13003899 ERX121572 ERS151242 ERA140546 Genepool|Department of Biology, McMaster University Genepool|Department of Biology, McMaster University 2 0.95796 0.9583 0.02413 0.02313 0.83946 0.8338 0.51717 0.51633 101 101 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2012-08-21 Adult Adult Whole Organism All anatomical structures
9368 9368 ERR145654 ERX121560 ERS151233 ERP001552 PRJEB3112 The effects of temperature on gene expression in zebrafish E-MTAB-1155 Transcriptome Analysis Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.     Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction. WW4 F M pooled fish SAMEA1487359 Genepool AdultAcclimationTemperature:27 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T15:48:59Z|External Id:SAMEA1487359|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T15:48:59Z|INSDC status:public|Submitter Id:E MTAB 1155:WW4 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:27 degree C|sample name:E MTAB 1155:WW4 F M pooled fish|scientific name:Danio rerio|sex:mixed sex                 The effects of temperature on gene expression in zebrafish E MTAB 1155:WW4 A seq WW4 pooled extract The effects of temperature on gene expression in zebrafish Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations. Experimental Factor: EmbryonicTemperature:27 degree C|Experimental Factor: AdultAcclimationTemperature:27 degree C RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</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>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP001552 Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16 WW4_A_1.fq.gz WW4_A_2.fq.gz fastq fastq 80948470.0 400735.0 E MTAB 1155:WW4 A 0:101 1:101 A:21174054;C:19268727;G:19622428;T:20880804;N:2457 101 101     21174054 19268727 19622428 20880804 2457 ERX121560 ERS151233 ERA140546 Genepool|Department of Biology, McMaster University Genepool|Department of Biology, McMaster University 2 0.93674 0.92652 0.0383 0.03971 0.84776 0.86028 0.52028 0.51601 101 101 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2012-08-21 Adult Adult Whole Organism All anatomical structures
9369 9369 ERR145639 ERX121583 ERS151247 ERP001552 PRJEB3112 The effects of temperature on gene expression in zebrafish E-MTAB-1155 Transcriptome Analysis Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.     Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction. CW4 F M pooled fish SAMEA1487357 Genepool AdultAcclimationTemperature:16 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T15:49:00Z|External Id:SAMEA1487357|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T15:49:00Z|INSDC status:public|Submitter Id:E MTAB 1155:CW4 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:27 degree C|sample name:E MTAB 1155:CW4 F M pooled fish|scientific name:Danio rerio|sex:mixed sex                 The effects of temperature on gene expression in zebrafish E MTAB 1155:CW4 seq CW4 pooled extract The effects of temperature on gene expression in zebrafish Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations. Experimental Factor: EmbryonicTemperature:27 degree C|Experimental Factor: AdultAcclimationTemperature:16 degree C RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</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>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP001552 Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16 CW4_1.fq.gz CW4_2.fq.gz fastq fastq 7322391324.0 36249462.0 E MTAB 1155:CW4 0:101 1:101 A:1915177797;C:1750141576;G:1768328049;T:1887892000;N:851902 101 101     1915177797 1750141576 1768328049 1887892000 851902 ERX121583 ERS151247 ERA140546 Genepool|Department of Biology, McMaster University Genepool|Department of Biology, McMaster University 2 0.94177 0.93855 0.04669 0.04835 0.81227 0.81663 0.5297 0.53381 101 101 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2012-08-21 Adult Adult Whole Organism All anatomical structures
9370 9370 ERR145632 ERX121582 ERS151246 ERP001552 PRJEB3112 The effects of temperature on gene expression in zebrafish E-MTAB-1155 Transcriptome Analysis Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.     Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction. CH2 F M pooled fish SAMEA1487358 Genepool AdultAcclimationTemperature:16 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T15:49:00Z|External Id:SAMEA1487358|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T15:49:00Z|INSDC status:public|Submitter Id:E MTAB 1155:CH2 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:32 degree C|sample name:E MTAB 1155:CH2 F M pooled fish|scientific name:Danio rerio|sex:mixed sex                 The effects of temperature on gene expression in zebrafish E MTAB 1155:CH2 seq CH2 pooled extract The effects of temperature on gene expression in zebrafish Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations. Experimental Factor: EmbryonicTemperature:32 degree C|Experimental Factor: AdultAcclimationTemperature:16 degree C RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</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>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP001552 Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16 CH2_1.fq.gz CH2_2.fq.gz fastq fastq 6008384960.0 29744480.0 E MTAB 1155:CH2 0:101 1:101 A:1551084475;C:1456651824;G:1467972620;T:1531930144;N:745897 101 101     1551084475 1456651824 1467972620 1531930144 745897 ERX121582 ERS151246 ERA140546 Genepool|Department of Biology, McMaster University Genepool|Department of Biology, McMaster University 2 0.94484 0.94325 0.04187 0.04238 0.81448 0.8172 0.46639 0.50253 101 101 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2012-08-21 Adult Adult Whole Organism All anatomical structures
9371 9371 ERR145634 ERX121581 ERS151245 ERP001552 PRJEB3112 The effects of temperature on gene expression in zebrafish E-MTAB-1155 Transcriptome Analysis Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.     Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction. CH4 F M pooled fish SAMEA1487361 Genepool AdultAcclimationTemperature:16 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T15:49:00Z|External Id:SAMEA1487361|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T15:49:00Z|INSDC status:public|Submitter Id:E MTAB 1155:CH4 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:32 degree C|sample name:E MTAB 1155:CH4 F M pooled fish|scientific name:Danio rerio|sex:mixed sex                 The effects of temperature on gene expression in zebrafish E MTAB 1155:CH4 seq CH4 pooled extract The effects of temperature on gene expression in zebrafish Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations. Experimental Factor: EmbryonicTemperature:32 degree C|Experimental Factor: AdultAcclimationTemperature:16 degree C RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</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>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP001552 Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16 CH4_1.fq.gz CH4_2.fq.gz fastq fastq 5647385104.0 27957352.0 E MTAB 1155:CH4 0:101 1:101 A:1469982057;C:1356659164;G:1371916498;T:1448143269;N:684116 101 101     1469982057 1356659164 1371916498 1448143269 684116 ERX121581 ERS151245 ERA140546 Genepool|Department of Biology, McMaster University Genepool|Department of Biology, McMaster University 2 0.93865 0.93633 0.0439 0.04446 0.80549 0.80864 0.53045 0.51098 101 101 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2012-08-21 Adult Adult Whole Organism All anatomical structures
9372 9372 ERR145651 ERX121579 ERS151239 ERP001552 PRJEB3112 The effects of temperature on gene expression in zebrafish E-MTAB-1155 Transcriptome Analysis Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.     Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction. WW2 F M pooled fish SAMEA1487360 Genepool AdultAcclimationTemperature:27 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T15:48:59Z|External Id:SAMEA1487360|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T15:48:59Z|INSDC status:public|Submitter Id:E MTAB 1155:WW2 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:27 degree C|sample name:E MTAB 1155:WW2 F M pooled fish|scientific name:Danio rerio|sex:mixed sex                 The effects of temperature on gene expression in zebrafish E MTAB 1155:WW2 B seq WW2 pooled extract The effects of temperature on gene expression in zebrafish Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations. Experimental Factor: EmbryonicTemperature:27 degree C|Experimental Factor: AdultAcclimationTemperature:27 degree C RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</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>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP001552 Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16 WW2_B_1.fq.gz WW2_B_2.fq.gz fastq fastq 4738967672.0 23460236.0 E MTAB 1155:WW2 B 0:101 1:101 A:1175576318;C:1183749238;G:1198839519;T:1166587116;N:14215481 101 101     1175576318 1183749238 1198839519 1166587116 14215481 ERX121579 ERS151239 ERA140546 Genepool|Department of Biology, McMaster University Genepool|Department of Biology, McMaster University 2 0.95497 0.95617 0.02438 0.0233 0.82909 0.82455 0.51164 0.51189 101 101 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2012-08-21 Adult Adult Whole Organism All anatomical structures
9373 9373 ERR145652 ERX121578 ERS151242 ERP001552 PRJEB3112 The effects of temperature on gene expression in zebrafish E-MTAB-1155 Transcriptome Analysis Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.     Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction. WW3 F M pooled fish SAMEA1487368 Genepool AdultAcclimationTemperature:27 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T16:01:13Z|External Id:SAMEA1487368|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T16:01:13Z|INSDC status:public|Submitter Id:E MTAB 1155:WW3 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:27 degree C|sample name:E MTAB 1155:WW3 F M pooled fish|scientific name:Danio rerio|sex:mixed sex                 The effects of temperature on gene expression in zebrafish E MTAB 1155:WW3 A seq WW3 pooled extract The effects of temperature on gene expression in zebrafish Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations. Experimental Factor: EmbryonicTemperature:27 degree C|Experimental Factor: AdultAcclimationTemperature:27 degree C RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</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>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP001552 Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16 WW3_A_1.fq.gz WW3_A_2.fq.gz fastq fastq 229808532.0 1137666.0 E MTAB 1155:WW3 A 0:101 1:101 A:59360822;C:55502890;G:56337453;T:58600433;N:6934 101 101     59360822 55502890 56337453 58600433 6934 ERX121578 ERS151242 ERA140546 Genepool|Department of Biology, McMaster University Genepool|Department of Biology, McMaster University 2 0.93623 0.92715 0.03151 0.03268 0.83735 0.84952 0.52265 0.5038 101 101 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2012-08-21 Adult Adult Whole Organism All anatomical structures
9374 9374 ERR145649 ERX121577 ERS151234 ERP001552 PRJEB3112 The effects of temperature on gene expression in zebrafish E-MTAB-1155 Transcriptome Analysis Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.     Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction. WW1 F M pooled fish SAMEA1487370 Genepool AdultAcclimationTemperature:27 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T15:48:59Z|External Id:SAMEA1487370|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T15:48:59Z|INSDC status:public|Submitter Id:E MTAB 1155:WW1 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:27 degree C|sample name:E MTAB 1155:WW1 F M pooled fish|scientific name:Danio rerio|sex:mixed sex                 The effects of temperature on gene expression in zebrafish E MTAB 1155:WW1 B seq WW1 pooled extract The effects of temperature on gene expression in zebrafish Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations. Experimental Factor: EmbryonicTemperature:27 degree C|Experimental Factor: AdultAcclimationTemperature:27 degree C RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</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>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP001552 Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16 WW1_B_1.fq.gz WW1_B_2.fq.gz fastq fastq 7635373356.0 37798878.0 E MTAB 1155:WW1 B 0:101 1:101 A:1902965653;C:1900547622;G:1920575326;T:1888470954;N:22813801 101 101     1902965653 1900547622 1920575326 1888470954 22813801 ERX121577 ERS151234 ERA140546 Genepool|Department of Biology, McMaster University Genepool|Department of Biology, McMaster University 2 0.95977 0.95988 0.02636 0.02563 0.84279 0.83808 0.52131 0.45646 101 101 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2012-08-21 Adult Adult Whole Organism All anatomical structures
9375 9375 ERR145636 ERX121576 ERS151244 ERP001552 PRJEB3112 The effects of temperature on gene expression in zebrafish E-MTAB-1155 Transcriptome Analysis Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.     Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction. CW2 F M pooled fish SAMEA1487364 Genepool AdultAcclimationTemperature:16 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T15:49:00Z|External Id:SAMEA1487364|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T15:49:00Z|INSDC status:public|Submitter Id:E MTAB 1155:CW2 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:27 degree C|sample name:E MTAB 1155:CW2 F M pooled fish|scientific name:Danio rerio|sex:mixed sex                 The effects of temperature on gene expression in zebrafish E MTAB 1155:CW2 seq CW2 pooled extract The effects of temperature on gene expression in zebrafish Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations. Experimental Factor: EmbryonicTemperature:27 degree C|Experimental Factor: AdultAcclimationTemperature:16 degree C RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</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>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP001552 Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16 CW2_1.fq.gz CW2_2.fq.gz fastq fastq 7748012798.0 38356499.0 E MTAB 1155:CW2 0:101 1:101 A:2015650126;C:1864022271;G:1874527501;T:1992894699;N:918201 101 101     2015650126 1864022271 1874527501 1992894699 918201 ERX121576 ERS151244 ERA140546 Genepool|Department of Biology, McMaster University Genepool|Department of Biology, McMaster University 2 0.94537 0.94243 0.04249 0.04301 0.82213 0.82552 0.52811 0.53747 101 101 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2012-08-21 Adult Adult Whole Organism All anatomical structures
9376 9376 ERR145646 ERX121571 ERS151241 ERP001552 PRJEB3112 The effects of temperature on gene expression in zebrafish E-MTAB-1155 Transcriptome Analysis Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.     Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction. WH4 F M pooled fish SAMEA1487367 Genepool AdultAcclimationTemperature:27 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T15:49:00Z|External Id:SAMEA1487367|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T15:49:00Z|INSDC status:public|Submitter Id:E MTAB 1155:WH4 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:32 degree C|sample name:E MTAB 1155:WH4 F M pooled fish|scientific name:Danio rerio|sex:mixed sex                 The effects of temperature on gene expression in zebrafish E MTAB 1155:WH4 A seq WH4 pooled extract The effects of temperature on gene expression in zebrafish Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations. Experimental Factor: EmbryonicTemperature:32 degree C|Experimental Factor: AdultAcclimationTemperature:27 degree C RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</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>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP001552 Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16 WH4_A_1.fq.gz WH4_A_2.fq.gz fastq fastq 812883148.0 4024174.0 E MTAB 1155:WH4 A 0:101 1:101 A:209997189;C:196285019;G:198925947;T:207278009;N:396984 101 101     209997189 196285019 198925947 207278009 396984 ERX121571 ERS151241 ERA140546 Genepool|Department of Biology, McMaster University Genepool|Department of Biology, McMaster University 2 0.94663 0.91942 0.03602 0.03591 0.8424 0.85462 0.51702 0.51147 101 101 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2012-08-21 Adult Adult Whole Organism All anatomical structures
9377 9377 ERR145647 ERX121570 ERS151241 ERP001552 PRJEB3112 The effects of temperature on gene expression in zebrafish E-MTAB-1155 Transcriptome Analysis Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.     Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction. WH4 F M pooled fish SAMEA1487367 Genepool AdultAcclimationTemperature:27 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T15:49:00Z|External Id:SAMEA1487367|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T15:49:00Z|INSDC status:public|Submitter Id:E MTAB 1155:WH4 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:32 degree C|sample name:E MTAB 1155:WH4 F M pooled fish|scientific name:Danio rerio|sex:mixed sex                 The effects of temperature on gene expression in zebrafish E MTAB 1155:WH4 B seq WH4 pooled extract The effects of temperature on gene expression in zebrafish Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations. Experimental Factor: EmbryonicTemperature:32 degree C|Experimental Factor: AdultAcclimationTemperature:27 degree C RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</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>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP001552 Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16 WH4_B_1.fq.gz WH4_B_2.fq.gz fastq fastq 10768144694.0 53307647.0 E MTAB 1155:WH4 B 0:101 1:101 A:2682817583;C:2706807352;G:2714533015;T:2652309644;N:11677100 101 101     2682817583 2706807352 2714533015 2652309644 11677100 ERX121570 ERS151241 ERA140546 Genepool|Department of Biology, McMaster University Genepool|Department of Biology, McMaster University 2 0.95867 0.96056 0.02378 0.02413 0.83609 0.83889 0.43331 0.44066 101 101 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2012-08-21 Adult Adult Whole Organism All anatomical structures
9378 9378 ERR145655 ERX121569 ERS151233 ERP001552 PRJEB3112 The effects of temperature on gene expression in zebrafish E-MTAB-1155 Transcriptome Analysis Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.     Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction. WW4 F M pooled fish SAMEA1487359 Genepool AdultAcclimationTemperature:27 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T15:48:59Z|External Id:SAMEA1487359|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T15:48:59Z|INSDC status:public|Submitter Id:E MTAB 1155:WW4 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:27 degree C|sample name:E MTAB 1155:WW4 F M pooled fish|scientific name:Danio rerio|sex:mixed sex                 The effects of temperature on gene expression in zebrafish E MTAB 1155:WW4 B seq WW4 pooled extract The effects of temperature on gene expression in zebrafish Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations. Experimental Factor: EmbryonicTemperature:27 degree C|Experimental Factor: AdultAcclimationTemperature:27 degree C RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</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>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP001552 Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16 WW4_B_1.fq.gz WW4_B_2.fq.gz fastq fastq 6455936968.0 31960084.0 E MTAB 1155:WW4 B 0:101 1:101 A:1610738878;C:1605252294;G:1623372987;T:1597311219;N:19261590 101 101     1610738878 1605252294 1623372987 1597311219 19261590 ERX121569 ERS151233 ERA140546 Genepool|Department of Biology, McMaster University Genepool|Department of Biology, McMaster University 2 0.96085 0.96101 0.02863 0.02731 0.84995 0.8452 0.52157 0.51189 101 101 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2012-08-21 Adult Adult Whole Organism All anatomical structures
9379 9379 ERR145633 ERX121568 ERS151240 ERP001552 PRJEB3112 The effects of temperature on gene expression in zebrafish E-MTAB-1155 Transcriptome Analysis Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.     Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction. CH3 F M pooled fish SAMEA1487363 Genepool AdultAcclimationTemperature:16 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T15:48:59Z|External Id:SAMEA1487363|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T15:48:59Z|INSDC status:public|Submitter Id:E MTAB 1155:CH3 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:32 degree C|sample name:E MTAB 1155:CH3 F M pooled fish|scientific name:Danio rerio|sex:mixed sex                 The effects of temperature on gene expression in zebrafish E MTAB 1155:CH3 seq CH3 pooled extract The effects of temperature on gene expression in zebrafish Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations. Experimental Factor: EmbryonicTemperature:32 degree C|Experimental Factor: AdultAcclimationTemperature:16 degree C RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</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>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP001552 Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16 CH3_1.fq.gz CH3_2.fq.gz fastq fastq 6146419640.0 30427820.0 E MTAB 1155:CH3 0:101 1:101 A:1596666196;C:1479913350;G:1493612614;T:1575480940;N:746540 101 101     1596666196 1479913350 1493612614 1575480940 746540 ERX121568 ERS151240 ERA140546 Genepool|Department of Biology, McMaster University Genepool|Department of Biology, McMaster University 2 0.93901 0.93723 0.04362 0.04417 0.79715 0.7977 0.51473 0.52412 101 101 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2012-08-21 Adult Adult Whole Organism All anatomical structures
9380 9380 ERR145650 ERX121567 ERS151239 ERP001552 PRJEB3112 The effects of temperature on gene expression in zebrafish E-MTAB-1155 Transcriptome Analysis Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.     Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction. WW2 F M pooled fish SAMEA1487360 Genepool AdultAcclimationTemperature:27 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T15:48:59Z|External Id:SAMEA1487360|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T15:48:59Z|INSDC status:public|Submitter Id:E MTAB 1155:WW2 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:27 degree C|sample name:E MTAB 1155:WW2 F M pooled fish|scientific name:Danio rerio|sex:mixed sex                 The effects of temperature on gene expression in zebrafish E MTAB 1155:WW2 A seq WW2 pooled extract The effects of temperature on gene expression in zebrafish Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations. Experimental Factor: EmbryonicTemperature:27 degree C|Experimental Factor: AdultAcclimationTemperature:27 degree C RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</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>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP001552 Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16 WW2_A_1.fq.gz WW2_A_2.fq.gz fastq fastq 280038054.0 1386327.0 E MTAB 1155:WW2 A 0:101 1:101 A:72831492;C:67021049;G:68232991;T:71942949;N:9573 101 101     72831492 67021049 68232991 71942949 9573 ERX121567 ERS151239 ERA140546 Genepool|Department of Biology, McMaster University Genepool|Department of Biology, McMaster University 2 0.93032 0.9187 0.03207 0.03356 0.82852 0.84139 0.52376 0.52436 101 101 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2012-08-21 Adult Adult Whole Organism All anatomical structures
9381 9381 ERR145637 ERX121565 ERS151232 ERP001552 PRJEB3112 The effects of temperature on gene expression in zebrafish E-MTAB-1155 Transcriptome Analysis Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.     Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction. CW3 F M pooled fish SAMEA1487355 Genepool AdultAcclimationTemperature:16 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T15:48:59Z|External Id:SAMEA1487355|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T15:48:59Z|INSDC status:public|Submitter Id:E MTAB 1155:CW3 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:27 degree C|sample name:E MTAB 1155:CW3 F M pooled fish|scientific name:Danio rerio|sex:mixed sex                 The effects of temperature on gene expression in zebrafish E MTAB 1155:CW3 A seq CW3 pooled extract The effects of temperature on gene expression in zebrafish Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations. Experimental Factor: EmbryonicTemperature:27 degree C|Experimental Factor: AdultAcclimationTemperature:16 degree C RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</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>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP001552 Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16 CW3_A_1.fq.gz CW3_A_2.fq.gz fastq fastq 2104292580.0 10417290.0 E MTAB 1155:CW3 A 0:101 1:101 A:547829220;C:504948167;G:510803037;T:540521191;N:190965 101 101     547829220 504948167 510803037 540521191 190965 ERX121565 ERS151232 ERA140546 Genepool|Department of Biology, McMaster University Genepool|Department of Biology, McMaster University 2 0.93423 0.92981 0.04776 0.04835 0.81245 0.81471 0.51349 0.4822 101 101 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2012-08-21 Adult Adult Whole Organism All anatomical structures
9382 9382 ERR145631 ERX121564 ERS151237 ERP001552 PRJEB3112 The effects of temperature on gene expression in zebrafish E-MTAB-1155 Transcriptome Analysis Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.     Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction. CH1 F M pooled fish SAMEA1487356 Genepool AdultAcclimationTemperature:16 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T15:48:59Z|External Id:SAMEA1487356|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T15:48:59Z|INSDC status:public|Submitter Id:E MTAB 1155:CH1 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:32 degree C|sample name:E MTAB 1155:CH1 F M pooled fish|scientific name:Danio rerio|sex:mixed sex                 The effects of temperature on gene expression in zebrafish E MTAB 1155:CH1 seq CH1 pooled extract The effects of temperature on gene expression in zebrafish Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations. Experimental Factor: EmbryonicTemperature:32 degree C|Experimental Factor: AdultAcclimationTemperature:16 degree C RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</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>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP001552 Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16 CH1_1.fq.gz CH1_2.fq.gz fastq fastq 7734471526.0 38289463.0 E MTAB 1155:CH1 0:101 1:101 A:1980474194;C:1892305985;G:1907192207;T:1953595996;N:903144 101 101     1980474194 1892305985 1907192207 1953595996 903144 ERX121564 ERS151237 ERA140546 Genepool|Department of Biology, McMaster University Genepool|Department of Biology, McMaster University 2 0.94403 0.94213 0.03862 0.03913 0.82309 0.82556 0.49626 0.49773 101 101 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2012-08-21 Adult Adult Whole Organism All anatomical structures
9383 9383 ERR145635 ERX121562 ERS151235 ERP001552 PRJEB3112 The effects of temperature on gene expression in zebrafish E-MTAB-1155 Transcriptome Analysis Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.     Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction. CW1 F M pooled fish SAMEA1487366 Genepool AdultAcclimationTemperature:16 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T15:48:59Z|External Id:SAMEA1487366|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T15:48:59Z|INSDC status:public|Submitter Id:E MTAB 1155:CW1 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:27 degree C|sample name:E MTAB 1155:CW1 F M pooled fish|scientific name:Danio rerio|sex:mixed sex                 The effects of temperature on gene expression in zebrafish E MTAB 1155:CW1 seq CW1 pooled extract The effects of temperature on gene expression in zebrafish Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations. Experimental Factor: EmbryonicTemperature:27 degree C|Experimental Factor: AdultAcclimationTemperature:16 degree C RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</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>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP001552 Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16 CW1_1.fq.gz CW1_2.fq.gz fastq fastq 6202716838.0 30706519.0 E MTAB 1155:CW1 0:101 1:101 A:1612950873;C:1492406749;G:1504306823;T:1592361004;N:691389 101 101     1612950873 1492406749 1504306823 1592361004 691389 ERX121562 ERS151235 ERA140546 Genepool|Department of Biology, McMaster University Genepool|Department of Biology, McMaster University 2 0.94448 0.94226 0.04304 0.04379 0.81296 0.81489 0.5237 0.52588 101 101 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2012-08-21 Adult Adult Whole Organism All anatomical structures
9384 9384 ERR145648 ERX121561 ERS151234 ERP001552 PRJEB3112 The effects of temperature on gene expression in zebrafish E-MTAB-1155 Transcriptome Analysis Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.     Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction. WW1 F M pooled fish SAMEA1487370 Genepool AdultAcclimationTemperature:27 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T15:48:59Z|External Id:SAMEA1487370|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T15:48:59Z|INSDC status:public|Submitter Id:E MTAB 1155:WW1 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:27 degree C|sample name:E MTAB 1155:WW1 F M pooled fish|scientific name:Danio rerio|sex:mixed sex                 The effects of temperature on gene expression in zebrafish E MTAB 1155:WW1 A seq WW1 pooled extract The effects of temperature on gene expression in zebrafish Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations. Experimental Factor: EmbryonicTemperature:27 degree C|Experimental Factor: AdultAcclimationTemperature:27 degree C RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</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>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP001552 Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16 WW1_A_1.fq.gz WW1_A_2.fq.gz fastq fastq 330954174.0 1638387.0 E MTAB 1155:WW1 A 0:101 1:101 A:86485807;C:78916128;G:80103844;T:85437370;N:11025 101 101     86485807 78916128 80103844 85437370 11025 ERX121561 ERS151234 ERA140546 Genepool|Department of Biology, McMaster University Genepool|Department of Biology, McMaster University 2 0.93321 0.92294 0.03445 0.03581 0.84133 0.85267 0.54253 0.53593 101 101 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2012-08-21 Adult Adult Whole Organism All anatomical structures
9385 9385 ERR145638 ERX121559 ERS151232 ERP001552 PRJEB3112 The effects of temperature on gene expression in zebrafish E-MTAB-1155 Transcriptome Analysis Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.     Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction. CW3 F M pooled fish SAMEA1487355 Genepool AdultAcclimationTemperature:16 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T15:48:59Z|External Id:SAMEA1487355|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T15:48:59Z|INSDC status:public|Submitter Id:E MTAB 1155:CW3 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:27 degree C|sample name:E MTAB 1155:CW3 F M pooled fish|scientific name:Danio rerio|sex:mixed sex                 The effects of temperature on gene expression in zebrafish E MTAB 1155:CW3 B seq CW3 pooled extract The effects of temperature on gene expression in zebrafish Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations. Experimental Factor: EmbryonicTemperature:27 degree C|Experimental Factor: AdultAcclimationTemperature:16 degree C RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</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>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP001552 Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16 CW3_B_1.fq.gz CW3_B_2.fq.gz fastq fastq 6504819756.0 32202078.0 E MTAB 1155:CW3 B 0:101 1:101 A:1653674963;C:1600212014;G:1606437826;T:1637400265;N:7094688 101 101     1653674963 1600212014 1606437826 1637400265 7094688 ERX121559 ERS151232 ERA140546 Genepool|Department of Biology, McMaster University Genepool|Department of Biology, McMaster University 2 0.94253 0.94443 0.03782 0.03856 0.80661 0.80801 0.49414 0.51667 101 101 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2012-08-21 Adult Adult Whole Organism All anatomical structures
9386 9386 ERR147028 ERX122956 ERS151238 ERP001552 PRJEB3112 The effects of temperature on gene expression in zebrafish E-MTAB-1155 Transcriptome Analysis Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.     Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction. WH3 F M pooled fish SAMEA1487362 Genepool AdultAcclimationTemperature:27 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T15:48:59Z|External Id:SAMEA1487362|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T15:48:59Z|INSDC status:public|Submitter Id:E MTAB 1155:WH3 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:32 degree C|sample name:E MTAB 1155:WH3 F M pooled fish|scientific name:Danio rerio|sex:mixed sex                 The effects of temperature on gene expression in zebrafish E MTAB 1155:WH3 seq WH3 pooled extract The effects of temperature on gene expression in zebrafish Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations. Experimental Factor: EmbryonicTemperature:32 degree C|Experimental Factor: AdultAcclimationTemperature:27 degree C RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</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>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP001552 Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16 WH3_1.fq.gz WH3_2.fq.gz fastq fastq 3197103894.0 15827247.0 E MTAB 1155:WH3 0:101 1:101 A:829020337;C:767623553;G:780642278;T:818288216;N:1529510 101 101     829020337 767623553 780642278 818288216 1529510 ERX122956 ERS151238 ERA142144 Genepool|Department of Biology, McMaster University Genepool|Department of Biology, McMaster University 2 0.94791 0.91975 0.03726 0.03735 0.84291 0.85622 0.4972 0.50314 101 101 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2012-08-21 Adult Adult Whole Organism All anatomical structures
9387 9387 ERR147027 ERX122955 ERS151236 ERP001552 PRJEB3112 The effects of temperature on gene expression in zebrafish E-MTAB-1155 Transcriptome Analysis Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.     Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction. WH2 F M pooled fish SAMEA1487365 Genepool AdultAcclimationTemperature:27 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T15:48:59Z|External Id:SAMEA1487365|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T15:48:59Z|INSDC status:public|Submitter Id:E MTAB 1155:WH2 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:32 degree C|sample name:E MTAB 1155:WH2 F M pooled fish|scientific name:Danio rerio|sex:mixed sex                 The effects of temperature on gene expression in zebrafish E MTAB 1155:WH2 seq WH2 pooled extract The effects of temperature on gene expression in zebrafish Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations. Experimental Factor: EmbryonicTemperature:32 degree C|Experimental Factor: AdultAcclimationTemperature:27 degree C RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</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>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP001552 Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16 WH2_1.fq.gz WH2_2.fq.gz fastq fastq 3455989922.0 17108861.0 E MTAB 1155:WH2 0:101 1:101 A:902145358;C:824320050;G:837200815;T:890816825;N:1506874 101 101     902145358 824320050 837200815 890816825 1506874 ERX122955 ERS151236 ERA142144 Genepool|Department of Biology, McMaster University Genepool|Department of Biology, McMaster University 2 0.94863 0.92001 0.04084 0.04066 0.83796 0.85263 0.5275 0.51735 101 101 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2012-08-21 Adult Adult Whole Organism All anatomical structures
9388 9388 ERR147026 ERX122954 ERS151243 ERP001552 PRJEB3112 The effects of temperature on gene expression in zebrafish E-MTAB-1155 Transcriptome Analysis Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.     Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction. WH1 F M pooled fish SAMEA1487369 Genepool AdultAcclimationTemperature:27 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T15:49:00Z|External Id:SAMEA1487369|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T15:49:00Z|INSDC status:public|Submitter Id:E MTAB 1155:WH1 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:32 degree C|sample name:E MTAB 1155:WH1 F M pooled fish|scientific name:Danio rerio|sex:mixed sex                 The effects of temperature on gene expression in zebrafish E MTAB 1155:WH1 seq WH1 pooled extract The effects of temperature on gene expression in zebrafish Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations. Experimental Factor: EmbryonicTemperature:32 degree C|Experimental Factor: AdultAcclimationTemperature:27 degree C RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</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>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP001552 Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16 WH1_1.fq.gz WH1_2.fq.gz fastq fastq 3005524064.0 14878832.0 E MTAB 1155:WH1 0:101 1:101 A:780146739;C:722416478;G:730307409;T:771476282;N:1177156 101 101     780146739 722416478 730307409 771476282 1177156 ERX122954 ERS151243 ERA142144 Genepool|Department of Biology, McMaster University Genepool|Department of Biology, McMaster University 2 0.94764 0.92072 0.03746 0.03773 0.83416 0.84831 0.42239 0.51505 101 101 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2012-08-21 Adult Adult Whole Organism All anatomical structures
9711 9711 ERR3366000 ERX3390288 ERS3506636 ERP115705 PRJEB32960 RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type E-MTAB-8029 Transcriptome Analysis RNA was extracted from 5 dpf embyros with and without xxx c.386C>T p.Ser129Phe variant in wdr37. Three independent RNA samples were prepared with each sample containing RNA from five individual embryos. ENA FIRST PUBLIC:2019 07 19|ENA LAST UPDATE:2019 06 10   Protocols: Five dpf zebrafish embryos were genotyped. Three independent RNA samples were prepared for both WT and mutant with 5 embryos pooled for each sample. RNA samples were prepared using Direct zol™ RNA MiniPrep kit Zymo Research. TruSeq RNA Sample Prep Kit v2 was used with protocol TruSeq RNA Sample Preparation v2 Guide Part # 15026495 Rev. F. WT 5dpf whole 3 SAMEA5702979 Medical College of Wisconsin ENA FIRST PUBLIC:2019 07 19T04:04:05Z|ENA LAST UPDATE:2019 06 10T11:46:52Z|External Id:SAMEA5702979|INSDC center name:Medical College of Wisconsin|INSDC first public:2019 07 19T04:04:05Z|INSDC last update:2019 06 10T11:46:52Z|INSDC status:public|Submitter Id:E MTAB 8029:WT 5dpf whole 3|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 5|genotype:wild type genotype|individual:mixed pool of 5 embryos|organism part:whole organism|sample name:E MTAB 8029:WT 5dpf whole 3|scientific name:Danio rerio                 HiSeq X Ten paired end sequencing; RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type E MTAB 8029:WT 5dpf whole 3 p WT 5dpf whole 3 p RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type Five dpf zebrafish embryos were genotyped. Three independent RNA samples were prepared for both WT and mutant with 5 embryos pooled for each sample. RNA samples were prepared using Direct zol™ RNA MiniPrep kit Zymo Research. TruSeq RNA Sample Prep Kit v2 was used with protocol TruSeq RNA Sample Preparation v2 Guide Part # 15026495 Rev. F. Experimental Factor: genotype:wild type genotype RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq X Ten   ERP115705 HiSeq X Ten paired end sequencing; RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type ENA FIRST PUBLIC:2019 07 19|ENA LAST UPDATE:2019 06 10|instrument model:HiSeq X Ten WT-5dpf-whole-3_1.fastq.gz WT-5dpf-whole-3_2.fastq.gz fastq fastq 7638506536.0 25293068.0 E MTAB 8029:WT 5dpf whole 3 0:151 1:151 A:2033085216;C:1787203019;G:1834311569;T:1982924179;N:982553 151 151     2033085216 1787203019 1834311569 1982924179 982553 ERX3390288 ERS3506636 ERA1993466 European Nucleotide Archive European Nucleotide Archive 2 0.92943 0.93349 0.06443 0.06476 0.67008 0.68489 0.45244 0.47512 151 151 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   Unknown 2019-06-10 Larval Larval Whole Organism All anatomical structures
9712 9712 ERR3365999 ERX3390287 ERS3506635 ERP115705 PRJEB32960 RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type E-MTAB-8029 Transcriptome Analysis RNA was extracted from 5 dpf embyros with and without xxx c.386C>T p.Ser129Phe variant in wdr37. Three independent RNA samples were prepared with each sample containing RNA from five individual embryos. ENA FIRST PUBLIC:2019 07 19|ENA LAST UPDATE:2019 06 10   Protocols: Five dpf zebrafish embryos were genotyped. Three independent RNA samples were prepared for both WT and mutant with 5 embryos pooled for each sample. RNA samples were prepared using Direct zol™ RNA MiniPrep kit Zymo Research. TruSeq RNA Sample Prep Kit v2 was used with protocol TruSeq RNA Sample Preparation v2 Guide Part # 15026495 Rev. F. WT 5dpf whole 2 SAMEA5702978 Medical College of Wisconsin ENA FIRST PUBLIC:2019 07 19T04:04:05Z|ENA LAST UPDATE:2019 06 10T11:46:52Z|External Id:SAMEA5702978|INSDC center name:Medical College of Wisconsin|INSDC first public:2019 07 19T04:04:05Z|INSDC last update:2019 06 10T11:46:52Z|INSDC status:public|Submitter Id:E MTAB 8029:WT 5dpf whole 2|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 5|genotype:wild type genotype|individual:mixed pool of 5 embryos|organism part:whole organism|sample name:E MTAB 8029:WT 5dpf whole 2|scientific name:Danio rerio                 HiSeq X Ten paired end sequencing; RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type E MTAB 8029:WT 5dpf whole 2 p WT 5dpf whole 2 p RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type Five dpf zebrafish embryos were genotyped. Three independent RNA samples were prepared for both WT and mutant with 5 embryos pooled for each sample. RNA samples were prepared using Direct zol™ RNA MiniPrep kit Zymo Research. TruSeq RNA Sample Prep Kit v2 was used with protocol TruSeq RNA Sample Preparation v2 Guide Part # 15026495 Rev. F. Experimental Factor: genotype:wild type genotype RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq X Ten   ERP115705 HiSeq X Ten paired end sequencing; RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type ENA FIRST PUBLIC:2019 07 19|ENA LAST UPDATE:2019 06 10|instrument model:HiSeq X Ten WT-5dpf--whole-2_1.fastq.gz WT-5dpf--whole-2_2.fastq.gz fastq fastq 8029356446.0 26587273.0 E MTAB 8029:WT 5dpf whole 2 0:151 1:151 A:2111720421;C:1902949602;G:1956400199;T:2057162414;N:1123810 151 151     2111720421 1902949602 1956400199 2057162414 1123810 ERX3390287 ERS3506635 ERA1993466 European Nucleotide Archive European Nucleotide Archive 2 0.93664 0.9394 0.06211 0.06234 0.67036 0.68416 0.44709 0.4713 151 151 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   Unknown 2019-06-10 Larval Larval Whole Organism All anatomical structures
9713 9713 ERR3365998 ERX3390286 ERS3506634 ERP115705 PRJEB32960 RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type E-MTAB-8029 Transcriptome Analysis RNA was extracted from 5 dpf embyros with and without xxx c.386C>T p.Ser129Phe variant in wdr37. Three independent RNA samples were prepared with each sample containing RNA from five individual embryos. ENA FIRST PUBLIC:2019 07 19|ENA LAST UPDATE:2019 06 10   Protocols: Five dpf zebrafish embryos were genotyped. Three independent RNA samples were prepared for both WT and mutant with 5 embryos pooled for each sample. RNA samples were prepared using Direct zol™ RNA MiniPrep kit Zymo Research. TruSeq RNA Sample Prep Kit v2 was used with protocol TruSeq RNA Sample Preparation v2 Guide Part # 15026495 Rev. F. WT 5dpf whole 1 SAMEA5702977 Medical College of Wisconsin ENA FIRST PUBLIC:2019 07 19T04:04:05Z|ENA LAST UPDATE:2019 06 10T11:46:52Z|External Id:SAMEA5702977|INSDC center name:Medical College of Wisconsin|INSDC first public:2019 07 19T04:04:05Z|INSDC last update:2019 06 10T11:46:52Z|INSDC status:public|Submitter Id:E MTAB 8029:WT 5dpf whole 1|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 5|genotype:wild type genotype|individual:mixed pool of 5 embryos|organism part:whole organism|sample name:E MTAB 8029:WT 5dpf whole 1|scientific name:Danio rerio                 HiSeq X Ten paired end sequencing; RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type E MTAB 8029:WT 5dpf whole 1 p WT 5dpf whole 1 p RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type Five dpf zebrafish embryos were genotyped. Three independent RNA samples were prepared for both WT and mutant with 5 embryos pooled for each sample. RNA samples were prepared using Direct zol™ RNA MiniPrep kit Zymo Research. TruSeq RNA Sample Prep Kit v2 was used with protocol TruSeq RNA Sample Preparation v2 Guide Part # 15026495 Rev. F. Experimental Factor: genotype:wild type genotype RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq X Ten   ERP115705 HiSeq X Ten paired end sequencing; RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type ENA FIRST PUBLIC:2019 07 19|ENA LAST UPDATE:2019 06 10|instrument model:HiSeq X Ten WT-5dpf-whole-1_1.fastq.gz WT-5dpf-whole-1_2.fastq.gz fastq fastq 7581314682.0 25103691.0 E MTAB 8029:WT 5dpf whole 1 0:151 1:151 A:2028089715;C:1768357820;G:1809746152;T:1974047455;N:1073540 151 151     2028089715 1768357820 1809746152 1974047455 1073540 ERX3390286 ERS3506634 ERA1993466 European Nucleotide Archive European Nucleotide Archive 2 0.92712 0.93122 0.06876 0.06853 0.66464 0.67537 0.46592 0.47176 151 151 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   Unknown 2019-06-10 Larval Larval Whole Organism All anatomical structures
9714 9714 ERR3365997 ERX3390285 ERS3506633 ERP115705 PRJEB32960 RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type E-MTAB-8029 Transcriptome Analysis RNA was extracted from 5 dpf embyros with and without xxx c.386C>T p.Ser129Phe variant in wdr37. Three independent RNA samples were prepared with each sample containing RNA from five individual embryos. ENA FIRST PUBLIC:2019 07 19|ENA LAST UPDATE:2019 06 10   Protocols: Five dpf zebrafish embryos were genotyped. Three independent RNA samples were prepared for both WT and mutant with 5 embryos pooled for each sample. RNA samples were prepared using Direct zol™ RNA MiniPrep kit Zymo Research. TruSeq RNA Sample Prep Kit v2 was used with protocol TruSeq RNA Sample Preparation v2 Guide Part # 15026495 Rev. F. c386C T het 5dpf whl2 SAMEA5702976 Medical College of Wisconsin ENA FIRST PUBLIC:2019 07 19T04:04:05Z|ENA LAST UPDATE:2019 06 10T11:46:52Z|External Id:SAMEA5702976|INSDC center name:Medical College of Wisconsin|INSDC first public:2019 07 19T04:04:05Z|INSDC last update:2019 06 10T11:46:52Z|INSDC status:public|Submitter Id:E MTAB 8029:c386C T het 5dpf whl2|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 5|genotype:wdr37 mutant c.386C>T p.Ser129Phe|individual:mixed pool of 5 embryos|organism part:whole organism|sample name:E MTAB 8029:c386C T het 5dpf whl2|scientific name:Danio rerio                 HiSeq X Ten paired end sequencing; RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type E MTAB 8029:c386C T het 5dpf whl2 p c386C T het 5dpf whl2 p RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type Five dpf zebrafish embryos were genotyped. Three independent RNA samples were prepared for both WT and mutant with 5 embryos pooled for each sample. RNA samples were prepared using Direct zol™ RNA MiniPrep kit Zymo Research. TruSeq RNA Sample Prep Kit v2 was used with protocol TruSeq RNA Sample Preparation v2 Guide Part # 15026495 Rev. F. Experimental Factor: genotype:wdr37 mutant c.386C>T p.Ser129Phe RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq X Ten   ERP115705 HiSeq X Ten paired end sequencing; RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type ENA FIRST PUBLIC:2019 07 19|ENA LAST UPDATE:2019 06 10|instrument model:HiSeq X Ten c386C-T-het-5dpf-whl-2_1.fastq.gz c386C-T-het-5dpf-whl-2_2.fastq.gz fastq fastq 7431512716.0 24607658.0 E MTAB 8029:c386C T het 5dpf whl 2 0:151 1:151 A:1981584337;C:1740735155;G:1776201259;T:1931922393;N:1069572 151 151     1981584337 1740735155 1776201259 1931922393 1069572 ERX3390285 ERS3506633 ERA1993466 European Nucleotide Archive European Nucleotide Archive 2 0.92957 0.933 0.0653 0.06445 0.66967 0.6788 0.46228 0.46392 151 151 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   Unknown 2019-06-10 Larval Larval Whole Organism All anatomical structures
9715 9715 ERR3365996 ERX3390284 ERS3506632 ERP115705 PRJEB32960 RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type E-MTAB-8029 Transcriptome Analysis RNA was extracted from 5 dpf embyros with and without xxx c.386C>T p.Ser129Phe variant in wdr37. Three independent RNA samples were prepared with each sample containing RNA from five individual embryos. ENA FIRST PUBLIC:2019 07 19|ENA LAST UPDATE:2019 06 10   Protocols: Five dpf zebrafish embryos were genotyped. Three independent RNA samples were prepared for both WT and mutant with 5 embryos pooled for each sample. RNA samples were prepared using Direct zol™ RNA MiniPrep kit Zymo Research. TruSeq RNA Sample Prep Kit v2 was used with protocol TruSeq RNA Sample Preparation v2 Guide Part # 15026495 Rev. F. c386C T het 5dpf whl1 SAMEA5702975 Medical College of Wisconsin ENA FIRST PUBLIC:2019 07 19T04:04:05Z|ENA LAST UPDATE:2019 06 10T11:46:52Z|External Id:SAMEA5702975|INSDC center name:Medical College of Wisconsin|INSDC first public:2019 07 19T04:04:05Z|INSDC last update:2019 06 10T11:46:52Z|INSDC status:public|Submitter Id:E MTAB 8029:c386C T het 5dpf whl1|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 5|genotype:wdr37 mutant c.386C>T p.Ser129Phe|individual:mixed pool of 5 embryos|organism part:whole organism|sample name:E MTAB 8029:c386C T het 5dpf whl1|scientific name:Danio rerio                 HiSeq X Ten paired end sequencing; RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type E MTAB 8029:c386C T het 5dpf whl1 p c386C T het 5dpf whl1 p RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type Five dpf zebrafish embryos were genotyped. Three independent RNA samples were prepared for both WT and mutant with 5 embryos pooled for each sample. RNA samples were prepared using Direct zol™ RNA MiniPrep kit Zymo Research. TruSeq RNA Sample Prep Kit v2 was used with protocol TruSeq RNA Sample Preparation v2 Guide Part # 15026495 Rev. F. Experimental Factor: genotype:wdr37 mutant c.386C>T p.Ser129Phe RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq X Ten   ERP115705 HiSeq X Ten paired end sequencing; RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type ENA FIRST PUBLIC:2019 07 19|ENA LAST UPDATE:2019 06 10|instrument model:HiSeq X Ten c386C-T-het-5dpf-whl-1_1.fastq.gz c386C-T-het-5dpf-whl-1_2.fastq.gz fastq fastq 7350140024.0 24338212.0 E MTAB 8029:c386C T het 5dpf whl 1 0:151 1:151 A:1930881649;C:1748604586;G:1790297791;T:1879354724;N:1001274 151 151     1930881649 1748604586 1790297791 1879354724 1001274 ERX3390284 ERS3506632 ERA1993466 European Nucleotide Archive European Nucleotide Archive 2 0.93663 0.9384 0.05835 0.05828 0.66557 0.67588 0.467 0.46407 151 151 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   Unknown 2019-06-10 Larval Larval Whole Organism All anatomical structures
9716 9716 ERR3365995 ERX3390283 ERS3506631 ERP115705 PRJEB32960 RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type E-MTAB-8029 Transcriptome Analysis RNA was extracted from 5 dpf embyros with and without xxx c.386C>T p.Ser129Phe variant in wdr37. Three independent RNA samples were prepared with each sample containing RNA from five individual embryos. ENA FIRST PUBLIC:2019 07 19|ENA LAST UPDATE:2019 06 10   Protocols: Five dpf zebrafish embryos were genotyped. Three independent RNA samples were prepared for both WT and mutant with 5 embryos pooled for each sample. RNA samples were prepared using Direct zol™ RNA MiniPrep kit Zymo Research. TruSeq RNA Sample Prep Kit v2 was used with protocol TruSeq RNA Sample Preparation v2 Guide Part # 15026495 Rev. F. c.386C T het 5dpf whl3 SAMEA5702974 Medical College of Wisconsin ENA FIRST PUBLIC:2019 07 19T04:04:05Z|ENA LAST UPDATE:2019 06 10T11:46:52Z|External Id:SAMEA5702974|INSDC center name:Medical College of Wisconsin|INSDC first public:2019 07 19T04:04:05Z|INSDC last update:2019 06 10T11:46:52Z|INSDC status:public|Submitter Id:E MTAB 8029:c.386C T het 5dpf whl3|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 5|genotype:wdr37 mutant c.386C>T p.Ser129Phe|individual:mixed pool of 5 embryos|organism part:whole organism|sample name:E MTAB 8029:c.386C T het 5dpf whl3|scientific name:Danio rerio                 HiSeq X Ten paired end sequencing; RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type E MTAB 8029:c.386C T het 5dpf whl3 p c.386C T het 5dpf whl3 p RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type Five dpf zebrafish embryos were genotyped. Three independent RNA samples were prepared for both WT and mutant with 5 embryos pooled for each sample. RNA samples were prepared using Direct zol™ RNA MiniPrep kit Zymo Research. TruSeq RNA Sample Prep Kit v2 was used with protocol TruSeq RNA Sample Preparation v2 Guide Part # 15026495 Rev. F. Experimental Factor: genotype:wdr37 mutant c.386C>T p.Ser129Phe RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq X Ten   ERP115705 HiSeq X Ten paired end sequencing; RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type ENA FIRST PUBLIC:2019 07 19|ENA LAST UPDATE:2019 06 12|instrument model:HiSeq X Ten c386C-T-het-5dpf-whl-3_1.fastq.gz c386C-T-het-5dpf-whl-3_2.fastq.gz fastq fastq 6059681642.0 20065171.0 E MTAB 8029:c386C T het 5dpf whl 3 0:151 1:151 A:1604034432;C:1423963595;G:1467519505;T:1563303018;N:861092 151 151     1604034432 1423963595 1467519505 1563303018 861092 ERX3390283 ERS3506631 ERA1993466 European Nucleotide Archive European Nucleotide Archive 2 0.93301 0.9374 0.0658 0.06581 0.66681 0.68503 0.46139 0.47743 151 151 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   Unknown 2019-06-10 Larval Larval Whole Organism All anatomical structures
9825 9825 ERR2102841 ERX2160152 ERS1883528 ERP040145 PRJEB37796 Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf E-MTAB-5992 Transcriptome Analysis We wanted to compare gene expression from control untreated zebrafish larvae and 2 mM NaBu treated larvae for 24 hours in order to assess the effect of inhibition of the HDAC pathway in these animals ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2017 08 23|ArrayExpress:E MTAB 5992   Protocols: zebrafish were isolated during pharyngula stage daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001 N3 nabu RNA SAMEA104224510 Fundacao Champalimaud ENA first public:2017 08 29|ENA last update:2017 08 23|External Id:SAMEA104224510|INSDC center alias:Fundacao Champalimaud|INSDC center name:Fundacao Champalimaud|INSDC first public:2017 08 29T17:02:02Z|INSDC last update:2017 08 23T09:55:35Z|INSDC status:public|Submitter Id:E MTAB 5992:N3 nabu RNA|age:8|broker name:ArrayExpress|common name:zebrafish|disease:normal|genotype:wild type genotype|sample name:E MTAB 5992:N3 nabu RNA|strain:AB                 Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf E MTAB 5992:N3 nabu RNA s N3 nabu RNA s Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf zebrafish were isolated during pharyngula stage daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001 Experimental Factor: compound:NaBu|Experimental Factor: dose:2 RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina Genome Analyzer IIx   ERP040145 Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2018 11 16 N3_R1_all.fastq.gz fastq 1410139550.0 18670564.0 E MTAB 5992:N3 nabu RNA 0:75.53 1:0 A:353294009;C:340727934;G:322476371;T:393200193;N:441043 75 0     353294009 340727934 322476371 393200193 441043 ERX2160152 ERS1883528 ERA1011308 Fundacao Champalimaud|European Nucleotide Archive Fundacao Champalimaud|European Nucleotide Archive 1 0.95434   0.08906   0.66935   0.47788   76   B   usable mapping rate illumina early_illumina unknown random_priming trueseq bulk unknown unknown   Portugal 2017-08-23 Multi-stage Multi-stage Whole Organism All anatomical structures
9826 9826 ERR2102840 ERX2160151 ERS1883527 ERP040145 PRJEB37796 Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf E-MTAB-5992 Transcriptome Analysis We wanted to compare gene expression from control untreated zebrafish larvae and 2 mM NaBu treated larvae for 24 hours in order to assess the effect of inhibition of the HDAC pathway in these animals ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2017 08 23|ArrayExpress:E MTAB 5992   Protocols: zebrafish were isolated during pharyngula stage daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001 N2 nabu RNA SAMEA104224509 Fundacao Champalimaud ENA first public:2017 08 29|ENA last update:2017 08 23|External Id:SAMEA104224509|INSDC center alias:Fundacao Champalimaud|INSDC center name:Fundacao Champalimaud|INSDC first public:2017 08 29T17:02:02Z|INSDC last update:2017 08 23T09:55:35Z|INSDC status:public|Submitter Id:E MTAB 5992:N2 nabu RNA|age:8|broker name:ArrayExpress|common name:zebrafish|disease:normal|genotype:wild type genotype|sample name:E MTAB 5992:N2 nabu RNA|strain:AB                 Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf E MTAB 5992:N2 nabu RNA s N2 nabu RNA s Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf zebrafish were isolated during pharyngula stage daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001 Experimental Factor: compound:NaBu|Experimental Factor: dose:2 RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina Genome Analyzer IIx   ERP040145 Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2018 11 16 N2_R1_all.fastq.gz fastq 1478621168.0 19576865.0 E MTAB 5992:N2 nabu RNA 0:75.53 1:0 A:369453299;C:359092235;G:341176884;T:408389810;N:508940 75 0     369453299 359092235 341176884 408389810 508940 ERX2160151 ERS1883527 ERA1011308 Fundacao Champalimaud|European Nucleotide Archive Fundacao Champalimaud|European Nucleotide Archive 1 0.95582   0.08202   0.67718   0.47812   76   B   usable mapping rate illumina early_illumina unknown random_priming trueseq bulk unknown unknown   Portugal 2017-08-23 Multi-stage Multi-stage Whole Organism All anatomical structures
9827 9827 ERR2102839 ERX2160150 ERS1883526 ERP040145 PRJEB37796 Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf E-MTAB-5992 Transcriptome Analysis We wanted to compare gene expression from control untreated zebrafish larvae and 2 mM NaBu treated larvae for 24 hours in order to assess the effect of inhibition of the HDAC pathway in these animals ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2017 08 23|ArrayExpress:E MTAB 5992   Protocols: zebrafish were isolated during pharyngula stage daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001 N1 nabu RNA SAMEA104224508 Fundacao Champalimaud ENA first public:2017 08 29|ENA last update:2017 08 23|External Id:SAMEA104224508|INSDC center alias:Fundacao Champalimaud|INSDC center name:Fundacao Champalimaud|INSDC first public:2017 08 29T17:02:02Z|INSDC last update:2017 08 23T09:55:35Z|INSDC status:public|Submitter Id:E MTAB 5992:N1 nabu RNA|age:8|broker name:ArrayExpress|common name:zebrafish|disease:normal|genotype:wild type genotype|sample name:E MTAB 5992:N1 nabu RNA|strain:AB                 Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf E MTAB 5992:N1 nabu RNA s N1 nabu RNA s Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf zebrafish were isolated during pharyngula stage daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001 Experimental Factor: compound:NaBu|Experimental Factor: dose:2 RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina Genome Analyzer IIx   ERP040145 Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2018 11 16 N1_R1_all.fastq.gz fastq 1531713181.0 20277882.0 E MTAB 5992:N1 nabu RNA 0:75.54 1:0 A:386600603;C:373317031;G:350339456;T:420938891;N:517200 75 0     386600603 373317031 350339456 420938891 517200 ERX2160150 ERS1883526 ERA1011308 Fundacao Champalimaud|European Nucleotide Archive Fundacao Champalimaud|European Nucleotide Archive 1 0.9552   0.08124   0.67685   0.47578   76   B   usable mapping rate illumina early_illumina unknown random_priming trueseq bulk unknown unknown   Portugal 2017-08-23 Multi-stage Multi-stage Whole Organism All anatomical structures
9828 9828 ERR2102838 ERX2160149 ERS1883525 ERP040145 PRJEB37796 Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf E-MTAB-5992 Transcriptome Analysis We wanted to compare gene expression from control untreated zebrafish larvae and 2 mM NaBu treated larvae for 24 hours in order to assess the effect of inhibition of the HDAC pathway in these animals ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2017 08 23|ArrayExpress:E MTAB 5992   Protocols: zebrafish were isolated during pharyngula stage daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001 C3 control RNA SAMEA104224507 Fundacao Champalimaud ENA first public:2017 08 29|ENA last update:2017 08 23|External Id:SAMEA104224507|INSDC center alias:Fundacao Champalimaud|INSDC center name:Fundacao Champalimaud|INSDC first public:2017 08 29T17:02:02Z|INSDC last update:2017 08 23T09:55:35Z|INSDC status:public|Submitter Id:E MTAB 5992:C3 control RNA|age:8|broker name:ArrayExpress|common name:zebrafish|disease:normal|genotype:wild type genotype|sample name:E MTAB 5992:C3 control RNA|strain:AB                 Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf E MTAB 5992:C3 control RNA s C3 control RNA s Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf zebrafish were isolated during pharyngula stage daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001 Experimental Factor: compound:PBS RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina Genome Analyzer IIx   ERP040145 Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2018 11 16 C3_R1_all.fastq.gz fastq 1380662008.0 18279108.0 E MTAB 5992:C3 control RNA 0:75.53 1:0 A:345997031;C:338444594;G:316575258;T:379195977;N:449148 75 0     345997031 338444594 316575258 379195977 449148 ERX2160149 ERS1883525 ERA1011308 Fundacao Champalimaud|European Nucleotide Archive Fundacao Champalimaud|European Nucleotide Archive 1 0.95615   0.08131   0.68694   0.45267   74   B   usable mapping rate illumina early_illumina unknown random_priming trueseq bulk unknown unknown   Portugal 2017-08-23 Multi-stage Multi-stage Whole Organism All anatomical structures
9829 9829 ERR2102837 ERX2160148 ERS1883524 ERP040145 PRJEB37796 Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf E-MTAB-5992 Transcriptome Analysis We wanted to compare gene expression from control untreated zebrafish larvae and 2 mM NaBu treated larvae for 24 hours in order to assess the effect of inhibition of the HDAC pathway in these animals ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2017 08 23|ArrayExpress:E MTAB 5992   Protocols: zebrafish were isolated during pharyngula stage daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001 C2 control RNA SAMEA104224506 Fundacao Champalimaud ENA first public:2017 08 29|ENA last update:2017 08 23|External Id:SAMEA104224506|INSDC center alias:Fundacao Champalimaud|INSDC center name:Fundacao Champalimaud|INSDC first public:2017 08 29T17:02:02Z|INSDC last update:2017 08 23T09:55:35Z|INSDC status:public|Submitter Id:E MTAB 5992:C2 control RNA|age:8|broker name:ArrayExpress|common name:zebrafish|disease:normal|genotype:wild type genotype|sample name:E MTAB 5992:C2 control RNA|strain:AB                 Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf E MTAB 5992:C2 control RNA s C2 control RNA s Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf zebrafish were isolated during pharyngula stage daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001 Experimental Factor: compound:PBS RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina Genome Analyzer IIx   ERP040145 Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2018 11 16 C2_R1_all.fastq.gz fastq 1336640735.0 17695627.0 E MTAB 5992:C2 control RNA 0:75.54 1:0 A:338213530;C:326808990;G:303983789;T:367147896;N:486530 75 0     338213530 326808990 303983789 367147896 486530 ERX2160148 ERS1883524 ERA1011308 Fundacao Champalimaud|European Nucleotide Archive Fundacao Champalimaud|European Nucleotide Archive 1 0.95427   0.08628   0.67706   0.47245   76   B   usable mapping rate illumina early_illumina unknown random_priming trueseq bulk unknown unknown   Portugal 2017-08-23 Multi-stage Multi-stage Whole Organism All anatomical structures
9830 9830 ERR2102836 ERX2160147 ERS1883523 ERP040145 PRJEB37796 Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf E-MTAB-5992 Transcriptome Analysis We wanted to compare gene expression from control untreated zebrafish larvae and 2 mM NaBu treated larvae for 24 hours in order to assess the effect of inhibition of the HDAC pathway in these animals ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2017 08 23|ArrayExpress:E MTAB 5992   Protocols: zebrafish were isolated during pharyngula stage daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001 C1 control RNA SAMEA104224505 Fundacao Champalimaud ENA first public:2017 08 29|ENA last update:2017 08 23|External Id:SAMEA104224505|INSDC center alias:Fundacao Champalimaud|INSDC center name:Fundacao Champalimaud|INSDC first public:2017 08 29T17:02:02Z|INSDC last update:2017 08 23T09:55:35Z|INSDC status:public|Submitter Id:E MTAB 5992:C1 control RNA|age:8|broker name:ArrayExpress|common name:zebrafish|disease:normal|genotype:wild type genotype|sample name:E MTAB 5992:C1 control RNA|strain:AB                 Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf E MTAB 5992:C1 control RNA s C1 control RNA s Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf zebrafish were isolated during pharyngula stage daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001 Experimental Factor: compound:PBS RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina Genome Analyzer IIx   ERP040145 Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2018 11 16 C1_R1_all.fastq.gz fastq 1297694845.0 17180544.0 E MTAB 5992:C1 control RNA 0:75.53 1:0 A:322048172;C:316542683;G:299227724;T:359449433;N:426833 75 0     322048172 316542683 299227724 359449433 426833 ERX2160147 ERS1883523 ERA1011308 Fundacao Champalimaud|European Nucleotide Archive Fundacao Champalimaud|European Nucleotide Archive 1 0.95505   0.08541   0.67659   0.48159   75   B   usable mapping rate illumina early_illumina unknown random_priming trueseq bulk unknown unknown   Portugal 2017-08-23 Multi-stage Multi-stage Whole Organism All anatomical structures
9842 9842 ERR4029259 ERX4030575 ERS4514128 ERP121190 PRJEB37851 Zebrafish il 4 il 10 regulated immunity in gills E-MTAB-8958 Transcriptome Analysis The evolutionary origin of vertebrate type 2 immunity is a topic of great interest. Several studies have focused on the immune cell components of evolutionary older vertebrates such as fish. However how fish cytokines function and whether they have similar roles as in mammals is still a matter of speculation. Here we have used the zebrafish Danio rerio to gain insights into il4/13a and il4/13b genes and characterized their role under both homeostatic and inflammatory conditions. We established knockouts for both il4/13a and il4/13b genes and showed that they are needed to suppress inflammation in larvae and in the gill mucosa. As a counterpoint we examined the gills of il10 defective zebrafish and revealed the importance of il10 in maintaining homeostasis in this mucosal tissue. As in mammals zebrafish il10 appears to have an anti inflammatory function. ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16   Protocols: This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494 7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end. Sample 4 SAMEA6786449 UNIVERSITY OF MANCHESTER ENA FIRST PUBLIC:2020 05 28T17:07:47Z|ENA LAST UPDATE:2020 04 16T14:58:15Z|External Id:SAMEA6786449|INSDC center name:UNIVERSITY OF MANCHESTER|INSDC first public:2020 05 28T17:07:47Z|INSDC last update:2020 04 16T14:58:15Z|INSDC status:public|Submitter Id:E MTAB 8958:Sample 4|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|organism part:gill|sample name:E MTAB 8958:Sample 4|scientific name:Danio rerio                 Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills E MTAB 8958:Sample 4 p Sample 4 p Zebrafish il 4 il 10 regulated immunity in gills This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494–7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end. Experimental Factor: genotype:wild type genotype RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   ERP121190 Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16 FB4_S41_R1_001.fastq.gz FB4_S41_R2_001.fastq.gz fastq fastq 4354809436.0 29071030.0 E MTAB 8958:FB4 S41 R 0:74.90 1:74.90 A:1140431810;C:1005396495;G:1008528915;T:1171220102;N:29232114 74 74     1140431810 1005396495 1008528915 1171220102 29232114 ERX4030575 ERS4514128 ERA2508092 UNIVERSITY OF MANCHESTER|European Nucleotide Archive UNIVERSITY OF MANCHESTER|European Nucleotide Archive 2 0.91143 0.91076 0.10123 0.09941 0.68235 0.68452 0.48713 0.48998 76 74 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   United Kingdom 2020-04-16 Adult Adult Gill Respiratory System
9843 9843 ERR4029258 ERX4030574 ERS4514127 ERP121190 PRJEB37851 Zebrafish il 4 il 10 regulated immunity in gills E-MTAB-8958 Transcriptome Analysis The evolutionary origin of vertebrate type 2 immunity is a topic of great interest. Several studies have focused on the immune cell components of evolutionary older vertebrates such as fish. However how fish cytokines function and whether they have similar roles as in mammals is still a matter of speculation. Here we have used the zebrafish Danio rerio to gain insights into il4/13a and il4/13b genes and characterized their role under both homeostatic and inflammatory conditions. We established knockouts for both il4/13a and il4/13b genes and showed that they are needed to suppress inflammation in larvae and in the gill mucosa. As a counterpoint we examined the gills of il10 defective zebrafish and revealed the importance of il10 in maintaining homeostasis in this mucosal tissue. As in mammals zebrafish il10 appears to have an anti inflammatory function. ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16   Protocols: This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494 7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end. Sample 3 SAMEA6786448 UNIVERSITY OF MANCHESTER ENA FIRST PUBLIC:2020 05 28T17:07:47Z|ENA LAST UPDATE:2020 04 16T14:58:15Z|External Id:SAMEA6786448|INSDC center name:UNIVERSITY OF MANCHESTER|INSDC first public:2020 05 28T17:07:47Z|INSDC last update:2020 04 16T14:58:15Z|INSDC status:public|Submitter Id:E MTAB 8958:Sample 3|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|organism part:gill|sample name:E MTAB 8958:Sample 3|scientific name:Danio rerio                 Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills E MTAB 8958:Sample 3 p Sample 3 p Zebrafish il 4 il 10 regulated immunity in gills This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494–7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end. Experimental Factor: genotype:wild type genotype RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   ERP121190 Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16 FB3_S40_R1_001.fastq.gz FB3_S40_R2_001.fastq.gz fastq fastq 3973860397.0 26559713.0 E MTAB 8958:FB3 S40 R 0:74.80 1:74.82 A:1038749031;C:917944667;G:920080717;T:1066160216;N:30925766 74 74     1038749031 917944667 920080717 1066160216 30925766 ERX4030574 ERS4514127 ERA2508092 UNIVERSITY OF MANCHESTER|European Nucleotide Archive UNIVERSITY OF MANCHESTER|European Nucleotide Archive 2 0.91065 0.90981 0.10133 0.09911 0.68789 0.68945 0.47182 0.49996 76 76 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   United Kingdom 2020-04-16 Adult Adult Gill Respiratory System
9844 9844 ERR4029257 ERX4030573 ERS4514126 ERP121190 PRJEB37851 Zebrafish il 4 il 10 regulated immunity in gills E-MTAB-8958 Transcriptome Analysis The evolutionary origin of vertebrate type 2 immunity is a topic of great interest. Several studies have focused on the immune cell components of evolutionary older vertebrates such as fish. However how fish cytokines function and whether they have similar roles as in mammals is still a matter of speculation. Here we have used the zebrafish Danio rerio to gain insights into il4/13a and il4/13b genes and characterized their role under both homeostatic and inflammatory conditions. We established knockouts for both il4/13a and il4/13b genes and showed that they are needed to suppress inflammation in larvae and in the gill mucosa. As a counterpoint we examined the gills of il10 defective zebrafish and revealed the importance of il10 in maintaining homeostasis in this mucosal tissue. As in mammals zebrafish il10 appears to have an anti inflammatory function. ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16   Protocols: This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494 7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end. Sample 2 SAMEA6786447 UNIVERSITY OF MANCHESTER ENA FIRST PUBLIC:2020 05 28T17:07:47Z|ENA LAST UPDATE:2020 04 16T14:58:15Z|External Id:SAMEA6786447|INSDC center name:UNIVERSITY OF MANCHESTER|INSDC first public:2020 05 28T17:07:47Z|INSDC last update:2020 04 16T14:58:15Z|INSDC status:public|Submitter Id:E MTAB 8958:Sample 2|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|organism part:gill|sample name:E MTAB 8958:Sample 2|scientific name:Danio rerio                 Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills E MTAB 8958:Sample 2 p Sample 2 p Zebrafish il 4 il 10 regulated immunity in gills This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494–7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end. Experimental Factor: genotype:wild type genotype RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   ERP121190 Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16 FB2_S39_R1_001.fastq.gz FB2_S39_R2_001.fastq.gz fastq fastq 4135184845.0 27517010.0 E MTAB 8958:FB2 S39 R 0:75.15 1:75.13 A:1084253902;C:962303819;G:961163738;T:1111949967;N:15513419 75 75     1084253902 962303819 961163738 1111949967 15513419 ERX4030573 ERS4514126 ERA2508092 UNIVERSITY OF MANCHESTER|European Nucleotide Archive UNIVERSITY OF MANCHESTER|European Nucleotide Archive 2 0.91098 0.91057 0.09468 0.09311 0.68095 0.68282 0.49982 0.50146 75 75 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   United Kingdom 2020-04-16 Adult Adult Gill Respiratory System
9845 9845 ERR4029256 ERX4030572 ERS4514125 ERP121190 PRJEB37851 Zebrafish il 4 il 10 regulated immunity in gills E-MTAB-8958 Transcriptome Analysis The evolutionary origin of vertebrate type 2 immunity is a topic of great interest. Several studies have focused on the immune cell components of evolutionary older vertebrates such as fish. However how fish cytokines function and whether they have similar roles as in mammals is still a matter of speculation. Here we have used the zebrafish Danio rerio to gain insights into il4/13a and il4/13b genes and characterized their role under both homeostatic and inflammatory conditions. We established knockouts for both il4/13a and il4/13b genes and showed that they are needed to suppress inflammation in larvae and in the gill mucosa. As a counterpoint we examined the gills of il10 defective zebrafish and revealed the importance of il10 in maintaining homeostasis in this mucosal tissue. As in mammals zebrafish il10 appears to have an anti inflammatory function. ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16   Protocols: This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494 7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end. Sample 1 SAMEA6786446 UNIVERSITY OF MANCHESTER ENA FIRST PUBLIC:2020 05 28T17:07:47Z|ENA LAST UPDATE:2020 04 16T14:58:15Z|External Id:SAMEA6786446|INSDC center name:UNIVERSITY OF MANCHESTER|INSDC first public:2020 05 28T17:07:47Z|INSDC last update:2020 04 16T14:58:15Z|INSDC status:public|Submitter Id:E MTAB 8958:Sample 1|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|organism part:gill|sample name:E MTAB 8958:Sample 1|scientific name:Danio rerio                 Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills E MTAB 8958:Sample 1 p Sample 1 p Zebrafish il 4 il 10 regulated immunity in gills This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494–7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end. Experimental Factor: genotype:wild type genotype RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   ERP121190 Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 06 17 FB1_S38_R1_001.fastq FB1_S38_R2_001.fastq fastq fastq 4651073045.0 31021879.0 E MTAB 8958:FB1 S38 R 0:74.96 1:74.97 A:1225305023;C:1072643957;G:1069905162;T:1255950159;N:27268744 74 74     1225305023 1072643957 1069905162 1255950159 27268744 ERX4030572 ERS4514125 ERA2508092 UNIVERSITY OF MANCHESTER|European Nucleotide Archive UNIVERSITY OF MANCHESTER|European Nucleotide Archive 2 0.91441 0.91282 0.10095 0.09913 0.686 0.68745 0.49433 0.5047 76 76 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   United Kingdom 2020-04-16 Adult Adult Gill Respiratory System
9846 9846 ERR4029255 ERX4030571 ERS4514124 ERP121190 PRJEB37851 Zebrafish il 4 il 10 regulated immunity in gills E-MTAB-8958 Transcriptome Analysis The evolutionary origin of vertebrate type 2 immunity is a topic of great interest. Several studies have focused on the immune cell components of evolutionary older vertebrates such as fish. However how fish cytokines function and whether they have similar roles as in mammals is still a matter of speculation. Here we have used the zebrafish Danio rerio to gain insights into il4/13a and il4/13b genes and characterized their role under both homeostatic and inflammatory conditions. We established knockouts for both il4/13a and il4/13b genes and showed that they are needed to suppress inflammation in larvae and in the gill mucosa. As a counterpoint we examined the gills of il10 defective zebrafish and revealed the importance of il10 in maintaining homeostasis in this mucosal tissue. As in mammals zebrafish il10 appears to have an anti inflammatory function. ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16   Protocols: This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494 7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end. Sample 16 SAMEA6786445 UNIVERSITY OF MANCHESTER ENA FIRST PUBLIC:2020 05 28T17:07:47Z|ENA LAST UPDATE:2020 04 16T14:58:15Z|External Id:SAMEA6786445|INSDC center name:UNIVERSITY OF MANCHESTER|INSDC first public:2020 05 28T17:07:47Z|INSDC last update:2020 04 16T14:58:15Z|INSDC status:public|Submitter Id:E MTAB 8958:Sample 16|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:il4/13b / |organism part:gill|sample name:E MTAB 8958:Sample 16|scientific name:Danio rerio                 Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills E MTAB 8958:Sample 16 p Sample 16 p Zebrafish il 4 il 10 regulated immunity in gills This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494–7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end. Experimental Factor: genotype:il4/13b / RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   ERP121190 Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16 FB4_S20_R1_001.fastq.gz FB4_S20_R2_001.fastq.gz fastq fastq 5961540086.0 39717871.0 E MTAB 8958:FB4 S20 R 0:75.07 1:75.03 A:1565483441;C:1390303898;G:1372759826;T:1611361282;N:21631639 75 75     1565483441 1390303898 1372759826 1611361282 21631639 ERX4030571 ERS4514124 ERA2508092 UNIVERSITY OF MANCHESTER|European Nucleotide Archive UNIVERSITY OF MANCHESTER|European Nucleotide Archive 2 0.90959 0.90989 0.0925 0.09172 0.68787 0.68929 0.49093 0.49057 76 76 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   United Kingdom 2020-04-16 Adult Adult Gill Respiratory System
9847 9847 ERR4029254 ERX4030570 ERS4514123 ERP121190 PRJEB37851 Zebrafish il 4 il 10 regulated immunity in gills E-MTAB-8958 Transcriptome Analysis The evolutionary origin of vertebrate type 2 immunity is a topic of great interest. Several studies have focused on the immune cell components of evolutionary older vertebrates such as fish. However how fish cytokines function and whether they have similar roles as in mammals is still a matter of speculation. Here we have used the zebrafish Danio rerio to gain insights into il4/13a and il4/13b genes and characterized their role under both homeostatic and inflammatory conditions. We established knockouts for both il4/13a and il4/13b genes and showed that they are needed to suppress inflammation in larvae and in the gill mucosa. As a counterpoint we examined the gills of il10 defective zebrafish and revealed the importance of il10 in maintaining homeostasis in this mucosal tissue. As in mammals zebrafish il10 appears to have an anti inflammatory function. ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16   Protocols: This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494 7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end. Sample 15 SAMEA6786444 UNIVERSITY OF MANCHESTER ENA FIRST PUBLIC:2020 05 28T17:07:47Z|ENA LAST UPDATE:2020 04 16T14:58:15Z|External Id:SAMEA6786444|INSDC center name:UNIVERSITY OF MANCHESTER|INSDC first public:2020 05 28T17:07:47Z|INSDC last update:2020 04 16T14:58:15Z|INSDC status:public|Submitter Id:E MTAB 8958:Sample 15|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:il4/13b / |organism part:gill|sample name:E MTAB 8958:Sample 15|scientific name:Danio rerio                 Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills E MTAB 8958:Sample 15 p Sample 15 p Zebrafish il 4 il 10 regulated immunity in gills This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494–7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end. Experimental Factor: genotype:il4/13b / RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   ERP121190 Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16 FB3_S19_R1_001.fastq.gz FB3_S19_R2_001.fastq.gz fastq fastq 6835575760.0 45515064.0 E MTAB 8958:FB3 S19 R 0:75.11 1:75.07 A:1802176562;C:1589590146;G:1564279107;T:1858606235;N:20923710 75 75     1802176562 1589590146 1564279107 1858606235 20923710 ERX4030570 ERS4514123 ERA2508092 UNIVERSITY OF MANCHESTER|European Nucleotide Archive UNIVERSITY OF MANCHESTER|European Nucleotide Archive 2 0.90945 0.91123 0.09519 0.09378 0.67963 0.67961 0.49246 0.49476 76 76 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   United Kingdom 2020-04-16 Adult Adult Gill Respiratory System
9848 9848 ERR4029253 ERX4030569 ERS4514122 ERP121190 PRJEB37851 Zebrafish il 4 il 10 regulated immunity in gills E-MTAB-8958 Transcriptome Analysis The evolutionary origin of vertebrate type 2 immunity is a topic of great interest. Several studies have focused on the immune cell components of evolutionary older vertebrates such as fish. However how fish cytokines function and whether they have similar roles as in mammals is still a matter of speculation. Here we have used the zebrafish Danio rerio to gain insights into il4/13a and il4/13b genes and characterized their role under both homeostatic and inflammatory conditions. We established knockouts for both il4/13a and il4/13b genes and showed that they are needed to suppress inflammation in larvae and in the gill mucosa. As a counterpoint we examined the gills of il10 defective zebrafish and revealed the importance of il10 in maintaining homeostasis in this mucosal tissue. As in mammals zebrafish il10 appears to have an anti inflammatory function. ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16   Protocols: This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494 7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end. Sample 14 SAMEA6786443 UNIVERSITY OF MANCHESTER ENA FIRST PUBLIC:2020 05 28T17:07:47Z|ENA LAST UPDATE:2020 04 16T14:58:15Z|External Id:SAMEA6786443|INSDC center name:UNIVERSITY OF MANCHESTER|INSDC first public:2020 05 28T17:07:47Z|INSDC last update:2020 04 16T14:58:15Z|INSDC status:public|Submitter Id:E MTAB 8958:Sample 14|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:il4/13b / |organism part:gill|sample name:E MTAB 8958:Sample 14|scientific name:Danio rerio                 Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills E MTAB 8958:Sample 14 p Sample 14 p Zebrafish il 4 il 10 regulated immunity in gills This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494–7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end. Experimental Factor: genotype:il4/13b / RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   ERP121190 Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16 FB2_S18_R1_001.fastq.gz FB2_S18_R2_001.fastq.gz fastq fastq 5789923311.0 38517674.0 E MTAB 8958:FB2 S18 R 0:75.18 1:75.14 A:1520250885;C:1354960735;G:1336204150;T:1565011084;N:13496457 75 75     1520250885 1354960735 1336204150 1565011084 13496457 ERX4030569 ERS4514122 ERA2508092 UNIVERSITY OF MANCHESTER|European Nucleotide Archive UNIVERSITY OF MANCHESTER|European Nucleotide Archive 2 0.91863 0.91917 0.08923 0.08753 0.68848 0.68883 0.5042 0.50799 76 76 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   United Kingdom 2020-04-16 Adult Adult Gill Respiratory System
9849 9849 ERR4029252 ERX4030568 ERS4514121 ERP121190 PRJEB37851 Zebrafish il 4 il 10 regulated immunity in gills E-MTAB-8958 Transcriptome Analysis The evolutionary origin of vertebrate type 2 immunity is a topic of great interest. Several studies have focused on the immune cell components of evolutionary older vertebrates such as fish. However how fish cytokines function and whether they have similar roles as in mammals is still a matter of speculation. Here we have used the zebrafish Danio rerio to gain insights into il4/13a and il4/13b genes and characterized their role under both homeostatic and inflammatory conditions. We established knockouts for both il4/13a and il4/13b genes and showed that they are needed to suppress inflammation in larvae and in the gill mucosa. As a counterpoint we examined the gills of il10 defective zebrafish and revealed the importance of il10 in maintaining homeostasis in this mucosal tissue. As in mammals zebrafish il10 appears to have an anti inflammatory function. ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16   Protocols: This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494 7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end. Sample 13 SAMEA6786442 UNIVERSITY OF MANCHESTER ENA FIRST PUBLIC:2020 05 28T17:07:47Z|ENA LAST UPDATE:2020 04 16T14:58:15Z|External Id:SAMEA6786442|INSDC center name:UNIVERSITY OF MANCHESTER|INSDC first public:2020 05 28T17:07:47Z|INSDC last update:2020 04 16T14:58:15Z|INSDC status:public|Submitter Id:E MTAB 8958:Sample 13|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:il4/13b / |organism part:gill|sample name:E MTAB 8958:Sample 13|scientific name:Danio rerio                 Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills E MTAB 8958:Sample 13 p Sample 13 p Zebrafish il 4 il 10 regulated immunity in gills This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494–7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end. Experimental Factor: genotype:il4/13b / RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   ERP121190 Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16 FB1_S17_R1_001.fastq.gz FB1_S17_R2_001.fastq.gz fastq fastq 6951804793.0 46295025.0 E MTAB 8958:FB1 S17 R 0:75.10 1:75.06 A:1827618209;C:1618955946;G:1595802123;T:1884739421;N:24689094 75 75     1827618209 1618955946 1595802123 1884739421 24689094 ERX4030568 ERS4514121 ERA2508092 UNIVERSITY OF MANCHESTER|European Nucleotide Archive UNIVERSITY OF MANCHESTER|European Nucleotide Archive 2 0.90991 0.90972 0.09297 0.09193 0.68284 0.68392 0.49878 0.5017 74 75 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   United Kingdom 2020-04-16 Adult Adult Gill Respiratory System
9850 9850 ERR4029251 ERX4030567 ERS4514120 ERP121190 PRJEB37851 Zebrafish il 4 il 10 regulated immunity in gills E-MTAB-8958 Transcriptome Analysis The evolutionary origin of vertebrate type 2 immunity is a topic of great interest. Several studies have focused on the immune cell components of evolutionary older vertebrates such as fish. However how fish cytokines function and whether they have similar roles as in mammals is still a matter of speculation. Here we have used the zebrafish Danio rerio to gain insights into il4/13a and il4/13b genes and characterized their role under both homeostatic and inflammatory conditions. We established knockouts for both il4/13a and il4/13b genes and showed that they are needed to suppress inflammation in larvae and in the gill mucosa. As a counterpoint we examined the gills of il10 defective zebrafish and revealed the importance of il10 in maintaining homeostasis in this mucosal tissue. As in mammals zebrafish il10 appears to have an anti inflammatory function. ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16   Protocols: This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494 7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end. Sample 20 SAMEA6786441 UNIVERSITY OF MANCHESTER ENA FIRST PUBLIC:2020 05 28T17:07:47Z|ENA LAST UPDATE:2020 04 16T14:58:15Z|External Id:SAMEA6786441|INSDC center name:UNIVERSITY OF MANCHESTER|INSDC first public:2020 05 28T17:07:47Z|INSDC last update:2020 04 16T14:58:15Z|INSDC status:public|Submitter Id:E MTAB 8958:Sample 20|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:il4/13a / ; il4/13b / |organism part:gill|sample name:E MTAB 8958:Sample 20|scientific name:Danio rerio                 Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills E MTAB 8958:Sample 20 p Sample 20 p Zebrafish il 4 il 10 regulated immunity in gills This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494–7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end. Experimental Factor: genotype:il4/13a / ; il4/13b / RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   ERP121190 Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16 FB4_S44_R1_001.fastq.gz FB4_S44_R2_001.fastq.gz fastq fastq 9629684100.0 64667395.0 E MTAB 8958:FB4 S44 R 0:74.47 1:74.44 A:2552333346;C:2176006333;G:2180111416;T:2614191329;N:107041676 74 74     2552333346 2176006333 2180111416 2614191329 107041676 ERX4030567 ERS4514120 ERA2508092 UNIVERSITY OF MANCHESTER|European Nucleotide Archive UNIVERSITY OF MANCHESTER|European Nucleotide Archive 2 0.90795 0.90756 0.10044 0.09789 0.6888 0.69256 0.50043 0.4932 76 76 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   United Kingdom 2020-04-16 Adult Adult Gill Respiratory System
9851 9851 ERR4029250 ERX4030566 ERS4514119 ERP121190 PRJEB37851 Zebrafish il 4 il 10 regulated immunity in gills E-MTAB-8958 Transcriptome Analysis The evolutionary origin of vertebrate type 2 immunity is a topic of great interest. Several studies have focused on the immune cell components of evolutionary older vertebrates such as fish. However how fish cytokines function and whether they have similar roles as in mammals is still a matter of speculation. Here we have used the zebrafish Danio rerio to gain insights into il4/13a and il4/13b genes and characterized their role under both homeostatic and inflammatory conditions. We established knockouts for both il4/13a and il4/13b genes and showed that they are needed to suppress inflammation in larvae and in the gill mucosa. As a counterpoint we examined the gills of il10 defective zebrafish and revealed the importance of il10 in maintaining homeostasis in this mucosal tissue. As in mammals zebrafish il10 appears to have an anti inflammatory function. ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16   Protocols: This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494 7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end. Sample 19 SAMEA6786440 UNIVERSITY OF MANCHESTER ENA FIRST PUBLIC:2020 05 28T17:07:47Z|ENA LAST UPDATE:2020 04 16T14:58:15Z|External Id:SAMEA6786440|INSDC center name:UNIVERSITY OF MANCHESTER|INSDC first public:2020 05 28T17:07:47Z|INSDC last update:2020 04 16T14:58:15Z|INSDC status:public|Submitter Id:E MTAB 8958:Sample 19|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:il4/13a / ; il4/13b / |organism part:gill|sample name:E MTAB 8958:Sample 19|scientific name:Danio rerio                 Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills E MTAB 8958:Sample 19 p Sample 19 p Zebrafish il 4 il 10 regulated immunity in gills This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494–7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end. Experimental Factor: genotype:il4/13a / ; il4/13b / RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   ERP121190 Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16 FB3_S43_R1_001.fastq.gz FB3_S43_R2_001.fastq.gz fastq fastq 11268744444.0 75088756.0 E MTAB 8958:FB3 S43 R 0:75.06 1:75.01 A:2983863814;C:2608268633;G:2555098938;T:3072413168;N:49099891 75 75     2983863814 2608268633 2555098938 3072413168 49099891 ERX4030566 ERS4514119 ERA2508092 UNIVERSITY OF MANCHESTER|European Nucleotide Archive UNIVERSITY OF MANCHESTER|European Nucleotide Archive 2 0.9107 0.91089 0.09522 0.09428 0.69187 0.69266 0.49302 0.49463 76 76 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   United Kingdom 2020-04-16 Adult Adult Gill Respiratory System
9852 9852 ERR4029249 ERX4030565 ERS4514118 ERP121190 PRJEB37851 Zebrafish il 4 il 10 regulated immunity in gills E-MTAB-8958 Transcriptome Analysis The evolutionary origin of vertebrate type 2 immunity is a topic of great interest. Several studies have focused on the immune cell components of evolutionary older vertebrates such as fish. However how fish cytokines function and whether they have similar roles as in mammals is still a matter of speculation. Here we have used the zebrafish Danio rerio to gain insights into il4/13a and il4/13b genes and characterized their role under both homeostatic and inflammatory conditions. We established knockouts for both il4/13a and il4/13b genes and showed that they are needed to suppress inflammation in larvae and in the gill mucosa. As a counterpoint we examined the gills of il10 defective zebrafish and revealed the importance of il10 in maintaining homeostasis in this mucosal tissue. As in mammals zebrafish il10 appears to have an anti inflammatory function. ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16   Protocols: This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494 7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end. Sample 18 SAMEA6786439 UNIVERSITY OF MANCHESTER ENA FIRST PUBLIC:2020 05 28T17:07:47Z|ENA LAST UPDATE:2020 04 16T14:58:14Z|External Id:SAMEA6786439|INSDC center name:UNIVERSITY OF MANCHESTER|INSDC first public:2020 05 28T17:07:47Z|INSDC last update:2020 04 16T14:58:14Z|INSDC status:public|Submitter Id:E MTAB 8958:Sample 18|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:il4/13a / ; il4/13b / |organism part:gill|sample name:E MTAB 8958:Sample 18|scientific name:Danio rerio                 Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills E MTAB 8958:Sample 18 p Sample 18 p Zebrafish il 4 il 10 regulated immunity in gills This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494–7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end. Experimental Factor: genotype:il4/13a / ; il4/13b / RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   ERP121190 Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16 FB2_S42_R1_001.fastq.gz FB2_S42_R2_001.fastq.gz fastq fastq 10434072067.0 69530304.0 E MTAB 8958:FB2 S42 R 0:75.06 1:75.01 A:2749500618;C:2426208950;G:2375421255;T:2834879202;N:48062042 75 75     2749500618 2426208950 2375421255 2834879202 48062042 ERX4030565 ERS4514118 ERA2508092 UNIVERSITY OF MANCHESTER|European Nucleotide Archive UNIVERSITY OF MANCHESTER|European Nucleotide Archive 2 0.9084 0.90779 0.0926 0.0917 0.68809 0.68864 0.49817 0.49902 76 75 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   United Kingdom 2020-04-16 Adult Adult Gill Respiratory System
9853 9853 ERR4029248 ERX4030564 ERS4514117 ERP121190 PRJEB37851 Zebrafish il 4 il 10 regulated immunity in gills E-MTAB-8958 Transcriptome Analysis The evolutionary origin of vertebrate type 2 immunity is a topic of great interest. Several studies have focused on the immune cell components of evolutionary older vertebrates such as fish. However how fish cytokines function and whether they have similar roles as in mammals is still a matter of speculation. Here we have used the zebrafish Danio rerio to gain insights into il4/13a and il4/13b genes and characterized their role under both homeostatic and inflammatory conditions. We established knockouts for both il4/13a and il4/13b genes and showed that they are needed to suppress inflammation in larvae and in the gill mucosa. As a counterpoint we examined the gills of il10 defective zebrafish and revealed the importance of il10 in maintaining homeostasis in this mucosal tissue. As in mammals zebrafish il10 appears to have an anti inflammatory function. ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16   Protocols: This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494 7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end. Sample 17 SAMEA6786438 UNIVERSITY OF MANCHESTER ENA FIRST PUBLIC:2020 05 28T17:07:47Z|ENA LAST UPDATE:2020 04 16T14:58:14Z|External Id:SAMEA6786438|INSDC center name:UNIVERSITY OF MANCHESTER|INSDC first public:2020 05 28T17:07:47Z|INSDC last update:2020 04 16T14:58:14Z|INSDC status:public|Submitter Id:E MTAB 8958:Sample 17|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:il4/13a / ; il4/13b / |organism part:gill|sample name:E MTAB 8958:Sample 17|scientific name:Danio rerio                 Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills E MTAB 8958:Sample 17 p Sample 17 p Zebrafish il 4 il 10 regulated immunity in gills This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494–7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end. Experimental Factor: genotype:il4/13a / ; il4/13b / RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   ERP121190 Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16 FB1_S41_R1_001.fastq.gz FB1_S41_R2_001.fastq.gz fastq fastq 12125040750.0 80781224.0 E MTAB 8958:FB1 S41 R 0:75.08 1:75.02 A:3129480022;C:2890038396;G:2819859086;T:3233228646;N:52434600 75 75     3129480022 2890038396 2819859086 3233228646 52434600 ERX4030564 ERS4514117 ERA2508092 UNIVERSITY OF MANCHESTER|European Nucleotide Archive UNIVERSITY OF MANCHESTER|European Nucleotide Archive 2 0.91384 0.91301 0.10967 0.10615 0.69006 0.69041 0.51643 0.51985 76 76 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   United Kingdom 2020-04-16 Adult Adult Gill Respiratory System
9854 9854 ERR4029247 ERX4030563 ERS4514116 ERP121190 PRJEB37851 Zebrafish il 4 il 10 regulated immunity in gills E-MTAB-8958 Transcriptome Analysis The evolutionary origin of vertebrate type 2 immunity is a topic of great interest. Several studies have focused on the immune cell components of evolutionary older vertebrates such as fish. However how fish cytokines function and whether they have similar roles as in mammals is still a matter of speculation. Here we have used the zebrafish Danio rerio to gain insights into il4/13a and il4/13b genes and characterized their role under both homeostatic and inflammatory conditions. We established knockouts for both il4/13a and il4/13b genes and showed that they are needed to suppress inflammation in larvae and in the gill mucosa. As a counterpoint we examined the gills of il10 defective zebrafish and revealed the importance of il10 in maintaining homeostasis in this mucosal tissue. As in mammals zebrafish il10 appears to have an anti inflammatory function. ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16   Protocols: This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494 7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end. Sample 8 SAMEA6786437 UNIVERSITY OF MANCHESTER ENA FIRST PUBLIC:2020 05 28T17:07:47Z|ENA LAST UPDATE:2020 04 16T14:58:14Z|External Id:SAMEA6786437|INSDC center name:UNIVERSITY OF MANCHESTER|INSDC first public:2020 05 28T17:07:47Z|INSDC last update:2020 04 16T14:58:14Z|INSDC status:public|Submitter Id:E MTAB 8958:Sample 8|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:il4/13a / |organism part:gill|sample name:E MTAB 8958:Sample 8|scientific name:Danio rerio                 Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills E MTAB 8958:Sample 8 p Sample 8 p Zebrafish il 4 il 10 regulated immunity in gills This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494–7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end. Experimental Factor: genotype:il4/13a / RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   ERP121190 Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16 FB12_S49_R1_001.fastq.gz FB12_S49_R2_001.fastq.gz fastq fastq 4223131851.0 28165494.0 E MTAB 8958:FB12 S49 R 0:74.95 1:74.99 A:1121514270;C:962554300;G:967294488;T:1146544647;N:25224146 74 74     1121514270 962554300 967294488 1146544647 25224146 ERX4030563 ERS4514116 ERA2508092 UNIVERSITY OF MANCHESTER|European Nucleotide Archive UNIVERSITY OF MANCHESTER|European Nucleotide Archive 2 0.91639 0.91413 0.10604 0.10326 0.68162 0.68458 0.49921 0.50172 76 75 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   United Kingdom 2020-04-16 Adult Adult Gill Respiratory System
9855 9855 ERR4029246 ERX4030562 ERS4514115 ERP121190 PRJEB37851 Zebrafish il 4 il 10 regulated immunity in gills E-MTAB-8958 Transcriptome Analysis The evolutionary origin of vertebrate type 2 immunity is a topic of great interest. Several studies have focused on the immune cell components of evolutionary older vertebrates such as fish. However how fish cytokines function and whether they have similar roles as in mammals is still a matter of speculation. Here we have used the zebrafish Danio rerio to gain insights into il4/13a and il4/13b genes and characterized their role under both homeostatic and inflammatory conditions. We established knockouts for both il4/13a and il4/13b genes and showed that they are needed to suppress inflammation in larvae and in the gill mucosa. As a counterpoint we examined the gills of il10 defective zebrafish and revealed the importance of il10 in maintaining homeostasis in this mucosal tissue. As in mammals zebrafish il10 appears to have an anti inflammatory function. ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16   Protocols: This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494 7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end. Sample 7 SAMEA6786436 UNIVERSITY OF MANCHESTER ENA FIRST PUBLIC:2020 05 28T17:07:47Z|ENA LAST UPDATE:2020 04 16T14:58:14Z|External Id:SAMEA6786436|INSDC center name:UNIVERSITY OF MANCHESTER|INSDC first public:2020 05 28T17:07:47Z|INSDC last update:2020 04 16T14:58:14Z|INSDC status:public|Submitter Id:E MTAB 8958:Sample 7|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:il4/13a / |organism part:gill|sample name:E MTAB 8958:Sample 7|scientific name:Danio rerio                 Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills E MTAB 8958:Sample 7 p Sample 7 p Zebrafish il 4 il 10 regulated immunity in gills This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494–7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end. Experimental Factor: genotype:il4/13a / RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   ERP121190 Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16 FB11_S48_R1_001.fastq.gz FB11_S48_R2_001.fastq.gz fastq fastq 4670407305.0 31054128.0 E MTAB 8958:FB11 S48 R 0:75.20 1:75.19 A:1234494738;C:1078360233;G:1084251975;T:1258088405;N:15211954 75 75     1234494738 1078360233 1084251975 1258088405 15211954 ERX4030562 ERS4514115 ERA2508092 UNIVERSITY OF MANCHESTER|European Nucleotide Archive UNIVERSITY OF MANCHESTER|European Nucleotide Archive 2 0.92228 0.92038 0.09418 0.09222 0.68674 0.68862 0.48948 0.48842 75 75 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   United Kingdom 2020-04-16 Adult Adult Gill Respiratory System
9856 9856 ERR4029245 ERX4030561 ERS4514114 ERP121190 PRJEB37851 Zebrafish il 4 il 10 regulated immunity in gills E-MTAB-8958 Transcriptome Analysis The evolutionary origin of vertebrate type 2 immunity is a topic of great interest. Several studies have focused on the immune cell components of evolutionary older vertebrates such as fish. However how fish cytokines function and whether they have similar roles as in mammals is still a matter of speculation. Here we have used the zebrafish Danio rerio to gain insights into il4/13a and il4/13b genes and characterized their role under both homeostatic and inflammatory conditions. We established knockouts for both il4/13a and il4/13b genes and showed that they are needed to suppress inflammation in larvae and in the gill mucosa. As a counterpoint we examined the gills of il10 defective zebrafish and revealed the importance of il10 in maintaining homeostasis in this mucosal tissue. As in mammals zebrafish il10 appears to have an anti inflammatory function. ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16   Protocols: This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494 7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end. Sample 6 SAMEA6786435 UNIVERSITY OF MANCHESTER ENA FIRST PUBLIC:2020 05 28T17:07:47Z|ENA LAST UPDATE:2020 04 16T14:58:14Z|External Id:SAMEA6786435|INSDC center name:UNIVERSITY OF MANCHESTER|INSDC first public:2020 05 28T17:07:47Z|INSDC last update:2020 04 16T14:58:14Z|INSDC status:public|Submitter Id:E MTAB 8958:Sample 6|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:il4/13a / |organism part:gill|sample name:E MTAB 8958:Sample 6|scientific name:Danio rerio                 Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills E MTAB 8958:Sample 6 p Sample 6 p Zebrafish il 4 il 10 regulated immunity in gills This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494–7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end. Experimental Factor: genotype:il4/13a / RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   ERP121190 Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16 FB10_S47_R1_001.fastq.gz FB10_S47_R2_001.fastq.gz fastq fastq 3970723047.0 26597167.0 E MTAB 8958:FB10 S47 R 0:74.63 1:74.66 A:1037861230;C:915437247;G:922979694;T:1056625196;N:37819680 74 74     1037861230 915437247 922979694 1056625196 37819680 ERX4030561 ERS4514114 ERA2508092 UNIVERSITY OF MANCHESTER|European Nucleotide Archive UNIVERSITY OF MANCHESTER|European Nucleotide Archive 2 0.92474 0.92246 0.0934 0.0916 0.69106 0.69384 0.49058 0.48154 76 76 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   United Kingdom 2020-04-16 Adult Adult Gill Respiratory System
9857 9857 ERR4029244 ERX4030560 ERS4514113 ERP121190 PRJEB37851 Zebrafish il 4 il 10 regulated immunity in gills E-MTAB-8958 Transcriptome Analysis The evolutionary origin of vertebrate type 2 immunity is a topic of great interest. Several studies have focused on the immune cell components of evolutionary older vertebrates such as fish. However how fish cytokines function and whether they have similar roles as in mammals is still a matter of speculation. Here we have used the zebrafish Danio rerio to gain insights into il4/13a and il4/13b genes and characterized their role under both homeostatic and inflammatory conditions. We established knockouts for both il4/13a and il4/13b genes and showed that they are needed to suppress inflammation in larvae and in the gill mucosa. As a counterpoint we examined the gills of il10 defective zebrafish and revealed the importance of il10 in maintaining homeostasis in this mucosal tissue. As in mammals zebrafish il10 appears to have an anti inflammatory function. ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16   Protocols: This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494 7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end. Sample 5 SAMEA6786434 UNIVERSITY OF MANCHESTER ENA FIRST PUBLIC:2020 05 28T17:07:47Z|ENA LAST UPDATE:2020 04 16T14:58:14Z|External Id:SAMEA6786434|INSDC center name:UNIVERSITY OF MANCHESTER|INSDC first public:2020 05 28T17:07:47Z|INSDC last update:2020 04 16T14:58:14Z|INSDC status:public|Submitter Id:E MTAB 8958:Sample 5|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:il4/13a / |organism part:gill|sample name:E MTAB 8958:Sample 5|scientific name:Danio rerio                 Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills E MTAB 8958:Sample 5 p Sample 5 p Zebrafish il 4 il 10 regulated immunity in gills This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494–7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end. Experimental Factor: genotype:il4/13a / RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   ERP121190 Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16 FB9_S46_R1_001.fastq.gz FB9_S46_R2_001.fastq.gz fastq fastq 4267946165.0 28455064.0 E MTAB 8958:FB9 S46 R 0:75.00 1:74.99 A:1108310330;C:999732020;G:987857724;T:1148193980;N:23852111 75 74     1108310330 999732020 987857724 1148193980 23852111 ERX4030560 ERS4514113 ERA2508092 UNIVERSITY OF MANCHESTER|European Nucleotide Archive UNIVERSITY OF MANCHESTER|European Nucleotide Archive 2 0.9223 0.91737 0.09304 0.09006 0.69063 0.6929 0.48978 0.49675 76 75 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   United Kingdom 2020-04-16 Adult Adult Gill Respiratory System
9858 9858 ERR4029243 ERX4030559 ERS4514112 ERP121190 PRJEB37851 Zebrafish il 4 il 10 regulated immunity in gills E-MTAB-8958 Transcriptome Analysis The evolutionary origin of vertebrate type 2 immunity is a topic of great interest. Several studies have focused on the immune cell components of evolutionary older vertebrates such as fish. However how fish cytokines function and whether they have similar roles as in mammals is still a matter of speculation. Here we have used the zebrafish Danio rerio to gain insights into il4/13a and il4/13b genes and characterized their role under both homeostatic and inflammatory conditions. We established knockouts for both il4/13a and il4/13b genes and showed that they are needed to suppress inflammation in larvae and in the gill mucosa. As a counterpoint we examined the gills of il10 defective zebrafish and revealed the importance of il10 in maintaining homeostasis in this mucosal tissue. As in mammals zebrafish il10 appears to have an anti inflammatory function. ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16   Protocols: This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494 7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end. Sample 9 SAMEA6786433 UNIVERSITY OF MANCHESTER ENA FIRST PUBLIC:2020 05 28T17:07:47Z|ENA LAST UPDATE:2020 04 16T14:58:14Z|External Id:SAMEA6786433|INSDC center name:UNIVERSITY OF MANCHESTER|INSDC first public:2020 05 28T17:07:47Z|INSDC last update:2020 04 16T14:58:14Z|INSDC status:public|Submitter Id:E MTAB 8958:Sample 9|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:il10 / |organism part:gill|sample name:E MTAB 8958:Sample 9|scientific name:Danio rerio                 Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills E MTAB 8958:Sample 9 p Sample 9 p Zebrafish il 4 il 10 regulated immunity in gills This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494–7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end. Experimental Factor: genotype:il10 / RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   ERP121190 Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16 FB17_S54_R1_001.fastq.gz FB17_S54_R2_001.fastq.gz fastq fastq 3847723303.0 25764874.0 E MTAB 8958:FB17 S54 R 0:74.65 1:74.69 A:1009950686;C:883047473;G:885821368;T:1035313325;N:33590451 74 74     1009950686 883047473 885821368 1035313325 33590451 ERX4030559 ERS4514112 ERA2508092 UNIVERSITY OF MANCHESTER|European Nucleotide Archive UNIVERSITY OF MANCHESTER|European Nucleotide Archive 2 0.91088 0.90785 0.09899 0.09623 0.68822 0.69055 0.48686 0.49337 76 75 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   United Kingdom 2020-04-16 Adult Adult Gill Respiratory System
9859 9859 ERR4029242 ERX4030558 ERS4514111 ERP121190 PRJEB37851 Zebrafish il 4 il 10 regulated immunity in gills E-MTAB-8958 Transcriptome Analysis The evolutionary origin of vertebrate type 2 immunity is a topic of great interest. Several studies have focused on the immune cell components of evolutionary older vertebrates such as fish. However how fish cytokines function and whether they have similar roles as in mammals is still a matter of speculation. Here we have used the zebrafish Danio rerio to gain insights into il4/13a and il4/13b genes and characterized their role under both homeostatic and inflammatory conditions. We established knockouts for both il4/13a and il4/13b genes and showed that they are needed to suppress inflammation in larvae and in the gill mucosa. As a counterpoint we examined the gills of il10 defective zebrafish and revealed the importance of il10 in maintaining homeostasis in this mucosal tissue. As in mammals zebrafish il10 appears to have an anti inflammatory function. ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16   Protocols: This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494 7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end. Sample 12 SAMEA6786432 UNIVERSITY OF MANCHESTER ENA FIRST PUBLIC:2020 05 28T17:07:47Z|ENA LAST UPDATE:2020 04 16T14:58:14Z|External Id:SAMEA6786432|INSDC center name:UNIVERSITY OF MANCHESTER|INSDC first public:2020 05 28T17:07:47Z|INSDC last update:2020 04 16T14:58:14Z|INSDC status:public|Submitter Id:E MTAB 8958:Sample 12|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:il10 / |organism part:gill|sample name:E MTAB 8958:Sample 12|scientific name:Danio rerio                 Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills E MTAB 8958:Sample 12 p Sample 12 p Zebrafish il 4 il 10 regulated immunity in gills This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494–7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end. Experimental Factor: genotype:il10 / RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   ERP121190 Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16 FB20_S57_R1_001.fastq.gz FB20_S57_R2_001.fastq.gz fastq fastq 4534822065.0 30209756.0 E MTAB 8958:FB20 S57 R 0:75.06 1:75.06 A:1181838544;C:1056097162;G:1066594521;T:1207484216;N:22807622 75 75     1181838544 1056097162 1066594521 1207484216 22807622 ERX4030558 ERS4514111 ERA2508092 UNIVERSITY OF MANCHESTER|European Nucleotide Archive UNIVERSITY OF MANCHESTER|European Nucleotide Archive 2 0.91577 0.91513 0.09598 0.09473 0.68931 0.69132 0.49181 0.49786 74 76 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   United Kingdom 2020-04-16 Adult Adult Gill Respiratory System
9860 9860 ERR4029241 ERX4030557 ERS4514110 ERP121190 PRJEB37851 Zebrafish il 4 il 10 regulated immunity in gills E-MTAB-8958 Transcriptome Analysis The evolutionary origin of vertebrate type 2 immunity is a topic of great interest. Several studies have focused on the immune cell components of evolutionary older vertebrates such as fish. However how fish cytokines function and whether they have similar roles as in mammals is still a matter of speculation. Here we have used the zebrafish Danio rerio to gain insights into il4/13a and il4/13b genes and characterized their role under both homeostatic and inflammatory conditions. We established knockouts for both il4/13a and il4/13b genes and showed that they are needed to suppress inflammation in larvae and in the gill mucosa. As a counterpoint we examined the gills of il10 defective zebrafish and revealed the importance of il10 in maintaining homeostasis in this mucosal tissue. As in mammals zebrafish il10 appears to have an anti inflammatory function. ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16   Protocols: This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494 7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end. Sample 11 SAMEA6786431 UNIVERSITY OF MANCHESTER ENA FIRST PUBLIC:2020 05 28T17:07:47Z|ENA LAST UPDATE:2020 04 16T14:58:14Z|External Id:SAMEA6786431|INSDC center name:UNIVERSITY OF MANCHESTER|INSDC first public:2020 05 28T17:07:47Z|INSDC last update:2020 04 16T14:58:14Z|INSDC status:public|Submitter Id:E MTAB 8958:Sample 11|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:il10 / |organism part:gill|sample name:E MTAB 8958:Sample 11|scientific name:Danio rerio                 Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills E MTAB 8958:Sample 11 p Sample 11 p Zebrafish il 4 il 10 regulated immunity in gills This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494–7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end. Experimental Factor: genotype:il10 / RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   ERP121190 Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16 FB19_S56_R1_001.fastq.gz FB19_S56_R2_001.fastq.gz fastq fastq 5070571422.0 33987501.0 E MTAB 8958:FB19 S56 R 0:74.58 1:74.61 A:1327496786;C:1163563377;G:1162870630;T:1365191685;N:51448944 74 74     1327496786 1163563377 1162870630 1365191685 51448944 ERX4030557 ERS4514110 ERA2508092 UNIVERSITY OF MANCHESTER|European Nucleotide Archive UNIVERSITY OF MANCHESTER|European Nucleotide Archive 2 0.91091 0.91003 0.09944 0.09748 0.68745 0.69016 0.49706 0.49287 76 75 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   United Kingdom 2020-04-16 Adult Adult Gill Respiratory System
9861 9861 ERR4029240 ERX4030556 ERS4514109 ERP121190 PRJEB37851 Zebrafish il 4 il 10 regulated immunity in gills E-MTAB-8958 Transcriptome Analysis The evolutionary origin of vertebrate type 2 immunity is a topic of great interest. Several studies have focused on the immune cell components of evolutionary older vertebrates such as fish. However how fish cytokines function and whether they have similar roles as in mammals is still a matter of speculation. Here we have used the zebrafish Danio rerio to gain insights into il4/13a and il4/13b genes and characterized their role under both homeostatic and inflammatory conditions. We established knockouts for both il4/13a and il4/13b genes and showed that they are needed to suppress inflammation in larvae and in the gill mucosa. As a counterpoint we examined the gills of il10 defective zebrafish and revealed the importance of il10 in maintaining homeostasis in this mucosal tissue. As in mammals zebrafish il10 appears to have an anti inflammatory function. ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16   Protocols: This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494 7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end. Sample 10 SAMEA6786430 UNIVERSITY OF MANCHESTER ENA FIRST PUBLIC:2020 05 28T17:07:47Z|ENA LAST UPDATE:2020 04 16T14:58:14Z|External Id:SAMEA6786430|INSDC center name:UNIVERSITY OF MANCHESTER|INSDC first public:2020 05 28T17:07:47Z|INSDC last update:2020 04 16T14:58:14Z|INSDC status:public|Submitter Id:E MTAB 8958:Sample 10|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:il10 / |organism part:gill|sample name:E MTAB 8958:Sample 10|scientific name:Danio rerio                 Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills E MTAB 8958:Sample 10 p Sample 10 p Zebrafish il 4 il 10 regulated immunity in gills This submission contains RNA seq samples from the gill tissue of five zebrafish strains: Wildtype il4/13a KO il4/13b KO il4/13a;b KO and il10 KO. The strains il4/13a KO il4/13b KO and il4/13a;b KO were generated using CRISPR/Cas9 system whereas the il10 KO was generated by the Sanger Institute through the Zebrafish Mutation Project Kettleborough RNW Busch nentwich EM Harvey SA Dooley CM Bruijn E De Eeden F Van et al. Europe PMC Funders Group Europe PMC Funders Author Manuscripts A systematic genome wide analysis of zebrafish protein coding gene function. 2013;4967446:494–7. Zebrafish Danio rerio were maintained under standard conditions 28 °C under a 14 h light/10 h dark cycle within the Biological Services Unit The University of Manchester. Gill tissue was harvested from adult 6 mpf male and female zebrafish. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Gills were harvested from four fish for each strain n=4 one fish per sample and total RNA was isolated from each sample using the RNeasy mini kit Qiagen. Prior to performing RNA seq the integrity of RNA samples was assessed using a 2200 TapeStation Agilent Technologies according to the manufacturer's instructions. Truseq stranded mRNA Assay. Paired end. Experimental Factor: genotype:il10 / RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   ERP121190 Illumina HiSeq 4000 paired end sequencing; Zebrafish il 4 il 10 regulated immunity in gills ENA FIRST PUBLIC:2020 05 28|ENA LAST UPDATE:2020 04 16 FB18_S55_R1_001.fastq.gz FB18_S55_R2_001.fastq.gz fastq fastq 4411576023.0 29389076.0 E MTAB 8958:FB18 S55 R 0:75.05 1:75.06 A:1153821133;C:1024593137;G:1029312154;T:1181989770;N:21859829 75 75     1153821133 1024593137 1029312154 1181989770 21859829 ERX4030556 ERS4514109 ERA2508092 UNIVERSITY OF MANCHESTER|European Nucleotide Archive UNIVERSITY OF MANCHESTER|European Nucleotide Archive 2 0.90933 0.90999 0.09581 0.09404 0.68917 0.69199 0.49527 0.49791 76 76 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   United Kingdom 2020-04-16 Adult Adult Gill Respiratory System
10374 10374 ERR8058375 ERX7625096 ERS10119356 ERP134902 PRJEB50332 RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine E-MTAB-11346 Transcriptome Analysis To determine the transcriptomic changes elicted by drugs of abuse zebrafish embryos were exposed to 10uM morphine from xxx hpf ttwo xxx hpf. Embryos were euthanized and deep frozen with N2l. RNA was extracted and an RNA seq assay was performed with Illumina Platform ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03   Protocols: At 72 hpf embryos were sacrificed by cold exposure incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs medium was removed and they were frozen in N2l. Tissue was stored at 80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented reverse transcrided using random hexamers three prime and five prime adapters were attached and library was amplified by PCR Morphine 3 SAMEA12512752 Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain. ENA FIRST PUBLIC:2022 12 31|ENA LAST UPDATE:2022 12 31|External Id:SAMEA12512752|INSDC center alias:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca Spain.|INSDC center name:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca Spain.|INSDC first public:2022 12 31T00:57:45Z|INSDC last update:2022 12 31T00:57:45Z|INSDC status:public|Submitter Id:E MTAB 11346:Morphine 3|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|developmental stage:72|genotype:wild type genotype|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11346:Morphine 3|strain:AB                 Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine E MTAB 11346:Morphine 3 p Morphine 3 p RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine At 72 hpf embryos were sacrificed by cold exposure incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs medium was removed and they were frozen in N2l. Tissue was stored at 80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented reverse transcrided using random hexamers three prime and five prime adapters were attached and library was amplified by PCR Experimental Factor: compound:morphine|Experimental Factor: dose:10 RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   ERP134902 Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03 NG-10331_4M_lib138515_4790_6_1.fastq.gz NG-10331_4M_lib138515_4790_6_2.fastq.gz fastq fastq 11175776640.0 44348320.0 E MTAB 11346:NG 10331 4M lib138515 4790 6 0:126 1:126 A:3058552548;C:2537121022;G:2531362154;T:3047376587;N:1364329 126 126     3058552548 2537121022 2531362154 3047376587 1364329 ERX7625096 ERS10119356 ERA8439547 Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive 2 0.93345 0.93836 0.09826 0.09482 0.69497 0.69968 0.46885 0.46966 126 126 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Spain 2022-12-31 Larval Larval Whole Organism All anatomical structures
10375 10375 ERR8058374 ERX7625095 ERS10119355 ERP134902 PRJEB50332 RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine E-MTAB-11346 Transcriptome Analysis To determine the transcriptomic changes elicted by drugs of abuse zebrafish embryos were exposed to 10uM morphine from xxx hpf ttwo xxx hpf. Embryos were euthanized and deep frozen with N2l. RNA was extracted and an RNA seq assay was performed with Illumina Platform ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03   Protocols: At 72 hpf embryos were sacrificed by cold exposure incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs medium was removed and they were frozen in N2l. Tissue was stored at 80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented reverse transcrided using random hexamers three prime and five prime adapters were attached and library was amplified by PCR Morphine 2 SAMEA12512751 Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain. ENA FIRST PUBLIC:2022 12 31|ENA LAST UPDATE:2022 12 31|External Id:SAMEA12512751|INSDC center alias:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca Spain.|INSDC center name:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca Spain.|INSDC first public:2022 12 31T00:57:45Z|INSDC last update:2022 12 31T00:57:45Z|INSDC status:public|Submitter Id:E MTAB 11346:Morphine 2|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|developmental stage:72|genotype:wild type genotype|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11346:Morphine 2|strain:AB                 Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine E MTAB 11346:Morphine 2 p Morphine 2 p RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine At 72 hpf embryos were sacrificed by cold exposure incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs medium was removed and they were frozen in N2l. Tissue was stored at 80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented reverse transcrided using random hexamers three prime and five prime adapters were attached and library was amplified by PCR Experimental Factor: compound:morphine|Experimental Factor: dose:10 RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   ERP134902 Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03 NG-10331_3M_lib138512_4790_5_1.fastq.gz NG-10331_3M_lib138512_4790_5_2.fastq.gz fastq fastq 10428424776.0 41382638.0 E MTAB 11346:NG 10331 3M lib138512 4790 5 0:126 1:126 A:2840226558;C:2379827926;G:2389813154;T:2817428937;N:1128201 126 126     2840226558 2379827926 2389813154 2817428937 1128201 ERX7625095 ERS10119355 ERA8439547 Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive 2 0.94204 0.9476 0.09827 0.09565 0.7008 0.70483 0.47435 0.47651 126 126 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Spain 2022-12-31 Larval Larval Whole Organism All anatomical structures
10376 10376 ERR8058373 ERX7625094 ERS10119354 ERP134902 PRJEB50332 RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine E-MTAB-11346 Transcriptome Analysis To determine the transcriptomic changes elicted by drugs of abuse zebrafish embryos were exposed to 10uM morphine from xxx hpf ttwo xxx hpf. Embryos were euthanized and deep frozen with N2l. RNA was extracted and an RNA seq assay was performed with Illumina Platform ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03   Protocols: At 72 hpf embryos were sacrificed by cold exposure incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs medium was removed and they were frozen in N2l. Tissue was stored at 80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented reverse transcrided using random hexamers three prime and five prime adapters were attached and library was amplified by PCR Morphine 1 SAMEA12512750 Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain. ENA FIRST PUBLIC:2022 12 31|ENA LAST UPDATE:2022 12 31|External Id:SAMEA12512750|INSDC center alias:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca Spain.|INSDC center name:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca Spain.|INSDC first public:2022 12 31T00:57:45Z|INSDC last update:2022 12 31T00:57:45Z|INSDC status:public|Submitter Id:E MTAB 11346:Morphine 1|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|developmental stage:72|genotype:wild type genotype|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11346:Morphine 1|strain:AB                 Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine E MTAB 11346:Morphine 1 p Morphine 1 p RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine At 72 hpf embryos were sacrificed by cold exposure incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs medium was removed and they were frozen in N2l. Tissue was stored at 80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented reverse transcrided using random hexamers three prime and five prime adapters were attached and library was amplified by PCR Experimental Factor: compound:morphine|Experimental Factor: dose:10 RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   ERP134902 Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03 NG-10331_2M_lib138509_4790_5_1.fastq.gz NG-10331_2M_lib138509_4790_5_2.fastq.gz fastq fastq 13158093312.0 52214656.0 E MTAB 11346:NG 10331 2M lib138509 4790 5 0:126 1:126 A:3613282182;C:2969954628;G:2964948806;T:3608471124;N:1436572 126 126     3613282182 2969954628 2964948806 3608471124 1436572 ERX7625094 ERS10119354 ERA8439547 Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive 2 0.93755 0.93735 0.11204 0.10849 0.67838 0.68335 0.45142 0.46509 126 126 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Spain 2022-12-31 Larval Larval Whole Organism All anatomical structures
10377 10377 ERR8058372 ERX7625093 ERS10119353 ERP134902 PRJEB50332 RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine E-MTAB-11346 Transcriptome Analysis To determine the transcriptomic changes elicted by drugs of abuse zebrafish embryos were exposed to 10uM morphine from xxx hpf ttwo xxx hpf. Embryos were euthanized and deep frozen with N2l. RNA was extracted and an RNA seq assay was performed with Illumina Platform ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03   Protocols: At 72 hpf embryos were sacrificed by cold exposure incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs medium was removed and they were frozen in N2l. Tissue was stored at 80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented reverse transcrided using random hexamers three prime and five prime adapters were attached and library was amplified by PCR Control 3 SAMEA12512749 Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain. ENA FIRST PUBLIC:2022 12 31|ENA LAST UPDATE:2022 12 31|External Id:SAMEA12512749|INSDC center alias:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca Spain.|INSDC center name:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca Spain.|INSDC first public:2022 12 31T00:57:45Z|INSDC last update:2022 12 31T00:57:45Z|INSDC status:public|Submitter Id:E MTAB 11346:Control 3|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|developmental stage:72|genotype:wild type genotype|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11346:Control 3|strain:AB                 Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine E MTAB 11346:Control 3 p Control 3 p RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine At 72 hpf embryos were sacrificed by cold exposure incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs medium was removed and they were frozen in N2l. Tissue was stored at 80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented reverse transcrided using random hexamers three prime and five prime adapters were attached and library was amplified by PCR Experimental Factor: compound:n1 RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   ERP134902 Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03 NG-10331_4C_lib138514_4790_6_1.fastq.gz NG-10331_4C_lib138514_4790_6_2.fastq.gz fastq fastq 14106514968.0 55978234.0 E MTAB 11346:NG 10331 4C lib138514 4790 6 0:126 1:126 A:3862641975;C:3195634147;G:3187866318;T:3858673135;N:1699393 126 126     3862641975 3195634147 3187866318 3858673135 1699393 ERX7625093 ERS10119353 ERA8439547 Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive 2 0.93657 0.93813 0.09783 0.09438 0.68925 0.69605 0.4741 0.47037 126 126 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Spain 2022-12-31 Larval Larval Whole Organism All anatomical structures
10378 10378 ERR8058371 ERX7625092 ERS10119352 ERP134902 PRJEB50332 RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine E-MTAB-11346 Transcriptome Analysis To determine the transcriptomic changes elicted by drugs of abuse zebrafish embryos were exposed to 10uM morphine from xxx hpf ttwo xxx hpf. Embryos were euthanized and deep frozen with N2l. RNA was extracted and an RNA seq assay was performed with Illumina Platform ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03   Protocols: At 72 hpf embryos were sacrificed by cold exposure incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs medium was removed and they were frozen in N2l. Tissue was stored at 80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented reverse transcrided using random hexamers three prime and five prime adapters were attached and library was amplified by PCR Control 2 SAMEA12512748 Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain. ENA FIRST PUBLIC:2022 12 31|ENA LAST UPDATE:2022 12 31|External Id:SAMEA12512748|INSDC center alias:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca Spain.|INSDC center name:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca Spain.|INSDC first public:2022 12 31T00:57:45Z|INSDC last update:2022 12 31T00:57:45Z|INSDC status:public|Submitter Id:E MTAB 11346:Control 2|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|developmental stage:72|genotype:wild type genotype|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11346:Control 2|strain:AB                 Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine E MTAB 11346:Control 2 p Control 2 p RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine At 72 hpf embryos were sacrificed by cold exposure incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs medium was removed and they were frozen in N2l. Tissue was stored at 80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented reverse transcrided using random hexamers three prime and five prime adapters were attached and library was amplified by PCR Experimental Factor: compound:n1 RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   ERP134902 Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03 NG-10331_3C_lib138511_4790_5_1.fastq.gz NG-10331_3C_lib138511_4790_5_2.fastq.gz fastq fastq 8889952680.0 35277590.0 E MTAB 11346:NG 10331 3C lib138511 4790 5 0:126 1:126 A:2424658667;C:2024699093;G:2023098669;T:2416527349;N:968902 126 126     2424658667 2024699093 2023098669 2416527349 968902 ERX7625092 ERS10119352 ERA8439547 Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive 2 0.94168 0.94149 0.09632 0.09404 0.68996 0.69672 0.46007 0.47123 126 126 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Spain 2022-12-31 Larval Larval Whole Organism All anatomical structures
10379 10379 ERR8058370 ERX7625091 ERS10119351 ERP134902 PRJEB50332 RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine E-MTAB-11346 Transcriptome Analysis To determine the transcriptomic changes elicted by drugs of abuse zebrafish embryos were exposed to 10uM morphine from xxx hpf ttwo xxx hpf. Embryos were euthanized and deep frozen with N2l. RNA was extracted and an RNA seq assay was performed with Illumina Platform ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03   Protocols: At 72 hpf embryos were sacrificed by cold exposure incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs medium was removed and they were frozen in N2l. Tissue was stored at 80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented reverse transcrided using random hexamers three prime and five prime adapters were attached and library was amplified by PCR Control 1 SAMEA12512747 Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain. ENA FIRST PUBLIC:2022 12 31|ENA LAST UPDATE:2022 12 31|External Id:SAMEA12512747|INSDC center alias:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca Spain.|INSDC center name:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca Spain.|INSDC first public:2022 12 31T00:57:45Z|INSDC last update:2022 12 31T00:57:45Z|INSDC status:public|Submitter Id:E MTAB 11346:Control 1|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|developmental stage:72|genotype:wild type genotype|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11346:Control 1|strain:AB                 Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine E MTAB 11346:Control 1 p Control 1 p RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine At 72 hpf embryos were sacrificed by cold exposure incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs medium was removed and they were frozen in N2l. Tissue was stored at 80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented reverse transcrided using random hexamers three prime and five prime adapters were attached and library was amplified by PCR Experimental Factor: compound:n1 RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   ERP134902 Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03 NG-10331_2C_lib138508_4790_5_1.fastq.gz NG-10331_2C_lib138508_4790_5_2.fastq.gz fastq fastq 12714421356.0 50454053.0 E MTAB 11346:NG 10331 2C lib138508 4790 5 0:126 1:126 A:3470625985;C:2894721473;G:2886656166;T:3461036460;N:1381272 126 126     3470625985 2894721473 2886656166 3461036460 1381272 ERX7625091 ERS10119351 ERA8439547 Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive 2 0.93951 0.93975 0.10489 0.10173 0.68134 0.68702 0.45337 0.44545 126 126 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Spain 2022-12-31 Larval Larval Whole Organism All anatomical structures
10380 10380 ERR8058369 ERX7625090 ERS10119350 ERP134902 PRJEB50332 RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine E-MTAB-11346 Transcriptome Analysis To determine the transcriptomic changes elicted by drugs of abuse zebrafish embryos were exposed to 10uM morphine from xxx hpf ttwo xxx hpf. Embryos were euthanized and deep frozen with N2l. RNA was extracted and an RNA seq assay was performed with Illumina Platform ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03   Protocols: At 72 hpf embryos were sacrificed by cold exposure incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs medium was removed and they were frozen in N2l. Tissue was stored at 80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented reverse transcrided using random hexamers three prime and five prime adapters were attached and library was amplified by PCR Cocaine 3 SAMEA12512746 Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain. ENA FIRST PUBLIC:2022 12 31|ENA LAST UPDATE:2022 12 31|External Id:SAMEA12512746|INSDC center alias:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca Spain.|INSDC center name:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca Spain.|INSDC first public:2022 12 31T00:57:45Z|INSDC last update:2022 12 31T00:57:45Z|INSDC status:public|Submitter Id:E MTAB 11346:Cocaine 3|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|developmental stage:72|genotype:wild type genotype|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11346:Cocaine 3|strain:AB                 Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine E MTAB 11346:Cocaine 3 p Cocaine 3 p RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine At 72 hpf embryos were sacrificed by cold exposure incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs medium was removed and they were frozen in N2l. Tissue was stored at 80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented reverse transcrided using random hexamers three prime and five prime adapters were attached and library was amplified by PCR Experimental Factor: compound:cocaine|Experimental Factor: dose:15 RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   ERP134902 Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03 NG-10331_4CC_lib138516_4790_6_1.fastq.gz NG-10331_4CC_lib138516_4790_6_2.fastq.gz fastq fastq 9574359984.0 37993492.0 E MTAB 11346:NG 10331 4CC lib138516 4790 6 0:126 1:126 A:2623103101;C:2170327733;G:2166494677;T:2613276955;N:1157518 126 126     2623103101 2170327733 2166494677 2613276955 1157518 ERX7625090 ERS10119350 ERA8439547 Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive 2 0.9366 0.93856 0.10196 0.09901 0.69018 0.69611 0.46501 0.46917 126 126 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Spain 2022-12-31 Larval Larval Whole Organism All anatomical structures
10381 10381 ERR8058368 ERX7625089 ERS10119349 ERP134902 PRJEB50332 RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine E-MTAB-11346 Transcriptome Analysis To determine the transcriptomic changes elicted by drugs of abuse zebrafish embryos were exposed to 10uM morphine from xxx hpf ttwo xxx hpf. Embryos were euthanized and deep frozen with N2l. RNA was extracted and an RNA seq assay was performed with Illumina Platform ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03   Protocols: At 72 hpf embryos were sacrificed by cold exposure incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs medium was removed and they were frozen in N2l. Tissue was stored at 80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented reverse transcrided using random hexamers three prime and five prime adapters were attached and library was amplified by PCR Cocaine 2 SAMEA12512745 Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain. ENA FIRST PUBLIC:2022 12 31|ENA LAST UPDATE:2022 12 31|External Id:SAMEA12512745|INSDC center alias:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca Spain.|INSDC center name:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca Spain.|INSDC first public:2022 12 31T00:57:45Z|INSDC last update:2022 12 31T00:57:45Z|INSDC status:public|Submitter Id:E MTAB 11346:Cocaine 2|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|developmental stage:72|genotype:wild type genotype|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11346:Cocaine 2|strain:AB                 Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine E MTAB 11346:Cocaine 2 p Cocaine 2 p RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine At 72 hpf embryos were sacrificed by cold exposure incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs medium was removed and they were frozen in N2l. Tissue was stored at 80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented reverse transcrided using random hexamers three prime and five prime adapters were attached and library was amplified by PCR Experimental Factor: compound:cocaine|Experimental Factor: dose:15 RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   ERP134902 Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03 NG-10331_3CC_lib138513_4828_1_1.fastq.gz NG-10331_3CC_lib138513_4828_1_2.fastq.gz fastq fastq 6977861604.0 27689927.0 E MTAB 11346:NG 10331 3CC lib138513 4828 1 0:126 1:126 A:1938593544;C:1560242508;G:1564690065;T:1913028128;N:1307359 126 126     1938593544 1560242508 1564690065 1913028128 1307359 ERX7625089 ERS10119349 ERA8439547 Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive 2 0.94226 0.9472 0.10354 0.10202 0.69911 0.69891 0.4749 0.47595 126 126 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Spain 2022-12-31 Larval Larval Whole Organism All anatomical structures
10382 10382 ERR8058367 ERX7625088 ERS10119348 ERP134902 PRJEB50332 RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine E-MTAB-11346 Transcriptome Analysis To determine the transcriptomic changes elicted by drugs of abuse zebrafish embryos were exposed to 10uM morphine from xxx hpf ttwo xxx hpf. Embryos were euthanized and deep frozen with N2l. RNA was extracted and an RNA seq assay was performed with Illumina Platform ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03   Protocols: At 72 hpf embryos were sacrificed by cold exposure incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs medium was removed and they were frozen in N2l. Tissue was stored at 80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented reverse transcrided using random hexamers three prime and five prime adapters were attached and library was amplified by PCR Cocaine 1 SAMEA12512744 Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain. ENA FIRST PUBLIC:2022 12 31|ENA LAST UPDATE:2022 12 31|External Id:SAMEA12512744|INSDC center alias:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca Spain.|INSDC center name:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca Spain.|INSDC first public:2022 12 31T00:57:45Z|INSDC last update:2022 12 31T00:57:45Z|INSDC status:public|Submitter Id:E MTAB 11346:Cocaine 1|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|developmental stage:72|genotype:wild type genotype|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11346:Cocaine 1|strain:AB                 Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine E MTAB 11346:Cocaine 1 p Cocaine 1 p RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine At 72 hpf embryos were sacrificed by cold exposure incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs medium was removed and they were frozen in N2l. Tissue was stored at 80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented reverse transcrided using random hexamers three prime and five prime adapters were attached and library was amplified by PCR Experimental Factor: compound:cocaine|Experimental Factor: dose:15 RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   ERP134902 Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03 NG-10331_2CC_lib138510_4790_5_1.fastq.gz NG-10331_2CC_lib138510_4790_5_2.fastq.gz fastq fastq 13608728532.0 54002891.0 E MTAB 11346:NG 10331 2CC lib138510 4790 5 0:126 1:126 A:3713185950;C:3097562409;G:3088976816;T:3707538756;N:1464601 126 126     3713185950 3097562409 3088976816 3707538756 1464601 ERX7625088 ERS10119348 ERA8439547 Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive 2 0.93921 0.94011 0.104 0.10075 0.68043 0.68523 0.44482 0.4591 126 126 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Spain 2022-12-31 Larval Larval Whole Organism All anatomical structures
11238 11238 ERR10782555 ERX10233132 ERS14439197 ERP144048 PRJEB58983 RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling E-MTAB-12503 Transcriptome Analysis Defects in blood development are a major contributor to complex congenital anomalies. Thrombocytopenia Absent Radius TAR Syndrome is a rare congenital disease presenting with reduced blood platelets megakaryocytic thrombocytopenia and forelimb anomalies concurrent with variable heart and kidney defects caused by hypomorphic RBM8A/Y14 gene function. RBM8A encodes a component of the ubiquitous exon junction complex involved in mRNA splicing transport and nonsense mediated decay. How perturbing a general mRNA processing factor causes the distinct phenotypes of TAR Syndrome remains unknown. Here we connect zebrafish rbm8a perturbation to early hematopoiesis defects via attenuated planar cell polarity PCP signaling involved in controlling developmental cell arrangements. Combining different genetic means to reduce rbm8a function we find a significant reduction of cd41 positive thrombocytes in hypomorphic rbm8a larvae. Transcriptomics analysis documents rbm8a mutant zebrafish embryos already post gastrulation accumulate mRNAs with erroneously included introns a hallmark of defective nonsense mediated decay. Affected mRNAs include transcripts encoding components of the non canonical Wnt pathway involved in PCP signaling and rbm8a mutant embryos show hallmarks of Wnt/PCP dependent early convergent extension defects. We establish that reduced rbm8a function synergizes with perturbations in Wnt/PCP pathway genes including wnt5b wnt11f2 fzd7a and vangl2. Following axis formation rbm8a perturbation impairs the migration and architecture of the lateral plate mesoderm LPM that forms the hematopoietic cardiovascular kidney and forelimb skeleton progenitors. Subsequently rbm8a perturbation impairs expression of early hematopoietic/endothelial genes including runx1a kdrl sox7 and the megakaryocyte regulator gfi1aa. Lastly we document similar hematopoietic defects upon loss of vangl2. Together our data link reduced rbm8a function to LPM migration and hematopoietic defects via attenuated Wnt/PCP signaling. Our… ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31   Protocols: Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined pooled embryos by Trizol LS extraction as per manufacturer’s guidelines Invitrogen with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina. Sample 6 E MTAB 12503:Sample 6   strain:mixed AB and Tubingen|ENA FIRST PUBLIC:2023 03 31|individual:20170530.A 6|organism:Danio rerio|organism:Danio rerio|ENA LAST UPDATE:2023 03 31|scientific name:Danio rerio|common name:zebrafish|organism part:embryo|age:10|developmental stage:bud|genotype:wild type genotype|ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31                 Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling E MTAB 12503:Sample 6 p Sample 6 p RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined pooled embryos by Trizol LS extraction as per manufacturer’s guidelines Invitrogen with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina. Experimental Factor: developmental stage:bud|Experimental Factor: genotype:wild type genotype RNA-Seq TRANSCRIPTOMIC SINGLE CELL RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   ERP144048 Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31 20170530.A-6_R1.fastq.gz 20170530.A-6_R2.fastq.gz fastq fastq 14809693138.0 49038719.0 E MTAB 12503:20170530.A 6 R 0:151 1:151 A:4069749497;C:3367864217;G:3430269434;T:3928390721;N:13419269 151 151     4069749497 3367864217 3430269434 3928390721 13419269 ERX10233132 ERS14439197 ERA20162442 University of Zurich|European Nucleotide Archive University of Zurich|European Nucleotide Archive 2 0.83945 0.69977 0.27269 0.22488 0.74523 0.77654 0.4899 0.4358 151 151 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq sc unknown unknown   Switzerland 2023-03-31 Multi-stage Embryo Whole Organism All anatomical structures
11239 11239 ERR10782554 ERX10233131 ERS14439196 ERP144048 PRJEB58983 RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling E-MTAB-12503 Transcriptome Analysis Defects in blood development are a major contributor to complex congenital anomalies. Thrombocytopenia Absent Radius TAR Syndrome is a rare congenital disease presenting with reduced blood platelets megakaryocytic thrombocytopenia and forelimb anomalies concurrent with variable heart and kidney defects caused by hypomorphic RBM8A/Y14 gene function. RBM8A encodes a component of the ubiquitous exon junction complex involved in mRNA splicing transport and nonsense mediated decay. How perturbing a general mRNA processing factor causes the distinct phenotypes of TAR Syndrome remains unknown. Here we connect zebrafish rbm8a perturbation to early hematopoiesis defects via attenuated planar cell polarity PCP signaling involved in controlling developmental cell arrangements. Combining different genetic means to reduce rbm8a function we find a significant reduction of cd41 positive thrombocytes in hypomorphic rbm8a larvae. Transcriptomics analysis documents rbm8a mutant zebrafish embryos already post gastrulation accumulate mRNAs with erroneously included introns a hallmark of defective nonsense mediated decay. Affected mRNAs include transcripts encoding components of the non canonical Wnt pathway involved in PCP signaling and rbm8a mutant embryos show hallmarks of Wnt/PCP dependent early convergent extension defects. We establish that reduced rbm8a function synergizes with perturbations in Wnt/PCP pathway genes including wnt5b wnt11f2 fzd7a and vangl2. Following axis formation rbm8a perturbation impairs the migration and architecture of the lateral plate mesoderm LPM that forms the hematopoietic cardiovascular kidney and forelimb skeleton progenitors. Subsequently rbm8a perturbation impairs expression of early hematopoietic/endothelial genes including runx1a kdrl sox7 and the megakaryocyte regulator gfi1aa. Lastly we document similar hematopoietic defects upon loss of vangl2. Together our data link reduced rbm8a function to LPM migration and hematopoietic defects via attenuated Wnt/PCP signaling. Our… ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31   Protocols: Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined pooled embryos by Trizol LS extraction as per manufacturer’s guidelines Invitrogen with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina. Sample 5 E MTAB 12503:Sample 5   strain:mixed AB and Tubingen|ENA FIRST PUBLIC:2023 03 31|individual:20170530.A 5|organism:Danio rerio|organism:Danio rerio|ENA LAST UPDATE:2023 03 31|scientific name:Danio rerio|common name:zebrafish|organism part:embryo|age:10|developmental stage:bud|genotype:wild type genotype|ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31                 Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling E MTAB 12503:Sample 5 p Sample 5 p RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined pooled embryos by Trizol LS extraction as per manufacturer’s guidelines Invitrogen with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina. Experimental Factor: developmental stage:bud|Experimental Factor: genotype:wild type genotype RNA-Seq TRANSCRIPTOMIC SINGLE CELL RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   ERP144048 Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31 20170530.A-5_R1.fastq.gz 20170530.A-5_R2.fastq.gz fastq fastq 14954968728.0 49519764.0 E MTAB 12503:20170530.A 5 R 0:151 1:151 A:4063340262;C:3440933120;G:3455723079;T:3981396987;N:13575280 151 151     4063340262 3440933120 3455723079 3981396987 13575280 ERX10233131 ERS14439196 ERA20162442 University of Zurich|European Nucleotide Archive University of Zurich|European Nucleotide Archive 2 0.85891 0.86859 0.28842 0.28866 0.7349 0.75051 0.45532 0.49145 151 151 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq sc unknown unknown   Switzerland 2023-03-31 Multi-stage Embryo Whole Organism All anatomical structures
11240 11240 ERR10782553 ERX10233130 ERS14439195 ERP144048 PRJEB58983 RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling E-MTAB-12503 Transcriptome Analysis Defects in blood development are a major contributor to complex congenital anomalies. Thrombocytopenia Absent Radius TAR Syndrome is a rare congenital disease presenting with reduced blood platelets megakaryocytic thrombocytopenia and forelimb anomalies concurrent with variable heart and kidney defects caused by hypomorphic RBM8A/Y14 gene function. RBM8A encodes a component of the ubiquitous exon junction complex involved in mRNA splicing transport and nonsense mediated decay. How perturbing a general mRNA processing factor causes the distinct phenotypes of TAR Syndrome remains unknown. Here we connect zebrafish rbm8a perturbation to early hematopoiesis defects via attenuated planar cell polarity PCP signaling involved in controlling developmental cell arrangements. Combining different genetic means to reduce rbm8a function we find a significant reduction of cd41 positive thrombocytes in hypomorphic rbm8a larvae. Transcriptomics analysis documents rbm8a mutant zebrafish embryos already post gastrulation accumulate mRNAs with erroneously included introns a hallmark of defective nonsense mediated decay. Affected mRNAs include transcripts encoding components of the non canonical Wnt pathway involved in PCP signaling and rbm8a mutant embryos show hallmarks of Wnt/PCP dependent early convergent extension defects. We establish that reduced rbm8a function synergizes with perturbations in Wnt/PCP pathway genes including wnt5b wnt11f2 fzd7a and vangl2. Following axis formation rbm8a perturbation impairs the migration and architecture of the lateral plate mesoderm LPM that forms the hematopoietic cardiovascular kidney and forelimb skeleton progenitors. Subsequently rbm8a perturbation impairs expression of early hematopoietic/endothelial genes including runx1a kdrl sox7 and the megakaryocyte regulator gfi1aa. Lastly we document similar hematopoietic defects upon loss of vangl2. Together our data link reduced rbm8a function to LPM migration and hematopoietic defects via attenuated Wnt/PCP signaling. Our… ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31   Protocols: Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined pooled embryos by Trizol LS extraction as per manufacturer’s guidelines Invitrogen with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina. Sample 2 E MTAB 12503:Sample 2   strain:mixed AB and Tubingen|ENA FIRST PUBLIC:2023 03 31|individual:20170530.A 2|organism:Danio rerio|organism:Danio rerio|ENA LAST UPDATE:2023 03 31|scientific name:Danio rerio|common name:zebrafish|organism part:embryo|age:24|developmental stage:pharyngula prim 5|genotype:wild type genotype|ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31                 Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling E MTAB 12503:Sample 2 p Sample 2 p RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined pooled embryos by Trizol LS extraction as per manufacturer’s guidelines Invitrogen with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina. Experimental Factor: developmental stage:pharyngula prim 5|Experimental Factor: genotype:wild type genotype RNA-Seq TRANSCRIPTOMIC SINGLE CELL RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   ERP144048 Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31 20170530.A-2_R1.fastq.gz 20170530.A-2_R2.fastq.gz fastq fastq 16267571562.0 53866131.0 E MTAB 12503:20170530.A 2 R 0:151 1:151 A:4395815325;C:3765428574;G:3780844712;T:4310729283;N:14753668 151 151     4395815325 3765428574 3780844712 4310729283 14753668 ERX10233130 ERS14439195 ERA20162442 University of Zurich|European Nucleotide Archive University of Zurich|European Nucleotide Archive 2 0.86977 0.8727 0.28497 0.28427 0.70763 0.72301 0.47478 0.47986 151 151 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq sc unknown unknown   Switzerland 2023-03-31 Pharyngula Embryo Whole Organism All anatomical structures
11241 11241 ERR10782552 ERX10233129 ERS14439194 ERP144048 PRJEB58983 RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling E-MTAB-12503 Transcriptome Analysis Defects in blood development are a major contributor to complex congenital anomalies. Thrombocytopenia Absent Radius TAR Syndrome is a rare congenital disease presenting with reduced blood platelets megakaryocytic thrombocytopenia and forelimb anomalies concurrent with variable heart and kidney defects caused by hypomorphic RBM8A/Y14 gene function. RBM8A encodes a component of the ubiquitous exon junction complex involved in mRNA splicing transport and nonsense mediated decay. How perturbing a general mRNA processing factor causes the distinct phenotypes of TAR Syndrome remains unknown. Here we connect zebrafish rbm8a perturbation to early hematopoiesis defects via attenuated planar cell polarity PCP signaling involved in controlling developmental cell arrangements. Combining different genetic means to reduce rbm8a function we find a significant reduction of cd41 positive thrombocytes in hypomorphic rbm8a larvae. Transcriptomics analysis documents rbm8a mutant zebrafish embryos already post gastrulation accumulate mRNAs with erroneously included introns a hallmark of defective nonsense mediated decay. Affected mRNAs include transcripts encoding components of the non canonical Wnt pathway involved in PCP signaling and rbm8a mutant embryos show hallmarks of Wnt/PCP dependent early convergent extension defects. We establish that reduced rbm8a function synergizes with perturbations in Wnt/PCP pathway genes including wnt5b wnt11f2 fzd7a and vangl2. Following axis formation rbm8a perturbation impairs the migration and architecture of the lateral plate mesoderm LPM that forms the hematopoietic cardiovascular kidney and forelimb skeleton progenitors. Subsequently rbm8a perturbation impairs expression of early hematopoietic/endothelial genes including runx1a kdrl sox7 and the megakaryocyte regulator gfi1aa. Lastly we document similar hematopoietic defects upon loss of vangl2. Together our data link reduced rbm8a function to LPM migration and hematopoietic defects via attenuated Wnt/PCP signaling. Our… ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31   Protocols: Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined pooled embryos by Trizol LS extraction as per manufacturer’s guidelines Invitrogen with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina. Sample 1 E MTAB 12503:Sample 1   strain:mixed AB and Tubingen|ENA FIRST PUBLIC:2023 03 31|individual:20170530.A 1|organism:Danio rerio|organism:Danio rerio|ENA LAST UPDATE:2023 03 31|scientific name:Danio rerio|common name:zebrafish|organism part:embryo|age:24|developmental stage:pharyngula prim 5|genotype:wild type genotype|ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31                 Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling E MTAB 12503:Sample 1 p Sample 1 p RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined pooled embryos by Trizol LS extraction as per manufacturer’s guidelines Invitrogen with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina. Experimental Factor: developmental stage:pharyngula prim 5|Experimental Factor: genotype:wild type genotype RNA-Seq TRANSCRIPTOMIC SINGLE CELL RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   ERP144048 Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31 20170530.A-1_R1.fastq.gz 20170530.A-1_R2.fastq.gz fastq fastq 15446599662.0 51147681.0 E MTAB 12503:20170530.A 1 R 0:151 1:151 A:4289931639;C:3451135010;G:3474244788;T:4217248893;N:14039332 151 151     4289931639 3451135010 3474244788 4217248893 14039332 ERX10233129 ERS14439194 ERA20162442 University of Zurich|European Nucleotide Archive University of Zurich|European Nucleotide Archive 2 0.90114 0.90507 0.32128 0.32127 0.70232 0.71956 0.47336 0.47528 151 151 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq sc unknown unknown   Switzerland 2023-03-31 Pharyngula Embryo Whole Organism All anatomical structures
11242 11242 ERR10782551 ERX10233128 ERS14439193 ERP144048 PRJEB58983 RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling E-MTAB-12503 Transcriptome Analysis Defects in blood development are a major contributor to complex congenital anomalies. Thrombocytopenia Absent Radius TAR Syndrome is a rare congenital disease presenting with reduced blood platelets megakaryocytic thrombocytopenia and forelimb anomalies concurrent with variable heart and kidney defects caused by hypomorphic RBM8A/Y14 gene function. RBM8A encodes a component of the ubiquitous exon junction complex involved in mRNA splicing transport and nonsense mediated decay. How perturbing a general mRNA processing factor causes the distinct phenotypes of TAR Syndrome remains unknown. Here we connect zebrafish rbm8a perturbation to early hematopoiesis defects via attenuated planar cell polarity PCP signaling involved in controlling developmental cell arrangements. Combining different genetic means to reduce rbm8a function we find a significant reduction of cd41 positive thrombocytes in hypomorphic rbm8a larvae. Transcriptomics analysis documents rbm8a mutant zebrafish embryos already post gastrulation accumulate mRNAs with erroneously included introns a hallmark of defective nonsense mediated decay. Affected mRNAs include transcripts encoding components of the non canonical Wnt pathway involved in PCP signaling and rbm8a mutant embryos show hallmarks of Wnt/PCP dependent early convergent extension defects. We establish that reduced rbm8a function synergizes with perturbations in Wnt/PCP pathway genes including wnt5b wnt11f2 fzd7a and vangl2. Following axis formation rbm8a perturbation impairs the migration and architecture of the lateral plate mesoderm LPM that forms the hematopoietic cardiovascular kidney and forelimb skeleton progenitors. Subsequently rbm8a perturbation impairs expression of early hematopoietic/endothelial genes including runx1a kdrl sox7 and the megakaryocyte regulator gfi1aa. Lastly we document similar hematopoietic defects upon loss of vangl2. Together our data link reduced rbm8a function to LPM migration and hematopoietic defects via attenuated Wnt/PCP signaling. Our… ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31   Protocols: Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined pooled embryos by Trizol LS extraction as per manufacturer’s guidelines Invitrogen with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina. Sample 7 E MTAB 12503:Sample 7   strain:mixed AB and Tubingen|ENA FIRST PUBLIC:2023 03 31|individual:20170530.A 7|organism:Danio rerio|organism:Danio rerio|ENA LAST UPDATE:2023 03 31|scientific name:Danio rerio|common name:zebrafish|organism part:embryo|age:10|developmental stage:bud|genotype:rbm8a d5/d5|ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31                 Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling E MTAB 12503:Sample 7 p Sample 7 p RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined pooled embryos by Trizol LS extraction as per manufacturer’s guidelines Invitrogen with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina. Experimental Factor: developmental stage:bud|Experimental Factor: genotype:rbm8a d5/d5 RNA-Seq TRANSCRIPTOMIC SINGLE CELL RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   ERP144048 Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31 20170530.A-7_R1.fastq.gz 20170530.A-7_R2.fastq.gz fastq fastq 12726557236.0 42140918.0 E MTAB 12503:20170530.A 7 R 0:151 1:151 A:3510176970;C:2879679978;G:2932244172;T:3392911734;N:11544382 151 151     3510176970 2879679978 2932244172 3392911734 11544382 ERX10233128 ERS14439193 ERA20162442 University of Zurich|European Nucleotide Archive University of Zurich|European Nucleotide Archive 2 0.88531 0.88678 0.33279 0.3329 0.73545 0.74992 0.52548 0.52864 151 151 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq sc unknown unknown   Switzerland 2023-03-31 Multi-stage Embryo Whole Organism All anatomical structures
11243 11243 ERR10782550 ERX10233127 ERS14439192 ERP144048 PRJEB58983 RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling E-MTAB-12503 Transcriptome Analysis Defects in blood development are a major contributor to complex congenital anomalies. Thrombocytopenia Absent Radius TAR Syndrome is a rare congenital disease presenting with reduced blood platelets megakaryocytic thrombocytopenia and forelimb anomalies concurrent with variable heart and kidney defects caused by hypomorphic RBM8A/Y14 gene function. RBM8A encodes a component of the ubiquitous exon junction complex involved in mRNA splicing transport and nonsense mediated decay. How perturbing a general mRNA processing factor causes the distinct phenotypes of TAR Syndrome remains unknown. Here we connect zebrafish rbm8a perturbation to early hematopoiesis defects via attenuated planar cell polarity PCP signaling involved in controlling developmental cell arrangements. Combining different genetic means to reduce rbm8a function we find a significant reduction of cd41 positive thrombocytes in hypomorphic rbm8a larvae. Transcriptomics analysis documents rbm8a mutant zebrafish embryos already post gastrulation accumulate mRNAs with erroneously included introns a hallmark of defective nonsense mediated decay. Affected mRNAs include transcripts encoding components of the non canonical Wnt pathway involved in PCP signaling and rbm8a mutant embryos show hallmarks of Wnt/PCP dependent early convergent extension defects. We establish that reduced rbm8a function synergizes with perturbations in Wnt/PCP pathway genes including wnt5b wnt11f2 fzd7a and vangl2. Following axis formation rbm8a perturbation impairs the migration and architecture of the lateral plate mesoderm LPM that forms the hematopoietic cardiovascular kidney and forelimb skeleton progenitors. Subsequently rbm8a perturbation impairs expression of early hematopoietic/endothelial genes including runx1a kdrl sox7 and the megakaryocyte regulator gfi1aa. Lastly we document similar hematopoietic defects upon loss of vangl2. Together our data link reduced rbm8a function to LPM migration and hematopoietic defects via attenuated Wnt/PCP signaling. Our… ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31   Protocols: Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined pooled embryos by Trizol LS extraction as per manufacturer’s guidelines Invitrogen with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina. Sample 4 E MTAB 12503:Sample 4   strain:mixed AB and Tubingen|ENA FIRST PUBLIC:2023 03 31|individual:20170530.A 4|organism:Danio rerio|organism:Danio rerio|ENA LAST UPDATE:2023 03 31|scientific name:Danio rerio|common name:zebrafish|organism part:embryo|age:24|developmental stage:pharyngula prim 5|genotype:rbm8a d5/d5|ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31                 Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling E MTAB 12503:Sample 4 p Sample 4 p RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined pooled embryos by Trizol LS extraction as per manufacturer’s guidelines Invitrogen with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina. Experimental Factor: developmental stage:pharyngula prim 5|Experimental Factor: genotype:rbm8a d5/d5 RNA-Seq TRANSCRIPTOMIC SINGLE CELL RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   ERP144048 Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31 20170530.A-4_R1.fastq.gz 20170530.A-4_R2.fastq.gz fastq fastq 15697575554.0 51978727.0 E MTAB 12503:20170530.A 4 R 0:151 1:151 A:4256444510;C:3622485921;G:3650190489;T:4154211501;N:14243133 151 151     4256444510 3622485921 3650190489 4154211501 14243133 ERX10233127 ERS14439192 ERA20162442 University of Zurich|European Nucleotide Archive University of Zurich|European Nucleotide Archive 2 0.87714 0.88071 0.29319 0.29235 0.69844 0.7164 0.47594 0.47385 151 151 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq sc unknown unknown   Switzerland 2023-03-31 Pharyngula Embryo Whole Organism All anatomical structures
11244 11244 ERR10782549 ERX10233126 ERS14439191 ERP144048 PRJEB58983 RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling E-MTAB-12503 Transcriptome Analysis Defects in blood development are a major contributor to complex congenital anomalies. Thrombocytopenia Absent Radius TAR Syndrome is a rare congenital disease presenting with reduced blood platelets megakaryocytic thrombocytopenia and forelimb anomalies concurrent with variable heart and kidney defects caused by hypomorphic RBM8A/Y14 gene function. RBM8A encodes a component of the ubiquitous exon junction complex involved in mRNA splicing transport and nonsense mediated decay. How perturbing a general mRNA processing factor causes the distinct phenotypes of TAR Syndrome remains unknown. Here we connect zebrafish rbm8a perturbation to early hematopoiesis defects via attenuated planar cell polarity PCP signaling involved in controlling developmental cell arrangements. Combining different genetic means to reduce rbm8a function we find a significant reduction of cd41 positive thrombocytes in hypomorphic rbm8a larvae. Transcriptomics analysis documents rbm8a mutant zebrafish embryos already post gastrulation accumulate mRNAs with erroneously included introns a hallmark of defective nonsense mediated decay. Affected mRNAs include transcripts encoding components of the non canonical Wnt pathway involved in PCP signaling and rbm8a mutant embryos show hallmarks of Wnt/PCP dependent early convergent extension defects. We establish that reduced rbm8a function synergizes with perturbations in Wnt/PCP pathway genes including wnt5b wnt11f2 fzd7a and vangl2. Following axis formation rbm8a perturbation impairs the migration and architecture of the lateral plate mesoderm LPM that forms the hematopoietic cardiovascular kidney and forelimb skeleton progenitors. Subsequently rbm8a perturbation impairs expression of early hematopoietic/endothelial genes including runx1a kdrl sox7 and the megakaryocyte regulator gfi1aa. Lastly we document similar hematopoietic defects upon loss of vangl2. Together our data link reduced rbm8a function to LPM migration and hematopoietic defects via attenuated Wnt/PCP signaling. Our… ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31   Protocols: Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined pooled embryos by Trizol LS extraction as per manufacturer’s guidelines Invitrogen with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina. Sample 3 E MTAB 12503:Sample 3   strain:mixed AB and Tubingen|ENA FIRST PUBLIC:2023 03 31|individual:20170530.A 3|organism:Danio rerio|organism:Danio rerio|ENA LAST UPDATE:2023 03 31|scientific name:Danio rerio|common name:zebrafish|organism part:embryo|age:24|developmental stage:pharyngula prim 5|genotype:rbm8a d5/d5|ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31                 Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling E MTAB 12503:Sample 3 p Sample 3 p RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined pooled embryos by Trizol LS extraction as per manufacturer’s guidelines Invitrogen with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina. Experimental Factor: developmental stage:pharyngula prim 5|Experimental Factor: genotype:rbm8a d5/d5 RNA-Seq TRANSCRIPTOMIC SINGLE CELL RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   ERP144048 Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31 20170530.A-3_R1.fastq.gz 20170530.A-3_R2.fastq.gz fastq fastq 13839085674.0 45824787.0 E MTAB 12503:20170530.A 3 R 0:151 1:151 A:3812423011;C:3120168590;G:3163957945;T:3729983766;N:12552362 151 151     3812423011 3120168590 3163957945 3729983766 12552362 ERX10233126 ERS14439191 ERA20162442 University of Zurich|European Nucleotide Archive University of Zurich|European Nucleotide Archive 2 0.88987 0.74432 0.33651 0.27875 0.69229 0.72934 0.46981 0.46116 151 151 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq sc unknown unknown   Switzerland 2023-03-31 Pharyngula Embryo Whole Organism All anatomical structures
11747 11747 ERR11608177 ERX11010308 ERS15939662 ERP148707 PRJEB63561 RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors E-MTAB-13116 Transcriptome Analysis Transcriptomic differences of gata1+ erythrocytes between the kdm4b / mutants and the WT embryos at 48 hpf were analyzed by RNA sequencing. ENA FIRST PUBLIC:2024 07 01|ENA LAST UPDATE:2024 07 01   Protocols: The 48 hpf gata1+ erythrocytes were sorted FACSAria BD Bioscience CA USA Two independent groups of RNA from wt and kdm4b / erythrocytes were extracted using TRIzol® Reagent Life Technologies each group contains three biological repeats. post adenylation of three prime ends of double strand cDNA fragments Adaptor with hairpin loop structure were ligated to prepare for hybridization. The library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then PCR was performed with Phusion High Fidelity DNA polymerase. At last PCR products were purified and the library quality was assessed on the Agilent Bioanalyzer 2100 system. MU2 SAMEA113945412 Shanghai Institute of Nutrition and Diseases, Chinese Academy of Sciences ENA first public:2024 07 01|External Id:SAMEA113945412|INSDC center name:Shanghai Institute of Nutrition and Diseases Chinese Academy of Sciences|INSDC last update:2023 06 27T11:19:32Z|INSDC status:public|Submitter Id:E MTAB 13116:MU2|age:48|broker name:ArrayExpress|cell type:erythrocyte|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|disease:normal|genotype:kdm4b / |genotype:wild type genotype|geographic location country and/or sea:not collected|immunophenotype:gata1 positive|individual:mixed pool of 200 individuals|isolate:not applicable|organism part:embryo|sample name:E MTAB 13116:MU2|scientific name:Danio rerio|sex:mixed|strain:Tubingen                 RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors E MTAB 13116:MU2 p MU2 p RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors The 48 hpf gata1+ erythrocytes were sorted FACSAria BD Bioscience CA USA Two independent groups of RNA from wt and kdm4b / erythrocytes were extracted using TRIzol® Reagent Life Technologies each group contains three biological repeats. post adenylation of three prime ends of double strand cDNA fragments Adaptor with hairpin loop structure were ligated to prepare for hybridization. The library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then PCR was performed with Phusion High Fidelity DNA polymerase. At last PCR products were purified and the library quality was assessed on the Agilent Bioanalyzer 2100 system.   RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   ERP148707 Illumina NovaSeq 6000 paired end sequencing; RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors ENA FIRST PUBLIC:2024 07 01|ENA LAST UPDATE:2024 07 01 MU2_R1.fastq.gz MU2_R2.fastq.gz fastq fastq 8373912900.0 27913043.0 E MTAB 13116:MU2 R 0:150 1:150 A:2149105370;C:2028251580;G:2055193482;T:2141168979;N:193489 150 150     2149105370 2028251580 2055193482 2141168979 193489 ERX11010308 ERS15939662 ERA24542523 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive                       B B biological fallback assumption illumina novaseq_era 3prime random_priming unknown bulk unknown unknown   United Kingdom 2023-06-27 Hatching Embryo Whole Organism All anatomical structures
11748 11748 ERR11608179 ERX11010310 ERS15939664 ERP148707 PRJEB63561 RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors E-MTAB-13116 Transcriptome Analysis Transcriptomic differences of gata1+ erythrocytes between the kdm4b / mutants and the WT embryos at 48 hpf were analyzed by RNA sequencing. ENA FIRST PUBLIC:2024 07 01|ENA LAST UPDATE:2024 07 01   Protocols: The 48 hpf gata1+ erythrocytes were sorted FACSAria BD Bioscience CA USA Two independent groups of RNA from wt and kdm4b / erythrocytes were extracted using TRIzol® Reagent Life Technologies each group contains three biological repeats. post adenylation of three prime ends of double strand cDNA fragments Adaptor with hairpin loop structure were ligated to prepare for hybridization. The library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then PCR was performed with Phusion High Fidelity DNA polymerase. At last PCR products were purified and the library quality was assessed on the Agilent Bioanalyzer 2100 system. WT1 SAMEA113945414 Shanghai Institute of Nutrition and Diseases, Chinese Academy of Sciences ENA first public:2024 07 01|External Id:SAMEA113945414|INSDC center name:Shanghai Institute of Nutrition and Diseases Chinese Academy of Sciences|INSDC last update:2023 06 27T11:19:32Z|INSDC status:public|Submitter Id:E MTAB 13116:WT1|age:48|broker name:ArrayExpress|cell type:erythrocyte|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|disease:normal|genotype:wild type genotype|geographic location country and/or sea:not collected|immunophenotype:gata1 positive|individual:mixed pool of 200 individuals|isolate:not applicable|organism part:embryo|sample name:E MTAB 13116:WT1|scientific name:Danio rerio|sex:mixed|strain:Tubingen                 RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors E MTAB 13116:WT1 p WT1 p RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors The 48 hpf gata1+ erythrocytes were sorted FACSAria BD Bioscience CA USA Two independent groups of RNA from wt and kdm4b / erythrocytes were extracted using TRIzol® Reagent Life Technologies each group contains three biological repeats. post adenylation of three prime ends of double strand cDNA fragments Adaptor with hairpin loop structure were ligated to prepare for hybridization. The library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then PCR was performed with Phusion High Fidelity DNA polymerase. At last PCR products were purified and the library quality was assessed on the Agilent Bioanalyzer 2100 system.   RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   ERP148707 Illumina NovaSeq 6000 paired end sequencing; RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors ENA FIRST PUBLIC:2024 07 01|ENA LAST UPDATE:2024 07 01 WT1_R1.fastq.gz WT1_R2.fastq.gz fastq fastq 6729388500.0 22431295.0 E MTAB 13116:WT1 R 0:150 1:150 A:1730015872;C:1621295817;G:1657133586;T:1720858352;N:84873 150 150     1730015872 1621295817 1657133586 1720858352 84873 ERX11010310 ERS15939664 ERA24542523 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive                       B B biological fallback assumption illumina novaseq_era 3prime random_priming unknown bulk unknown unknown   United Kingdom 2023-06-27 Hatching Embryo Whole Organism All anatomical structures
11749 11749 ERR11608176 ERX11010307 ERS15939661 ERP148707 PRJEB63561 RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors E-MTAB-13116 Transcriptome Analysis Transcriptomic differences of gata1+ erythrocytes between the kdm4b / mutants and the WT embryos at 48 hpf were analyzed by RNA sequencing. ENA FIRST PUBLIC:2024 07 01|ENA LAST UPDATE:2024 07 01   Protocols: The 48 hpf gata1+ erythrocytes were sorted FACSAria BD Bioscience CA USA Two independent groups of RNA from wt and kdm4b / erythrocytes were extracted using TRIzol® Reagent Life Technologies each group contains three biological repeats. post adenylation of three prime ends of double strand cDNA fragments Adaptor with hairpin loop structure were ligated to prepare for hybridization. The library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then PCR was performed with Phusion High Fidelity DNA polymerase. At last PCR products were purified and the library quality was assessed on the Agilent Bioanalyzer 2100 system. MU1 SAMEA113945411 Shanghai Institute of Nutrition and Diseases, Chinese Academy of Sciences ENA first public:2024 07 01|External Id:SAMEA113945411|INSDC center name:Shanghai Institute of Nutrition and Diseases Chinese Academy of Sciences|INSDC last update:2023 06 27T11:19:32Z|INSDC status:public|Submitter Id:E MTAB 13116:MU1|age:48|broker name:ArrayExpress|cell type:erythrocyte|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|disease:normal|genotype:kdm4b / |genotype:wild type genotype|geographic location country and/or sea:not collected|immunophenotype:gata1 positive|individual:mixed pool of 200 individuals|isolate:not applicable|organism part:embryo|sample name:E MTAB 13116:MU1|scientific name:Danio rerio|sex:mixed|strain:Tubingen                 RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors E MTAB 13116:MU1 p MU1 p RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors The 48 hpf gata1+ erythrocytes were sorted FACSAria BD Bioscience CA USA Two independent groups of RNA from wt and kdm4b / erythrocytes were extracted using TRIzol® Reagent Life Technologies each group contains three biological repeats. post adenylation of three prime ends of double strand cDNA fragments Adaptor with hairpin loop structure were ligated to prepare for hybridization. The library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then PCR was performed with Phusion High Fidelity DNA polymerase. At last PCR products were purified and the library quality was assessed on the Agilent Bioanalyzer 2100 system.   RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   ERP148707 Illumina NovaSeq 6000 paired end sequencing; RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors ENA FIRST PUBLIC:2024 07 01|ENA LAST UPDATE:2024 07 01 MU1_R1.fastq.gz MU1_R2.fastq.gz fastq fastq 7310352000.0 24367840.0 E MTAB 13116:MU1 R 0:150 1:150 A:1888660247;C:1748082353;G:1788562372;T:1884958596;N:88432 150 150     1888660247 1748082353 1788562372 1884958596 88432 ERX11010307 ERS15939661 ERA24542523 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive                       B B biological fallback assumption illumina novaseq_era 3prime random_priming unknown bulk unknown unknown   United Kingdom 2023-06-27 Hatching Embryo Whole Organism All anatomical structures
11750 11750 ERR11608178 ERX11010309 ERS15939663 ERP148707 PRJEB63561 RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors E-MTAB-13116 Transcriptome Analysis Transcriptomic differences of gata1+ erythrocytes between the kdm4b / mutants and the WT embryos at 48 hpf were analyzed by RNA sequencing. ENA FIRST PUBLIC:2024 07 01|ENA LAST UPDATE:2024 07 01   Protocols: The 48 hpf gata1+ erythrocytes were sorted FACSAria BD Bioscience CA USA Two independent groups of RNA from wt and kdm4b / erythrocytes were extracted using TRIzol® Reagent Life Technologies each group contains three biological repeats. post adenylation of three prime ends of double strand cDNA fragments Adaptor with hairpin loop structure were ligated to prepare for hybridization. The library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then PCR was performed with Phusion High Fidelity DNA polymerase. At last PCR products were purified and the library quality was assessed on the Agilent Bioanalyzer 2100 system. MU3 SAMEA113945413 Shanghai Institute of Nutrition and Diseases, Chinese Academy of Sciences ENA first public:2024 07 01|External Id:SAMEA113945413|INSDC center name:Shanghai Institute of Nutrition and Diseases Chinese Academy of Sciences|INSDC last update:2023 06 27T11:19:32Z|INSDC status:public|Submitter Id:E MTAB 13116:MU3|age:48|broker name:ArrayExpress|cell type:erythrocyte|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|disease:normal|genotype:kdm4b / |genotype:wild type genotype|geographic location country and/or sea:not collected|immunophenotype:gata1 positive|individual:mixed pool of 200 individuals|isolate:not applicable|organism part:embryo|sample name:E MTAB 13116:MU3|scientific name:Danio rerio|sex:mixed|strain:Tubingen                 RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors E MTAB 13116:MU3 p MU3 p RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors The 48 hpf gata1+ erythrocytes were sorted FACSAria BD Bioscience CA USA Two independent groups of RNA from wt and kdm4b / erythrocytes were extracted using TRIzol® Reagent Life Technologies each group contains three biological repeats. post adenylation of three prime ends of double strand cDNA fragments Adaptor with hairpin loop structure were ligated to prepare for hybridization. The library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then PCR was performed with Phusion High Fidelity DNA polymerase. At last PCR products were purified and the library quality was assessed on the Agilent Bioanalyzer 2100 system.   RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   ERP148707 Illumina NovaSeq 6000 paired end sequencing; RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors ENA FIRST PUBLIC:2024 07 01|ENA LAST UPDATE:2024 07 01 MU3_R1.fastq.gz MU3_R2.fastq.gz fastq fastq 8826207900.0 29420693.0 E MTAB 13116:MU3 R 0:150 1:150 A:2298326835;C:2100185951;G:2130807919;T:2296678033;N:209162 150 150     2298326835 2100185951 2130807919 2296678033 209162 ERX11010309 ERS15939663 ERA24542523 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive                       B B biological fallback assumption illumina novaseq_era 3prime random_priming unknown bulk unknown unknown   United Kingdom 2023-06-27 Hatching Embryo Whole Organism All anatomical structures
11751 11751 ERR11608180 ERX11010311 ERS15939665 ERP148707 PRJEB63561 RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors E-MTAB-13116 Transcriptome Analysis Transcriptomic differences of gata1+ erythrocytes between the kdm4b / mutants and the WT embryos at 48 hpf were analyzed by RNA sequencing. ENA FIRST PUBLIC:2024 07 01|ENA LAST UPDATE:2024 07 01   Protocols: The 48 hpf gata1+ erythrocytes were sorted FACSAria BD Bioscience CA USA Two independent groups of RNA from wt and kdm4b / erythrocytes were extracted using TRIzol® Reagent Life Technologies each group contains three biological repeats. post adenylation of three prime ends of double strand cDNA fragments Adaptor with hairpin loop structure were ligated to prepare for hybridization. The library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then PCR was performed with Phusion High Fidelity DNA polymerase. At last PCR products were purified and the library quality was assessed on the Agilent Bioanalyzer 2100 system. WT2 E MTAB 13116:WT2   strain:Tubingen|disease:normal|individual:mixed pool of 200 individuals|organism:Danio rerio|organism:Danio rerio|collection date:not collected|sex:mixed|scientific name:Danio rerio|common name:zebrafish|organism part:embryo|developmental stage:embryo stage|genotype:wild type genotype|isolate:not applicable|immunophenotype:gata1 positive|cell type:erythrocyte|age:48|geographic location country and/or sea:not collected|ENA LAST UPDATE:2023 06 27                 RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors E MTAB 13116:WT2 p WT2 p RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors The 48 hpf gata1+ erythrocytes were sorted FACSAria BD Bioscience CA USA Two independent groups of RNA from wt and kdm4b / erythrocytes were extracted using TRIzol® Reagent Life Technologies each group contains three biological repeats. post adenylation of three prime ends of double strand cDNA fragments Adaptor with hairpin loop structure were ligated to prepare for hybridization. The library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then PCR was performed with Phusion High Fidelity DNA polymerase. At last PCR products were purified and the library quality was assessed on the Agilent Bioanalyzer 2100 system.   RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   ERP148707 Illumina NovaSeq 6000 paired end sequencing; RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors ENA FIRST PUBLIC:2024 07 01|ENA LAST UPDATE:2024 07 01 WT2_R1.fastq.gz WT2_R2.fastq.gz fastq fastq 8368621500.0 27895405.0 E MTAB 13116:WT2 R 0:150 1:150 A:2126734187;C:2050458346;G:2078646608;T:2112586140;N:196219 150 150     2126734187 2050458346 2078646608 2112586140 196219 ERX11010311 ERS15939665 ERA24542523 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive                       B B biological fallback assumption illumina novaseq_era 3prime random_priming unknown bulk unknown unknown   United Kingdom 2023-06-27 Hatching Embryo Whole Organism All anatomical structures
11752 11752 ERR11608181 ERX11010312 ERS15939666 ERP148707 PRJEB63561 RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors E-MTAB-13116 Transcriptome Analysis Transcriptomic differences of gata1+ erythrocytes between the kdm4b / mutants and the WT embryos at 48 hpf were analyzed by RNA sequencing. ENA FIRST PUBLIC:2024 07 01|ENA LAST UPDATE:2024 07 01   Protocols: The 48 hpf gata1+ erythrocytes were sorted FACSAria BD Bioscience CA USA Two independent groups of RNA from wt and kdm4b / erythrocytes were extracted using TRIzol® Reagent Life Technologies each group contains three biological repeats. post adenylation of three prime ends of double strand cDNA fragments Adaptor with hairpin loop structure were ligated to prepare for hybridization. The library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then PCR was performed with Phusion High Fidelity DNA polymerase. At last PCR products were purified and the library quality was assessed on the Agilent Bioanalyzer 2100 system. WT3 E MTAB 13116:WT3   strain:Tubingen|disease:normal|individual:mixed pool of 200 individuals|organism:Danio rerio|organism:Danio rerio|collection date:not collected|sex:mixed|scientific name:Danio rerio|common name:zebrafish|organism part:embryo|developmental stage:embryo stage|genotype:wild type genotype|isolate:not applicable|immunophenotype:gata1 positive|cell type:erythrocyte|age:48|geographic location country and/or sea:not collected|ENA LAST UPDATE:2023 06 27                 RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors E MTAB 13116:WT3 p WT3 p RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors The 48 hpf gata1+ erythrocytes were sorted FACSAria BD Bioscience CA USA Two independent groups of RNA from wt and kdm4b / erythrocytes were extracted using TRIzol® Reagent Life Technologies each group contains three biological repeats. post adenylation of three prime ends of double strand cDNA fragments Adaptor with hairpin loop structure were ligated to prepare for hybridization. The library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then PCR was performed with Phusion High Fidelity DNA polymerase. At last PCR products were purified and the library quality was assessed on the Agilent Bioanalyzer 2100 system.   RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   ERP148707 Illumina NovaSeq 6000 paired end sequencing; RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors ENA FIRST PUBLIC:2024 07 01|ENA LAST UPDATE:2024 07 01 WT3_R1.fastq.gz WT3_R2.fastq.gz fastq fastq 8718445500.0 29061485.0 E MTAB 13116:WT3 R 0:150 1:150 A:2244668655;C:2103611849;G:2135345835;T:2234609621;N:209540 150 150     2244668655 2103611849 2135345835 2234609621 209540 ERX11010312 ERS15939666 ERA24542523 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive                       B B biological fallback assumption illumina novaseq_era 3prime random_priming unknown bulk unknown unknown   United Kingdom 2023-06-27 Hatching Embryo Whole Organism All anatomical structures
28383 28383 SRR26319642 SRX22027776 SRS19100884 SRP463771 PRJNA1022139 Danio rerio strain:AB Transcriptome or Gene expression PRJNA1022139 Other Effects and Mechanisms of Porphyromonas gingivalis Outer Membrane Vesicles Induced Cardiovascular Injury         WT 3   strain:AB|age:larvae|dev stage:48 hpi|collection date:2022 11 06|geo loc name:China:Fujian|sex:not applicable|tissue:Whole body|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio:PBS treated WT 3 WT 3 PBS treated     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   SRP463771     WT_3_1.fq.gz WT_3_2.fq.gz fastq fastq 6638052600.0 22126842.0 WT 3 1.fq.gz 0:150 1:150 A:1795389898;C:1548955123;G:1524873816;T:1768758791;N:74972 150 150     1795389898 1548955123 1524873816 1768758791 74972 SRX22027776 SRS19100884 SRA1727571 Hospital of Stomatology, Fujian Medical University|Department of Orthodontics Hospital of Stomatology, Fujian Medical University 2 0.94512 0.94441 0.0675 0.06744 0.69457 0.69353 0.47279 0.46651 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2023-10-11 Larval Larval Trunk Surface Structure
28384 28384 SRR26316552 SRX22024811 SRS19097993 SRP463771 PRJNA1022139 Danio rerio strain:AB Transcriptome or Gene expression PRJNA1022139 Other Effects and Mechanisms of Porphyromonas gingivalis Outer Membrane Vesicles Induced Cardiovascular Injury       WT 1 WT 1   strain:AB|age:larvae|dev stage:48 hpi|collection date:2022 11 06|geo loc name:China:Fujian|sex:not applicable|tissue:Whole body|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio:PBS treated WT 1 WT 1 PBS treated     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   SRP463771     WT_1_1.fq.gz WT_1_2.fq.gz fastq fastq 6806096700.0 22686989.0 WT 1 1.fq.gz 0:150 1:150 A:1824700900;C:1607509679;G:1583685250;T:1790098957;N:101914 150 150     1824700900 1607509679 1583685250 1790098957 101914 SRX22024811 SRS19097993 SRA1727466 Hospital of Stomatology, Fujian Medical University|Department of Orthodontics Hospital of Stomatology, Fujian Medical University 2 0.94441 0.94413 0.0633 0.06243 0.69589 0.69603 0.47278 0.46311 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2023-10-11 Larval Larval Trunk Surface Structure
28385 28385 SRR26298124 SRX22006623 SRS19081287 SRP463771 PRJNA1022139 Danio rerio strain:AB Transcriptome or Gene expression PRJNA1022139 Other Effects and Mechanisms of Porphyromonas gingivalis Outer Membrane Vesicles Induced Cardiovascular Injury       Pg OMVs 3 Pg OMVs 3   strain:AB|age:larvae|dev stage:48 hpi|collection date:2022 11 06|geo loc name:China:Fujian|sex:not applicable|tissue:whole body|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio:Pg OMVs treated Pg OMVs 3 Pg OMVs 3 Pg OMVs treated     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   SRP463771     Pgom_3_1.fq.gz Pgom_3_2.fq.gz fastq fastq 6799556700.0 22665189.0 Pgom 3 1.fq.gz 0:150 1:150 A:1841955583;C:1578686846;G:1566584129;T:1812024582;N:305560 150 150     1841955583 1578686846 1566584129 1812024582 305560 SRX22006623 SRS19081287 SRA1726653 Hospital of Stomatology, Fujian Medical University|Department of Orthodontics Hospital of Stomatology, Fujian Medical University 2 0.93679 0.93643 0.0705 0.07046 0.69522 0.69572 0.46657 0.46769 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2023-10-09 Larval Larval Trunk Surface Structure
28386 28386 SRR26284600 SRX21993532 SRS19068394 SRP463771 PRJNA1022139 Danio rerio strain:AB Transcriptome or Gene expression PRJNA1022139 Other Effects and Mechanisms of Porphyromonas gingivalis Outer Membrane Vesicles Induced Cardiovascular Injury       Pg OMVs 2 Pg OMVs 2   strain:AB|age:larvae|dev stage:48 hpi|collection date:2022 11 06|geo loc name:China:Fujian|sex:not applicable|tissue:whole body|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio:Pg OMVs treated Pg OMVs 2 Pg OMVs 2 Pg OMVs treated     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   SRP463771     Pgom_2_2.fq.gz Pgom_2_1.fq.gz fastq fastq 6873087300.0 22910291.0 Pgom 2 1.fq.gz 0:150 1:150 A:1852244290;C:1608380801;G:1593161224;T:1819219541;N:81444 150 150     1852244290 1608380801 1593161224 1819219541 81444 SRX21993532 SRS19068394 SRA1726180 Hospital of Stomatology, Fujian Medical University|Department of Orthodontics Hospital of Stomatology, Fujian Medical University 2 0.93991 0.93977 0.06917 0.06976 0.68883 0.68931 0.47575 0.45981 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2023-10-06 Larval Larval Trunk Surface Structure
28387 28387 SRR26283523 SRX21992473 SRS19067399 SRP463771 PRJNA1022139 Danio rerio strain:AB Transcriptome or Gene expression PRJNA1022139 Other Effects and Mechanisms of Porphyromonas gingivalis Outer Membrane Vesicles Induced Cardiovascular Injury         WT 2   strain:AB|age:larvae|dev stage:48 hpi|collection date:2022 11 06|geo loc name:China:Fujian|sex:not applicable|tissue:whole body|BioSampleModel:Model organism or animal                 not applicable not applicable not applicable wild type     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   SRP463771     WT_2_1.fq.gz WT_2_2.fq.gz fastq fastq 6662879700.0 22209599.0 WT 2 1.fq.gz 0:150 1:150 A:1793163738;C:1560948295;G:1543048656;T:1765563975;N:155036 150 150     1793163738 1560948295 1543048656 1765563975 155036 SRX21992473 SRS19067399 SRA1726064 Hospital of Stomatology, Fujian Medical University|Department of Orthodontics Hospital of Stomatology, Fujian Medical University 2 0.94479 0.94546 0.06315 0.06307 0.69751 0.69627 0.46332 0.45959 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2023-10-06 Larval Larval Trunk Surface Structure
28388 28388 SRR26213372 SRX21923899 SRS19008410 SRP463771 PRJNA1022139 Danio rerio strain:AB Transcriptome or Gene expression PRJNA1022139 Other Effects and Mechanisms of Porphyromonas gingivalis Outer Membrane Vesicles Induced Cardiovascular Injury       Model organism or animal sample from Danio rerio Pg OMVs 1 a   strain:AB|dev stage:larvae|collection date:2022 11 06|geo loc name:China:Fujian|sex:not applicable|tissue:whole body|treatment:Pg OMVs injected|BioSampleModel:Model organism or animal                 RNA seq of zebrafish:48 hpi Pg OMVs group1a Pg OMVs group1a Pg OMVs injected     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   SRP463771     Pgom_1_1.fq.gz Pgom_1_2.fq.gz fastq fastq 6768097800.0 22560326.0 Pgom 1 1.fq.gz 0:150 1:150 A:1807197563;C:1591333381;G:1591884474;T:1777600011;N:82371 150 150     1807197563 1591333381 1591884474 1777600011 82371 SRX21923899 SRS19008410 SRA1722765 Hospital of Stomatology, Fujian Medical University|Department of Orthodontics Hospital of Stomatology, Fujian Medical University 2 0.93975 0.93898 0.05827 0.05801 0.68521 0.68517 0.46882 0.46802 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2023-09-28 Larval Larval Trunk Surface Structure

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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");;