{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_layout = \"PAIRED\", experiment.library_selection = \"RANDOM\" and experiment.library_source = \"TRANSCRIPTOMIC\"", "rows": [[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.", null, null, "zebrafish 5 day DsRed positive enteric neural crest derived cells replicate 3", "zebrafish ENCDC replicate 3", "SAMD00529468", null, "sample name:zebrafish ENCDC replicate 3|biological replicate:enteric neural crest derived cells 3|strain:Tgsox10:cre; EF3alpha:loxP gfp loxP dsred", null, null, null, null, null, null, null, null, "NextSeq 550 paired end sequencing of SAMD00529468", "DRX393854", "190326ENvsNC N706 5day;NeuralCrestDerivedCell;rep3", "1", "1", null, "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", null, null, null, 3803721121.0, 24526633.0, "DRR408248", "0:77.54 1:77.54", "A:999106107;C:897663781;G:921501114;T:979486853;N:5963266", 77, 77, null, null, 999106107, 897663781, 921501114, 979486853, 5963266, "DRX393854", "DRS407179", "DRA014886", "NIBB|NIBB core research facilities, National Institute for Basic Biology", "University of Hyogo", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2024-09-22", "Undetermined", "Larval", "Brain", "Nervous System"], [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.", null, null, "zebrafish 5 day DsRed positive enteric neural crest derived cells replicate 2", "zebrafish ENCDC replicate 2", "SAMD00529467", null, "sample name:zebrafish ENCDC replicate 2|biological replicate:enteric neural crest derived cells 2|strain:Tgsox10:cre; EF2alpha:loxP gfp loxP dsred", null, null, null, null, null, null, null, null, "NextSeq 550 paired end sequencing of SAMD00529467", "DRX393853", "190326ENvsNC N705 5day;NeuralCrestDerivedCell;rep2", "1", "1", null, "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", null, null, null, 3436798274.0, 22156202.0, "DRR408247", "0:77.56 1:77.56", "A:900848174;C:812031426;G:832960423;T:885671203;N:5287048", 77, 77, null, null, 900848174, 812031426, 832960423, 885671203, 5287048, "DRX393853", "DRS407178", "DRA014886", "NIBB|NIBB core research facilities, National Institute for Basic Biology", "University of Hyogo", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2024-09-22", "Undetermined", "Larval", "Brain", "Nervous System"], [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.", null, null, "zebrafish 5 day DsRed positive enteric neural crest derived cells replicate 1", "zebrafish ENCDC replicate 1", "SAMD00529466", null, "sample name:zebrafish ENCDC replicate 1|biological replicate:enteric neural crest derived cells 1|strain:Tgsox10:cre; EF1alpha:loxP gfp loxP dsred", null, null, null, null, null, null, null, null, "NextSeq 550 paired end sequencing of SAMD00529466", "DRX393852", "190326ENvsNC N704 5day;NeuralCrestDerivedCell;rep1", "1", "1", null, "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", null, null, null, 3582073512.0, 23135170.0, "DRR408246", "0:77.41 1:77.42", "A:943152815;C:841972211;G:863627245;T:927361159;N:5960082", 77, 77, null, null, 943152815, 841972211, 863627245, 927361159, 5960082, "DRX393852", "DRS407177", "DRA014886", "NIBB|NIBB core research facilities, National Institute for Basic Biology", "University of Hyogo", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2024-09-22", "Undetermined", "Larval", "Brain", "Nervous System"], [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.", null, null, "zebrafish 5 day GFP positive enteric neurons replicate 3", "zebrafish EN replicate 3", "SAMD00529465", null, "sample name:zebrafish EN replicate 3|biological replicate:eneteric neurons 3|strain:TgSAGFFLF219B; uas:gfp", null, null, null, null, null, null, null, null, "NextSeq 550 paired end sequencing of SAMD00529465", "DRX393851", "190326ENvsNC N703 5day;EntericNeuron;rep3", "1", "1", null, "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", null, null, null, 3729799291.0, 23985772.0, "DRR408245", "0:77.75 1:77.75", "A:978752781;C:879988139;G:903976580;T:962122970;N:4958821", 77, 77, null, null, 978752781, 879988139, 903976580, 962122970, 4958821, "DRX393851", "DRS407176", "DRA014886", "NIBB|NIBB core research facilities, National Institute for Basic Biology", "University of Hyogo", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2024-09-22", "Undetermined", "Larval", "Undetermined", "Undetermined"], [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.", null, null, "zebrafish 5 day GFP positive enteric neurons replicate 2", "zebrafish EN replicate 2", "SAMD00529464", null, "sample name:zebrafish EN replicate 2|biological replicate:eneteric neurons 2|strain:TgSAGFFLF218B; uas:gfp", null, null, null, null, null, null, null, null, "NextSeq 550 paired end sequencing of SAMD00529464", "DRX393850", "190326ENvsNC N702 5day;EntericNeuron;rep2", "1", "1", null, "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", null, null, null, 3315994810.0, 21477755.0, "DRR408244", "0:77.19 1:77.20", "A:873970427;C:778042505;G:798459853;T:859611841;N:5910184", 77, 77, null, null, 873970427, 778042505, 798459853, 859611841, 5910184, "DRX393850", "DRS407175", "DRA014886", "NIBB|NIBB core research facilities, National Institute for Basic Biology", "University of Hyogo", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2024-09-22", "Undetermined", "Larval", "Undetermined", "Undetermined"], [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.", null, null, "zebrafish 5 day GFP positive enteric neurons replicate 1", "zebrafish EN replicate 1", "SAMD00529463", null, "sample name:zebrafish EN replicate 1|biological replicate:eneteric neurons 1|strain:TgSAGFFLF217B; uas:gfp", null, null, null, null, null, null, null, null, "NextSeq 550 paired end sequencing of SAMD00529463", "DRX393849", "190326ENvsNC N701 5day;EntericNeuron;rep1", "1", "1", null, "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", null, null, null, 2999501518.0, 19455440.0, "DRR408243", "0:77.08 1:77.09", "A:788053541;C:705895776;G:724185148;T:775760738;N:5606315", 77, 77, null, null, 788053541, 705895776, 724185148, 775760738, 5606315, "DRX393849", "DRS407174", "DRA014886", "NIBB|NIBB core research facilities, National Institute for Basic Biology", "University of Hyogo", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2024-09-22", "Undetermined", "Larval", "Undetermined", "Undetermined"], [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", null, "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", null, null, null, null, null, null, null, null, "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, null, null, 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", null, "Unknown", "2018-10-30", "Larval", "Larval", "Brain", "Nervous System"], [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", null, "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", null, null, null, null, null, null, null, null, "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, null, null, 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", null, "Unknown", "2018-10-30", "Larval", "Larval", "Brain", "Nervous System"], [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", null, "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", null, null, null, null, null, null, null, null, "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, null, null, 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", null, "Unknown", "2018-10-30", "Larval", "Larval", "Brain", "Nervous System"], [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", null, "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", null, null, null, null, null, null, null, null, "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, null, null, 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", null, "Unknown", "2018-10-30", "Larval", "Larval", "Brain", "Nervous System"], [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", null, "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", null, null, null, null, null, null, null, null, "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, null, null, 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", null, "Unknown", "2018-10-30", "Larval", "Larval", "Brain", "Nervous System"], [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", null, "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", null, null, null, null, null, null, null, null, "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, null, null, 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", null, "Unknown", "2018-10-30", "Larval", "Larval", "Brain", "Nervous System"], [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.", null, null, "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", null, null, null, null, null, null, null, null, "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, null, null, 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", null, "Canada", "2012-08-21", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [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.", null, null, "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", null, null, null, null, null, null, null, null, "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, null, null, 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", null, "Canada", "2012-08-21", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [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.", null, null, "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", null, null, null, null, null, null, null, null, "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, null, null, 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", null, "Canada", "2012-08-21", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [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.", null, null, "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", null, null, null, null, null, null, null, null, "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, null, null, 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", null, "Canada", "2012-08-21", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [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.", null, null, "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", null, null, null, null, null, null, null, null, "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, null, null, 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", null, "Canada", "2012-08-21", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [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.", null, null, "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", null, null, null, null, null, null, null, null, "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, null, null, 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", null, "Canada", "2012-08-21", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [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.", null, null, "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", null, null, null, null, null, null, null, null, "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, null, null, 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", null, "Canada", "2012-08-21", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [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.", null, null, "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", null, null, null, null, null, null, null, null, "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, null, null, 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", null, "Canada", "2012-08-21", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [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.", null, null, "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", null, null, null, null, null, null, null, null, "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, null, null, 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", null, "Canada", "2012-08-21", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [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.", null, null, "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", null, null, null, null, null, null, null, null, "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, null, null, 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", null, "Canada", "2012-08-21", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [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.", null, null, "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", null, null, null, null, null, null, null, null, "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, null, null, 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", null, "Canada", "2012-08-21", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [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.", null, null, "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", null, null, null, null, null, null, null, null, "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, null, null, 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", null, "Canada", "2012-08-21", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [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.", null, null, "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", null, null, null, null, null, null, null, null, "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, null, null, 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", null, "Canada", "2012-08-21", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [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.", null, null, "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", null, null, null, null, null, null, null, null, "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, null, null, 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", null, "Canada", "2012-08-21", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [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.", null, null, "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", null, null, null, null, null, null, null, null, "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, null, null, 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", null, "Canada", "2012-08-21", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [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.", null, null, "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", null, null, null, null, null, null, null, null, "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, null, null, 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", null, "Canada", "2012-08-21", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [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.", null, null, "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", null, null, null, null, null, null, null, null, "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, null, null, 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", null, "Canada", "2012-08-21", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [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.", null, null, "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", null, null, null, null, null, null, null, null, "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, null, null, 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", null, "Canada", "2012-08-21", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [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.", null, null, "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", null, null, null, null, null, null, null, null, "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, null, null, 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", null, "Canada", "2012-08-21", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [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.", null, null, "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", null, null, null, null, null, null, null, null, "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, null, null, 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", null, "Canada", "2012-08-21", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [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.", null, null, "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", null, null, null, null, null, null, null, null, "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, null, null, 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", null, "Canada", "2012-08-21", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [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.", null, null, "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", null, null, null, null, null, null, null, null, "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, null, null, 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", null, "Canada", "2012-08-21", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [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", null, "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\u2122 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", null, null, null, null, null, null, null, null, "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\u2122 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", null, "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, null, null, 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", null, "Unknown", "2019-06-10", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [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", null, "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\u2122 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", null, null, null, null, null, null, null, null, "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\u2122 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", null, "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, null, null, 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", null, "Unknown", "2019-06-10", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [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", null, "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\u2122 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", null, null, null, null, null, null, null, null, "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\u2122 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", null, "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, null, null, 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", null, "Unknown", "2019-06-10", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [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", null, "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\u2122 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", null, null, null, null, null, null, null, null, "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\u2122 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", null, "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, null, null, 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", null, "Unknown", "2019-06-10", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [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", null, "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\u2122 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", null, null, null, null, null, null, null, null, "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\u2122 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", null, "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, null, null, 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", null, "Unknown", "2019-06-10", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [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", null, "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\u2122 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", null, null, null, null, null, null, null, null, "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\u2122 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", null, "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, null, null, 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", null, "Unknown", "2019-06-10", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [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", null, "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 \u00b0C 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", null, null, null, null, null, null, null, null, "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\u20137. Zebrafish Danio rerio were maintained under standard conditions 28 \u00b0C 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", null, "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, null, null, 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", null, "United Kingdom", "2020-04-16", "Adult", "Adult", "Gill", "Respiratory System"], [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", null, "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 \u00b0C 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", null, null, null, null, null, null, null, null, "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\u20137. Zebrafish Danio rerio were maintained under standard conditions 28 \u00b0C 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", null, "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, null, null, 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", null, "United Kingdom", "2020-04-16", "Adult", "Adult", "Gill", "Respiratory System"], [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", null, "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 \u00b0C 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", null, null, null, null, null, null, null, null, "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\u20137. Zebrafish Danio rerio were maintained under standard conditions 28 \u00b0C 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", null, "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, null, null, 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", null, "United Kingdom", "2020-04-16", "Adult", "Adult", "Gill", "Respiratory System"], [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", null, "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 \u00b0C 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", null, null, null, null, null, null, null, null, "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\u20137. Zebrafish Danio rerio were maintained under standard conditions 28 \u00b0C 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", null, "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, null, null, 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", null, "United Kingdom", "2020-04-16", "Adult", "Adult", "Gill", "Respiratory System"], [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", null, "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 \u00b0C 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", null, null, null, null, null, null, null, null, "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\u20137. Zebrafish Danio rerio were maintained under standard conditions 28 \u00b0C 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", null, "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, null, null, 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", null, "United Kingdom", "2020-04-16", "Adult", "Adult", "Gill", "Respiratory System"], [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", null, "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 \u00b0C 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", null, null, null, null, null, null, null, null, "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\u20137. Zebrafish Danio rerio were maintained under standard conditions 28 \u00b0C 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", null, "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, null, null, 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", null, "United Kingdom", "2020-04-16", "Adult", "Adult", "Gill", "Respiratory System"], [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", null, "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 \u00b0C 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", null, null, null, null, null, null, null, null, "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\u20137. Zebrafish Danio rerio were maintained under standard conditions 28 \u00b0C 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", null, "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, null, null, 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", null, "United Kingdom", "2020-04-16", "Adult", "Adult", "Gill", "Respiratory System"], [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", null, "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 \u00b0C 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", null, null, null, null, null, null, null, null, "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\u20137. Zebrafish Danio rerio were maintained under standard conditions 28 \u00b0C 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", null, "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, null, null, 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", null, "United Kingdom", "2020-04-16", "Adult", "Adult", "Gill", "Respiratory System"], [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", null, "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 \u00b0C 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", null, null, null, null, null, null, null, null, "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\u20137. Zebrafish Danio rerio were maintained under standard conditions 28 \u00b0C 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", null, "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, null, null, 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", null, "United Kingdom", "2020-04-16", "Adult", "Adult", "Gill", "Respiratory System"], [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", null, "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 \u00b0C 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", null, null, null, null, null, null, null, null, "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\u20137. Zebrafish Danio rerio were maintained under standard conditions 28 \u00b0C 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", null, "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, null, null, 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", null, "United Kingdom", "2020-04-16", "Adult", "Adult", "Gill", "Respiratory System"], [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", null, "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 \u00b0C 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", null, null, null, null, null, null, null, null, "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\u20137. Zebrafish Danio rerio were maintained under standard conditions 28 \u00b0C 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", null, "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, null, null, 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", null, "United Kingdom", "2020-04-16", "Adult", "Adult", "Gill", "Respiratory System"], [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", null, "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 \u00b0C 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", null, null, null, null, null, null, null, null, "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\u20137. Zebrafish Danio rerio were maintained under standard conditions 28 \u00b0C 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", null, "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, null, null, 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", null, "United Kingdom", "2020-04-16", "Adult", "Adult", "Gill", "Respiratory System"], [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", null, "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 \u00b0C 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", null, null, null, null, null, null, null, null, "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\u20137. Zebrafish Danio rerio were maintained under standard conditions 28 \u00b0C 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", null, "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, null, null, 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", null, "United Kingdom", "2020-04-16", "Adult", "Adult", "Gill", "Respiratory System"], [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", null, "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 \u00b0C 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", null, null, null, null, null, null, null, null, "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\u20137. Zebrafish Danio rerio were maintained under standard conditions 28 \u00b0C 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", null, "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, null, null, 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", null, "United Kingdom", "2020-04-16", "Adult", "Adult", "Gill", "Respiratory System"], [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", null, "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 \u00b0C 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", null, null, null, null, null, null, null, null, "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\u20137. Zebrafish Danio rerio were maintained under standard conditions 28 \u00b0C 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", null, "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, null, null, 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", null, "United Kingdom", "2020-04-16", "Adult", "Adult", "Gill", "Respiratory System"], [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", null, "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 \u00b0C 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", null, null, null, null, null, null, null, null, "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\u20137. Zebrafish Danio rerio were maintained under standard conditions 28 \u00b0C 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", null, "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, null, null, 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", null, "United Kingdom", "2020-04-16", "Adult", "Adult", "Gill", "Respiratory System"], [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", null, "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 \u00b0C 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", null, null, null, null, null, null, null, null, "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\u20137. Zebrafish Danio rerio were maintained under standard conditions 28 \u00b0C 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", null, "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, null, null, 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", null, "United Kingdom", "2020-04-16", "Adult", "Adult", "Gill", "Respiratory System"], [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", null, "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 \u00b0C 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", null, null, null, null, null, null, null, null, "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\u20137. Zebrafish Danio rerio were maintained under standard conditions 28 \u00b0C 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", null, "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, null, null, 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", null, "United Kingdom", "2020-04-16", "Adult", "Adult", "Gill", "Respiratory System"], [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", null, "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 \u00b0C 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", null, null, null, null, null, null, null, null, "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\u20137. Zebrafish Danio rerio were maintained under standard conditions 28 \u00b0C 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", null, "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, null, null, 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", null, "United Kingdom", "2020-04-16", "Adult", "Adult", "Gill", "Respiratory System"], [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", null, "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 \u00b0C 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", null, null, null, null, null, null, null, null, "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\u20137. Zebrafish Danio rerio were maintained under standard conditions 28 \u00b0C 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", null, "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, null, null, 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", null, "United Kingdom", "2020-04-16", "Adult", "Adult", "Gill", "Respiratory System"], [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", null, "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  80\u00baC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer\u00b4s 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\u2122 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", null, null, null, null, null, null, null, null, "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  80\u00baC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer\u00b4s 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\u2122  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", null, "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, null, null, 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", null, "Spain", "2022-12-31", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [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", null, "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  80\u00baC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer\u00b4s 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\u2122 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", null, null, null, null, null, null, null, null, "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  80\u00baC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer\u00b4s 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\u2122  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", null, "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, null, null, 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", null, "Spain", "2022-12-31", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [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", null, "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  80\u00baC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer\u00b4s 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\u2122 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", null, null, null, null, null, null, null, null, "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  80\u00baC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer\u00b4s 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\u2122  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", null, "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, null, null, 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", null, "Spain", "2022-12-31", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [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", null, "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  80\u00baC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer\u00b4s 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\u2122 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", null, null, null, null, null, null, null, null, "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  80\u00baC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer\u00b4s 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\u2122  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", null, "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, null, null, 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", null, "Spain", "2022-12-31", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [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", null, "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  80\u00baC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer\u00b4s 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\u2122 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", null, null, null, null, null, null, null, null, "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  80\u00baC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer\u00b4s 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\u2122  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", null, "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, null, null, 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", null, "Spain", "2022-12-31", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [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", null, "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  80\u00baC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer\u00b4s 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\u2122 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", null, null, null, null, null, null, null, null, "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  80\u00baC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer\u00b4s 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\u2122  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", null, "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, null, null, 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", null, "Spain", "2022-12-31", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [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", null, "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  80\u00baC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer\u00b4s 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\u2122 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", null, null, null, null, null, null, null, null, "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  80\u00baC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer\u00b4s 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\u2122  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", null, "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, null, null, 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", null, "Spain", "2022-12-31", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [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", null, "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  80\u00baC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer\u00b4s 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\u2122 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", null, null, null, null, null, null, null, null, "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  80\u00baC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer\u00b4s 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\u2122  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", null, "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, null, null, 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", null, "Spain", "2022-12-31", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [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", null, "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  80\u00baC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer\u00b4s 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\u2122 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", null, null, null, null, null, null, null, null, "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  80\u00baC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer\u00b4s 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\u2122  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", null, "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, null, null, 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", null, "Spain", "2022-12-31", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [10391, "ERR8516975", "ERX8083451", "ERS10521298", "ERP135383", "PRJEB50776", "Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue", "E-MTAB-11431", "Other", "Zebrafish primary neurons either sfpq sibling/control +/+  +/  or null  /  were cultured in transwell inserts. At DIV2  for each genotype  cellular and neurite tissues were separately isolated  RNA extracted and total RNAseq performed.", "ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19", null, "Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing  and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion", "Sibling neurite", "SAMEA12922152", "Centre for Developmental Neurobiology, King's College London", "ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922152|INSDC center alias:Centre for Developmental Neurobiology  King's College London|INSDC center name:Centre for Developmental Neurobiology  King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Sibling neurite|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq sibling +/+ and +/ |growth condition:transwell culture|organism part:neurite|sample name:E MTAB 11431:Sibling neurite", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue", "E MTAB 11431:Sibling neurite p", "Sibling neurite p", "Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue", "Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing  and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion", "Experimental Factor: genotype:sfpq sibling +/+ and +/ |Experimental Factor: organism part:neurite", "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP135383", "Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue", "ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py", "15812X4_190227_A00421_38_AH7523DRXX_S56_R1_001.fastq.gz 15812X4_190227_A00421_38_AH7523DRXX_S56_R2_001.fastq.gz", "fastq fastq", null, null, "E MTAB 11431:15812X4 190227 A00421 38 AH7523DRXX S56 R", "0:51 1:51", "A:1077092958;C:949537387;G:955020348;T:1099432979;N:20556852", 51, 51, null, null, 1077092958, 949537387, 955020348, 1099432979, 20556852, "ERX8083451", "ERS10521298", "ERA8932807", "Centre for Developmental Neurobiology, King", "Centre for Developmental Neurobiology, King", 2, 0.9053, 0.9259, 0.21658, 0.22155, 0.69369, 0.69179, 0.50726, 0.50871, 51, 51, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "ribozero", "bulk", "bulk", "bulk", null, "United Kingdom", "2022-02-19", "Undetermined", "Undetermined", "Brain", "Nervous System"], [10392, "ERR8516976", "ERX8083451", "ERS10521298", "ERP135383", "PRJEB50776", "Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue", "E-MTAB-11431", "Other", "Zebrafish primary neurons either sfpq sibling/control +/+  +/  or null  /  were cultured in transwell inserts. At DIV2  for each genotype  cellular and neurite tissues were separately isolated  RNA extracted and total RNAseq performed.", "ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19", null, "Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing  and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion", "Sibling neurite", "SAMEA12922152", "Centre for Developmental Neurobiology, King's College London", "ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922152|INSDC center alias:Centre for Developmental Neurobiology  King's College London|INSDC center name:Centre for Developmental Neurobiology  King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Sibling neurite|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq sibling +/+ and +/ |growth condition:transwell culture|organism part:neurite|sample name:E MTAB 11431:Sibling neurite", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue", "E MTAB 11431:Sibling neurite p", "Sibling neurite p", "Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue", "Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing  and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion", "Experimental Factor: genotype:sfpq sibling +/+ and +/ |Experimental Factor: organism part:neurite", "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP135383", "Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue", "ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py", "15812X5_190227_A00421_38_AH7523DRXX_S55_R1_001.fastq.gz 15812X5_190227_A00421_38_AH7523DRXX_S55_R2_001.fastq.gz", "fastq fastq", null, null, "E MTAB 11431:15812X5 190227 A00421 38 AH7523DRXX S55 R", "0:51 1:51", "A:972081222;C:890179393;G:888655698;T:998443264;N:18934747", 51, 51, null, null, 972081222, 890179393, 888655698, 998443264, 18934747, "ERX8083451", "ERS10521298", "ERA8932807", "Centre for Developmental Neurobiology, King", "Centre for Developmental Neurobiology, King", 2, 0.86107, 0.87807, 0.22063, 0.23029, 0.70859, 0.70561, 0.51656, 0.51946, 51, 51, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "ribozero", "bulk", "bulk", "bulk", null, "United Kingdom", "2022-02-19", "Undetermined", "Undetermined", "Brain", "Nervous System"], [10393, "ERR8516977", "ERX8083451", "ERS10521298", "ERP135383", "PRJEB50776", "Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue", "E-MTAB-11431", "Other", "Zebrafish primary neurons either sfpq sibling/control +/+  +/  or null  /  were cultured in transwell inserts. At DIV2  for each genotype  cellular and neurite tissues were separately isolated  RNA extracted and total RNAseq performed.", "ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19", null, "Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing  and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion", "Sibling neurite", "SAMEA12922152", "Centre for Developmental Neurobiology, King's College London", "ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922152|INSDC center alias:Centre for Developmental Neurobiology  King's College London|INSDC center name:Centre for Developmental Neurobiology  King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Sibling neurite|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq sibling +/+ and +/ |growth condition:transwell culture|organism part:neurite|sample name:E MTAB 11431:Sibling neurite", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue", "E MTAB 11431:Sibling neurite p", "Sibling neurite p", "Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue", "Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing  and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion", "Experimental Factor: genotype:sfpq sibling +/+ and +/ |Experimental Factor: organism part:neurite", "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP135383", "Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue", "ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py", "15812X6_190227_A00421_38_AH7523DRXX_S54_R1_001.fastq.gz 15812X6_190227_A00421_38_AH7523DRXX_S54_R2_001.fastq.gz", "fastq fastq", null, null, "E MTAB 11431:15812X6 190227 A00421 38 AH7523DRXX S54 R", "0:51 1:51", "A:728798881;C:962223604;G:958876331;T:735449513;N:17094231", 51, 51, null, null, 728798881, 962223604, 958876331, 735449513, 17094231, "ERX8083451", "ERS10521298", "ERA8932807", "Centre for Developmental Neurobiology, King", "Centre for Developmental Neurobiology, King", 2, 0.54616, 0.55881, 0.13313, 0.14036, 0.84295, 0.84185, 0.64193, 0.59762, 51, 51, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "ribozero", "bulk", "bulk", "bulk", null, "United Kingdom", "2022-02-19", "Undetermined", "Undetermined", "Brain", "Nervous System"], [10394, "ERR8516972", "ERX8083450", "ERS10521297", "ERP135383", "PRJEB50776", "Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue", "E-MTAB-11431", "Other", "Zebrafish primary neurons either sfpq sibling/control +/+  +/  or null  /  were cultured in transwell inserts. At DIV2  for each genotype  cellular and neurite tissues were separately isolated  RNA extracted and total RNAseq performed.", "ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19", null, "Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing  and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion", "Sibling cellular", "SAMEA12922151", "Centre for Developmental Neurobiology, King's College London", "ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922151|INSDC center alias:Centre for Developmental Neurobiology  King's College London|INSDC center name:Centre for Developmental Neurobiology  King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Sibling cellular|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq sibling +/+ and +/ |growth condition:transwell culture|organism part:neuron|sample name:E MTAB 11431:Sibling cellular", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue", "E MTAB 11431:Sibling cellular p", "Sibling cellular p", "Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue", "Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing  and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion", "Experimental Factor: genotype:sfpq sibling +/+ and +/ |Experimental Factor: organism part:neuron", "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP135383", "Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue", "ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py", "15812X1_190227_A00421_38_AH7523DRXX_S59_R1_001.fastq.gz 15812X1_190227_A00421_38_AH7523DRXX_S59_R2_001.fastq.gz", "fastq fastq", null, null, "E MTAB 11431:15812X1 190227 A00421 38 AH7523DRXX S59 R", "0:51 1:51", "A:837274632;C:1062368015;G:1049892288;T:853310517;N:19213786", 51, 51, null, null, 837274632, 1062368015, 1049892288, 853310517, 19213786, "ERX8083450", "ERS10521297", "ERA8932807", "Centre for Developmental Neurobiology, King", "Centre for Developmental Neurobiology, King", 2, 0.5726, 0.57788, 0.13781, 0.14082, 0.80616, 0.80452, 0.61581, 0.60389, 51, 51, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "ribozero", "bulk", "bulk", "bulk", null, "United Kingdom", "2022-02-19", "Undetermined", "Undetermined", "Brain", "Nervous System"], [10395, "ERR8516973", "ERX8083450", "ERS10521297", "ERP135383", "PRJEB50776", "Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue", "E-MTAB-11431", "Other", "Zebrafish primary neurons either sfpq sibling/control +/+  +/  or null  /  were cultured in transwell inserts. At DIV2  for each genotype  cellular and neurite tissues were separately isolated  RNA extracted and total RNAseq performed.", "ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19", null, "Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing  and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion", "Sibling cellular", "SAMEA12922151", "Centre for Developmental Neurobiology, King's College London", "ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922151|INSDC center alias:Centre for Developmental Neurobiology  King's College London|INSDC center name:Centre for Developmental Neurobiology  King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Sibling cellular|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq sibling +/+ and +/ |growth condition:transwell culture|organism part:neuron|sample name:E MTAB 11431:Sibling cellular", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue", "E MTAB 11431:Sibling cellular p", "Sibling cellular p", "Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue", "Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing  and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion", "Experimental Factor: genotype:sfpq sibling +/+ and +/ |Experimental Factor: organism part:neuron", "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP135383", "Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue", "ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py", "15812X2_190227_A00421_38_AH7523DRXX_S58_R1_001.fastq.gz 15812X2_190227_A00421_38_AH7523DRXX_S58_R2_001.fastq.gz", "fastq fastq", null, null, "E MTAB 11431:15812X2 190227 A00421 38 AH7523DRXX S58 R", "0:51 1:51", "A:897813231;C:796012893;G:794839496;T:923696030;N:17221274", 51, 51, null, null, 897813231, 796012893, 794839496, 923696030, 17221274, "ERX8083450", "ERS10521297", "ERA8932807", "Centre for Developmental Neurobiology, King", "Centre for Developmental Neurobiology, King", 2, 0.92095, 0.94156, 0.18892, 0.20024, 0.6901, 0.68905, 0.49377, 0.50086, 51, 51, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "ribozero", "bulk", "bulk", "bulk", null, "United Kingdom", "2022-02-19", "Undetermined", "Undetermined", "Brain", "Nervous System"], [10396, "ERR8516974", "ERX8083450", "ERS10521297", "ERP135383", "PRJEB50776", "Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue", "E-MTAB-11431", "Other", "Zebrafish primary neurons either sfpq sibling/control +/+  +/  or null  /  were cultured in transwell inserts. At DIV2  for each genotype  cellular and neurite tissues were separately isolated  RNA extracted and total RNAseq performed.", "ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19", null, "Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing  and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion", "Sibling cellular", "SAMEA12922151", "Centre for Developmental Neurobiology, King's College London", "ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922151|INSDC center alias:Centre for Developmental Neurobiology  King's College London|INSDC center name:Centre for Developmental Neurobiology  King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Sibling cellular|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq sibling +/+ and +/ |growth condition:transwell culture|organism part:neuron|sample name:E MTAB 11431:Sibling cellular", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue", "E MTAB 11431:Sibling cellular p", "Sibling cellular p", "Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue", "Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing  and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion", "Experimental Factor: genotype:sfpq sibling +/+ and +/ |Experimental Factor: organism part:neuron", "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP135383", "Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue", "ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py", "15812X3_190227_A00421_38_AH7523DRXX_S57_R1_001.fastq.gz 15812X3_190227_A00421_38_AH7523DRXX_S57_R2_001.fastq.gz", "fastq fastq", null, null, "E MTAB 11431:15812X3 190227 A00421 38 AH7523DRXX S57 R", "0:51 1:51", "A:951912827;C:1107150666;G:1086060798;T:973791571;N:20785248", 51, 51, null, null, 951912827, 1107150666, 1086060798, 973791571, 20785248, "ERX8083450", "ERS10521297", "ERA8932807", "Centre for Developmental Neurobiology, King", "Centre for Developmental Neurobiology, King", 2, 0.63792, 0.62667, 0.18547, 0.18671, 0.78756, 0.78549, 0.59274, 0.55478, 51, 51, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "ribozero", "bulk", "bulk", "bulk", null, "United Kingdom", "2022-02-19", "Undetermined", "Undetermined", "Brain", "Nervous System"], [10397, "ERR8516969", "ERX8083449", "ERS10521296", "ERP135383", "PRJEB50776", "Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue", "E-MTAB-11431", "Other", "Zebrafish primary neurons either sfpq sibling/control +/+  +/  or null  /  were cultured in transwell inserts. At DIV2  for each genotype  cellular and neurite tissues were separately isolated  RNA extracted and total RNAseq performed.", "ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19", null, "Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing  and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion", "Null neurite", "SAMEA12922150", "Centre for Developmental Neurobiology, King's College London", "ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922150|INSDC center alias:Centre for Developmental Neurobiology  King's College London|INSDC center name:Centre for Developmental Neurobiology  King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Null neurite|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq null  / |growth condition:transwell culture|organism part:neurite|sample name:E MTAB 11431:Null neurite", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue", "E MTAB 11431:Null neurite p", "Null neurite p", "Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue", "Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing  and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion", "Experimental Factor: genotype:sfpq null  / |Experimental Factor: organism part:neurite", "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP135383", "Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue", "ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py", "15812X10_190227_A00421_38_AH7523DRXX_S48_R1_001.fastq.gz 15812X10_190227_A00421_38_AH7523DRXX_S48_R2_001.fastq.gz", "fastq fastq", null, null, "E MTAB 11431:15812X10 190227 A00421 38 AH7523DRXX S48 R", "0:51 1:51", "A:925784769;C:934445856;G:959155668;T:924080408;N:18878983", 51, 51, null, null, 925784769, 934445856, 959155668, 924080408, 18878983, "ERX8083449", "ERS10521296", "ERA8932807", "Centre for Developmental Neurobiology, King", "Centre for Developmental Neurobiology, King", 2, 0.59503, 0.61112, 0.1947, 0.20225, 0.76512, 0.76337, 0.54584, 0.54345, 51, 51, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "ribozero", "bulk", "bulk", "bulk", null, "United Kingdom", "2022-02-19", "Undetermined", "Undetermined", "Brain", "Nervous System"], [10398, "ERR8516970", "ERX8083449", "ERS10521296", "ERP135383", "PRJEB50776", "Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue", "E-MTAB-11431", "Other", "Zebrafish primary neurons either sfpq sibling/control +/+  +/  or null  /  were cultured in transwell inserts. At DIV2  for each genotype  cellular and neurite tissues were separately isolated  RNA extracted and total RNAseq performed.", "ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19", null, "Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing  and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion", "Null neurite", "SAMEA12922150", "Centre for Developmental Neurobiology, King's College London", "ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922150|INSDC center alias:Centre for Developmental Neurobiology  King's College London|INSDC center name:Centre for Developmental Neurobiology  King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Null neurite|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq null  / |growth condition:transwell culture|organism part:neurite|sample name:E MTAB 11431:Null neurite", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue", "E MTAB 11431:Null neurite p", "Null neurite p", "Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue", "Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing  and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion", "Experimental Factor: genotype:sfpq null  / |Experimental Factor: organism part:neurite", "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP135383", "Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue", "ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py", "15812X11_190227_A00421_38_AH7523DRXX_S52_R1_001.fastq.gz 15812X11_190227_A00421_38_AH7523DRXX_S52_R2_001.fastq.gz", "fastq fastq", null, null, "E MTAB 11431:15812X11 190227 A00421 38 AH7523DRXX S52 R", "0:51 1:51", "A:991755033;C:864808531;G:892202564;T:992188806;N:18881958", 51, 51, null, null, 991755033, 864808531, 892202564, 992188806, 18881958, "ERX8083449", "ERS10521296", "ERA8932807", "Centre for Developmental Neurobiology, King", "Centre for Developmental Neurobiology, King", 2, 0.86612, 0.88689, 0.26181, 0.2728, 0.7094, 0.7091, 0.53639, 0.53906, 51, 51, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "ribozero", "bulk", "bulk", "bulk", null, "United Kingdom", "2022-02-19", "Undetermined", "Undetermined", "Brain", "Nervous System"], [10399, "ERR8516971", "ERX8083449", "ERS10521296", "ERP135383", "PRJEB50776", "Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue", "E-MTAB-11431", "Other", "Zebrafish primary neurons either sfpq sibling/control +/+  +/  or null  /  were cultured in transwell inserts. At DIV2  for each genotype  cellular and neurite tissues were separately isolated  RNA extracted and total RNAseq performed.", "ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19", null, "Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing  and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion", "Null neurite", "SAMEA12922150", "Centre for Developmental Neurobiology, King's College London", "ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922150|INSDC center alias:Centre for Developmental Neurobiology  King's College London|INSDC center name:Centre for Developmental Neurobiology  King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Null neurite|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq null  / |growth condition:transwell culture|organism part:neurite|sample name:E MTAB 11431:Null neurite", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue", "E MTAB 11431:Null neurite p", "Null neurite p", "Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue", "Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing  and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion", "Experimental Factor: genotype:sfpq null  / |Experimental Factor: organism part:neurite", "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP135383", "Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue", "ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py", "15812X12_190227_A00421_38_AH7523DRXX_S50_R1_001.fastq.gz 15812X12_190227_A00421_38_AH7523DRXX_S50_R2_001.fastq.gz", "fastq fastq", null, null, "E MTAB 11431:15812X12 190227 A00421 38 AH7523DRXX S50 R", "0:51 1:51", "A:766707527;C:798667604;G:818782599;T:773280942;N:15938306", 51, 51, null, null, 766707527, 798667604, 818782599, 773280942, 15938306, "ERX8083449", "ERS10521296", "ERA8932807", "Centre for Developmental Neurobiology, King", "Centre for Developmental Neurobiology, King", 2, 0.88811, 0.92834, 0.21869, 0.22669, 0.72878, 0.72604, 0.55598, 0.57831, 51, 51, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "ribozero", "bulk", "bulk", "bulk", null, "United Kingdom", "2022-02-19", "Undetermined", "Undetermined", "Brain", "Nervous System"], [10400, "ERR8516966", "ERX8083448", "ERS10521295", "ERP135383", "PRJEB50776", "Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue", "E-MTAB-11431", "Other", "Zebrafish primary neurons either sfpq sibling/control +/+  +/  or null  /  were cultured in transwell inserts. At DIV2  for each genotype  cellular and neurite tissues were separately isolated  RNA extracted and total RNAseq performed.", "ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19", null, "Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing  and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion", "Null cellular", "SAMEA12922149", "Centre for Developmental Neurobiology, King's College London", "ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922149|INSDC center alias:Centre for Developmental Neurobiology  King's College London|INSDC center name:Centre for Developmental Neurobiology  King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Null cellular|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq null  / |growth condition:transwell culture|organism part:neuron|sample name:E MTAB 11431:Null cellular", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue", "E MTAB 11431:Null cellular p", "Null cellular p", "Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue", "Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing  and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion", "Experimental Factor: genotype:sfpq null  / |Experimental Factor: organism part:neuron", "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP135383", "Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue", "ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py", "15812X7_190227_A00421_38_AH7523DRXX_S53_R1_001.fastq.gz 15812X7_190227_A00421_38_AH7523DRXX_S53_R2_001.fastq.gz", "fastq fastq", null, null, "E MTAB 11431:15812X7 190227 A00421 38 AH7523DRXX S53 R", "0:51 1:51", "A:774360373;C:720215184;G:719479745;T:796239200;N:15182374", 51, 51, null, null, 774360373, 720215184, 719479745, 796239200, 15182374, "ERX8083448", "ERS10521295", "ERA8932807", "Centre for Developmental Neurobiology, King", "Centre for Developmental Neurobiology, King", 2, 0.79643, 0.81194, 0.25554, 0.2603, 0.72236, 0.72021, 0.51775, 0.51678, 51, 51, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "ribozero", "bulk", "bulk", "bulk", null, "United Kingdom", "2022-02-19", "Undetermined", "Undetermined", "Brain", "Nervous System"], [10401, "ERR8516967", "ERX8083448", "ERS10521295", "ERP135383", "PRJEB50776", "Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue", "E-MTAB-11431", "Other", "Zebrafish primary neurons either sfpq sibling/control +/+  +/  or null  /  were cultured in transwell inserts. At DIV2  for each genotype  cellular and neurite tissues were separately isolated  RNA extracted and total RNAseq performed.", "ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19", null, "Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing  and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion", "Null cellular", "SAMEA12922149", "Centre for Developmental Neurobiology, King's College London", "ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922149|INSDC center alias:Centre for Developmental Neurobiology  King's College London|INSDC center name:Centre for Developmental Neurobiology  King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Null cellular|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq null  / |growth condition:transwell culture|organism part:neuron|sample name:E MTAB 11431:Null cellular", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue", "E MTAB 11431:Null cellular p", "Null cellular p", "Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue", "Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing  and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion", "Experimental Factor: genotype:sfpq null  / |Experimental Factor: organism part:neuron", "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP135383", "Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue", "ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py", "15812X8_190227_A00421_38_AH7523DRXX_S51_R1_001.fastq.gz 15812X8_190227_A00421_38_AH7523DRXX_S51_R2_001.fastq.gz", "fastq fastq", null, null, "E MTAB 11431:15812X8 190227 A00421 38 AH7523DRXX S51 R", "0:51 1:51", "A:739921027;C:667375549;G:663864111;T:764302396;N:14288091", 51, 51, null, null, 739921027, 667375549, 663864111, 764302396, 14288091, "ERX8083448", "ERS10521295", "ERA8932807", "Centre for Developmental Neurobiology, King", "Centre for Developmental Neurobiology, King", 2, 0.90817, 0.92909, 0.23387, 0.24814, 0.70088, 0.69842, 0.51238, 0.51267, 51, 51, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "ribozero", "bulk", "bulk", "bulk", null, "United Kingdom", "2022-02-19", "Undetermined", "Undetermined", "Brain", "Nervous System"], [10402, "ERR8516968", "ERX8083448", "ERS10521295", "ERP135383", "PRJEB50776", "Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue", "E-MTAB-11431", "Other", "Zebrafish primary neurons either sfpq sibling/control +/+  +/  or null  /  were cultured in transwell inserts. At DIV2  for each genotype  cellular and neurite tissues were separately isolated  RNA extracted and total RNAseq performed.", "ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19", null, "Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing  and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion", "Null cellular", "SAMEA12922149", "Centre for Developmental Neurobiology, King's College London", "ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922149|INSDC center alias:Centre for Developmental Neurobiology  King's College London|INSDC center name:Centre for Developmental Neurobiology  King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Null cellular|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq null  / |growth condition:transwell culture|organism part:neuron|sample name:E MTAB 11431:Null cellular", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue", "E MTAB 11431:Null cellular p", "Null cellular p", "Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue", "Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing  and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion", "Experimental Factor: genotype:sfpq null  / |Experimental Factor: organism part:neuron", "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP135383", "Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue", "ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py", "15812X9_190227_A00421_38_AH7523DRXX_S49_R1_001.fastq.gz 15812X9_190227_A00421_38_AH7523DRXX_S49_R2_001.fastq.gz", "fastq fastq", null, null, "E MTAB 11431:15812X9 190227 A00421 38 AH7523DRXX S49 R", "0:51 1:51", "A:882831441;C:935213418;G:957033335;T:879085993;N:18444957", 51, 51, null, null, 882831441, 935213418, 957033335, 879085993, 18444957, "ERX8083448", "ERS10521295", "ERA8932807", "Centre for Developmental Neurobiology, King", "Centre for Developmental Neurobiology, King", 2, 0.76218, 0.7682, 0.18357, 0.18521, 0.74444, 0.74272, 0.46714, 0.55518, 51, 51, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "ribozero", "bulk", "bulk", "bulk", null, "United Kingdom", "2022-02-19", "Undetermined", "Undetermined", "Brain", "Nervous System"], [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", null, "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\u00ae 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", null, null, null, null, null, null, null, null, "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\u00ae 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "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, null, null, 2149105370, 2028251580, 2055193482, 2141168979, 193489, "ERX11010308", "ERS15939662", "ERA24542523", "European Bioinformatics Institute|European Nucleotide Archive", "European Bioinformatics Institute|European Nucleotide Archive", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "3prime", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-06-27", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [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", null, "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\u00ae 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", null, null, null, null, null, null, null, null, "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\u00ae 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "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, null, null, 1730015872, 1621295817, 1657133586, 1720858352, 84873, "ERX11010310", "ERS15939664", "ERA24542523", "European Bioinformatics Institute|European Nucleotide Archive", "European Bioinformatics Institute|European Nucleotide Archive", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "3prime", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-06-27", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [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", null, "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\u00ae 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", null, null, null, null, null, null, null, null, "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\u00ae 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "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, null, null, 1888660247, 1748082353, 1788562372, 1884958596, 88432, "ERX11010307", "ERS15939661", "ERA24542523", "European Bioinformatics Institute|European Nucleotide Archive", "European Bioinformatics Institute|European Nucleotide Archive", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "3prime", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-06-27", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [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", null, "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\u00ae 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", null, null, null, null, null, null, null, null, "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\u00ae 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "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, null, null, 2298326835, 2100185951, 2130807919, 2296678033, 209162, "ERX11010309", "ERS15939663", "ERA24542523", "European Bioinformatics Institute|European Nucleotide Archive", "European Bioinformatics Institute|European Nucleotide Archive", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "3prime", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-06-27", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [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", null, "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\u00ae 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", null, "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", null, null, null, null, null, null, null, null, "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\u00ae 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "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, null, null, 2126734187, 2050458346, 2078646608, 2112586140, 196219, "ERX11010311", "ERS15939665", "ERA24542523", "European Bioinformatics Institute|European Nucleotide Archive", "European Bioinformatics Institute|European Nucleotide Archive", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "3prime", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-06-27", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [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", null, "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\u00ae 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", null, "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", null, null, null, null, null, null, null, null, "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\u00ae 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "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, null, null, 2244668655, 2103611849, 2135345835, 2234609621, 209540, "ERX11010312", "ERS15939666", "ERA24542523", "European Bioinformatics Institute|European Nucleotide Archive", "European Bioinformatics Institute|European Nucleotide Archive", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "3prime", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-06-27", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [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", null, null, null, null, "WT 3", null, "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", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio:PBS treated", "WT 3", "WT 3", "PBS treated", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP463771", null, null, "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, null, null, 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", null, "China", "2023-10-11", "Larval", "Larval", "Trunk", "Surface Structure"], [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", null, null, null, "WT 1", "WT 1", null, "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", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio:PBS treated", "WT 1", "WT 1", "PBS treated", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP463771", null, null, "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, null, null, 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", null, "China", "2023-10-11", "Larval", "Larval", "Trunk", "Surface Structure"], [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", null, null, null, "Pg OMVs 3", "Pg OMVs 3", null, "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", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio:Pg OMVs treated", "Pg OMVs 3", "Pg OMVs 3", "Pg OMVs treated", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP463771", null, null, "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, null, null, 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", null, "China", "2023-10-09", "Larval", "Larval", "Trunk", "Surface Structure"], [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", null, null, null, "Pg OMVs 2", "Pg OMVs 2", null, "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", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio:Pg OMVs treated", "Pg OMVs 2", "Pg OMVs 2", "Pg OMVs treated", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP463771", null, null, "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, null, null, 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", null, "China", "2023-10-06", "Larval", "Larval", "Trunk", "Surface Structure"], [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", null, null, null, null, "WT 2", null, "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", null, null, null, null, null, null, null, null, "not applicable", "not applicable", "not applicable", "wild type", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP463771", null, null, "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, null, null, 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", null, "China", "2023-10-06", "Larval", "Larval", "Trunk", "Surface Structure"], [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", null, null, null, "Model organism or animal sample from Danio rerio", "Pg OMVs 1 a", null, "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", null, null, null, null, null, null, null, null, "RNA seq of zebrafish:48 hpi", "Pg OMVs group1a", "Pg OMVs group1a", "Pg OMVs injected", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP463771", null, null, "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, null, null, 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", null, "China", "2023-09-28", "Larval", "Larval", "Trunk", "Surface Structure"], [31473, "SRR28362822", "SRX23967985", "SRS20767216", "SRP495638", "PRJNA1088730", "Effects of noxo1a deficiency on gene expression in zebrafish larvae upon exposure to cold warm stress", "PRJNA1088730", "Other", "Exposure of fish to cold warm stress was reported to elicit ROS generation and subsequent tissue damage. On the other hand  ROS signaling is essential for many physiological functions of the organism. As a NADPH oxidase NOX organizer  deficiency of Noxo1a is expected to decrease the content of hydrogen peroxide in fish tissue upon exposure to cold warm stress. In this study  the effect on Noxo1a deficiency on gene expression in zebrafish larvae under cold warm stress was characterized by RNA sequencing.", null, null, null, "WT re#2", "WT re#2", null, "strain:AB strain|dev stage:Larvae|collection date:2023 03 05|geo loc name:China: Wuhan|sex:not determined|tissue:Whole body|genotype:Wild type|treatment:Exposed to 10 \u00b0C for 12 h followed by recovery at 28 \u00b0C for 6 h|replicate:replicate = biological replicate 2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "WT re#2", "WT re#2", "WT re#2", "One microgram total RNA from each sample was used as the beginning material for sequencing library construction. Each treatment included 4 biological replicates. The NEBNext rRNA Depletion Kit was used for rRNA depletion. post rRNA depletion  Agencourt RNAClean XP Beads from Beckman Coulter were used for RNA purification. Then  the NEBNext Ultra Directional RNA Library Prep Kit for Illumina was used for RNA fragmentation  first and second strand cDNA synthesis  double stranded cDNA end repair. Double strand cDNAs were purified using the Agencourt AMPure XP from Beckman Coulter and ligated to adaptors of NEBNext Multiplex Oligos for Illumina. Finally  the Q5 Hot Start HiFi PCR Master Mix was used for PCR enrichment of the adaptor ligated DNA. The concentration and quality of the constructed sequencing libraries were measured by using the Agilent High Sensitivity DNA Kit and a Bioanalyzer 2100 from Agilent Technologies. The libraries were submitted to 51 bp single end high throughput sequencing by the Center for Advanced Technology CAT of the University of California  San Francisco using Hiseq 3000.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP495638", null, null, "wt-re-2_S42_L004_R1_001.fastq.gz wt-re-2_S42_L004_R2_001.fastq.gz", "fastq fastq", 7360107300.0, 24533691.0, "wt re 2 S42 L004 R1 001.fastq.gz", "0:150 1:150", "A:1953410192;C:1717566713;G:1749971750;T:1938773172;N:385473", 150, 150, null, null, 1953410192, 1717566713, 1749971750, 1938773172, 385473, "SRX23967985", "SRS20767216", "SRA1825819", "Chinese Academy of Sciences|Institute of Hydrobiology", "Chinese Academy of Sciences", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "nebnext", "bulk", "unknown", "unknown", null, "China", "2024-03-16", "Larval", "Larval", "Trunk", "Surface Structure"], [31474, "SRR28362829", "SRX23967984", "SRS20767215", "SRP495638", "PRJNA1088730", "Effects of noxo1a deficiency on gene expression in zebrafish larvae upon exposure to cold warm stress", "PRJNA1088730", "Other", "Exposure of fish to cold warm stress was reported to elicit ROS generation and subsequent tissue damage. On the other hand  ROS signaling is essential for many physiological functions of the organism. As a NADPH oxidase NOX organizer  deficiency of Noxo1a is expected to decrease the content of hydrogen peroxide in fish tissue upon exposure to cold warm stress. In this study  the effect on Noxo1a deficiency on gene expression in zebrafish larvae under cold warm stress was characterized by RNA sequencing.", null, null, null, "WT re#1", "WT re#1", null, "strain:AB strain|dev stage:Larvae|collection date:2023 03 05|geo loc name:China: Wuhan|sex:not determined|tissue:Whole body|genotype:Wild type|treatment:Exposed to 10 \u00b0C for 12 h followed by recovery at 28 \u00b0C for 6 h|replicate:replicate = biological replicate 1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "WT re#1", "WT re#1", "WT re#1", "One microgram total RNA from each sample was used as the beginning material for sequencing library construction. Each treatment included 4 biological replicates. The NEBNext rRNA Depletion Kit was used for rRNA depletion. post rRNA depletion  Agencourt RNAClean XP Beads from Beckman Coulter were used for RNA purification. Then  the NEBNext Ultra Directional RNA Library Prep Kit for Illumina was used for RNA fragmentation  first and second strand cDNA synthesis  double stranded cDNA end repair. Double strand cDNAs were purified using the Agencourt AMPure XP from Beckman Coulter and ligated to adaptors of NEBNext Multiplex Oligos for Illumina. Finally  the Q5 Hot Start HiFi PCR Master Mix was used for PCR enrichment of the adaptor ligated DNA. The concentration and quality of the constructed sequencing libraries were measured by using the Agilent High Sensitivity DNA Kit and a Bioanalyzer 2100 from Agilent Technologies. The libraries were submitted to 51 bp single end high throughput sequencing by the Center for Advanced Technology CAT of the University of California  San Francisco using Hiseq 3000.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP495638", null, null, "wt-re-1_S41_L004_R1_001.fastq.gz wt-re-1_S41_L004_R2_001.fastq.gz wt-re-1_S6_L002_R1_001.fastq.gz wt-re-1_S6_L002_R2_001.fastq.gz", "fastq fastq fastq fastq", 7304976300.0, 24349921.0, "wt re 1 S41 L004 R1 001.fastq.gz", "0:150 1:150", "A:1931654450;C:1711483982;G:1750280300;T:1911082544;N:475024", 150, 150, null, null, 1931654450, 1711483982, 1750280300, 1911082544, 475024, "SRX23967984", "SRS20767215", "SRA1825819", "Chinese Academy of Sciences|Institute of Hydrobiology", "Chinese Academy of Sciences", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "nebnext", "bulk", "unknown", "unknown", null, "China", "2024-03-16", "Larval", "Larval", "Trunk", "Surface Structure"], [31475, "SRR28362823", "SRX23967983", "SRS20767214", "SRP495638", "PRJNA1088730", "Effects of noxo1a deficiency on gene expression in zebrafish larvae upon exposure to cold warm stress", "PRJNA1088730", "Other", "Exposure of fish to cold warm stress was reported to elicit ROS generation and subsequent tissue damage. On the other hand  ROS signaling is essential for many physiological functions of the organism. As a NADPH oxidase NOX organizer  deficiency of Noxo1a is expected to decrease the content of hydrogen peroxide in fish tissue upon exposure to cold warm stress. In this study  the effect on Noxo1a deficiency on gene expression in zebrafish larvae under cold warm stress was characterized by RNA sequencing.", null, null, null, "WT cs#4", "WT cs#4", null, "strain:AB strain|dev stage:Larvae|collection date:2023 03 05|geo loc name:China: Wuhan|sex:not determined|tissue:Whole body|genotype:Wild type|treatment:Exposed to 10 \u00b0C for 12 h|replicate:replicate = biological replicate 4|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "WT cs#4", "WT cs#4", "WT cs#4", "One microgram total RNA from each sample was used as the beginning material for sequencing library construction. Each treatment included 4 biological replicates. The NEBNext rRNA Depletion Kit was used for rRNA depletion. post rRNA depletion  Agencourt RNAClean XP Beads from Beckman Coulter were used for RNA purification. Then  the NEBNext Ultra Directional RNA Library Prep Kit for Illumina was used for RNA fragmentation  first and second strand cDNA synthesis  double stranded cDNA end repair. Double strand cDNAs were purified using the Agencourt AMPure XP from Beckman Coulter and ligated to adaptors of NEBNext Multiplex Oligos for Illumina. Finally  the Q5 Hot Start HiFi PCR Master Mix was used for PCR enrichment of the adaptor ligated DNA. The concentration and quality of the constructed sequencing libraries were measured by using the Agilent High Sensitivity DNA Kit and a Bioanalyzer 2100 from Agilent Technologies. The libraries were submitted to 51 bp single end high throughput sequencing by the Center for Advanced Technology CAT of the University of California  San Francisco using Hiseq 3000.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP495638", null, null, "wt-cs-4_S38_L004_R1_001.fastq.gz wt-cs-4_S38_L004_R2_001.fastq.gz", "fastq fastq", 7117266300.0, 23724221.0, "wt cs 4 S38 L004 R1 001.fastq.gz", "0:150 1:150", "A:1893835105;C:1654405982;G:1690442550;T:1878207126;N:375537", 150, 150, null, null, 1893835105, 1654405982, 1690442550, 1878207126, 375537, "SRX23967983", "SRS20767214", "SRA1825819", "Chinese Academy of Sciences|Institute of Hydrobiology", "Chinese Academy of Sciences", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "nebnext", "bulk", "unknown", "unknown", null, "China", "2024-03-16", "Larval", "Larval", "Trunk", "Surface Structure"], [31476, "SRR28362824", "SRX23967982", "SRS20767213", "SRP495638", "PRJNA1088730", "Effects of noxo1a deficiency on gene expression in zebrafish larvae upon exposure to cold warm stress", "PRJNA1088730", "Other", "Exposure of fish to cold warm stress was reported to elicit ROS generation and subsequent tissue damage. On the other hand  ROS signaling is essential for many physiological functions of the organism. As a NADPH oxidase NOX organizer  deficiency of Noxo1a is expected to decrease the content of hydrogen peroxide in fish tissue upon exposure to cold warm stress. In this study  the effect on Noxo1a deficiency on gene expression in zebrafish larvae under cold warm stress was characterized by RNA sequencing.", null, null, null, "WT cs#3", "WT cs#3", null, "strain:AB strain|dev stage:Larvae|collection date:2023 03 05|geo loc name:China: Wuhan|sex:not determined|tissue:Whole body|genotype:Wild type|treatment:Exposed to 10 \u00b0C for 12 h|replicate:replicate = biological replicate 3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "WT cs#3", "WT cs#3", "WT cs#3", "One microgram total RNA from each sample was used as the beginning material for sequencing library construction. Each treatment included 4 biological replicates. The NEBNext rRNA Depletion Kit was used for rRNA depletion. post rRNA depletion  Agencourt RNAClean XP Beads from Beckman Coulter were used for RNA purification. Then  the NEBNext Ultra Directional RNA Library Prep Kit for Illumina was used for RNA fragmentation  first and second strand cDNA synthesis  double stranded cDNA end repair. Double strand cDNAs were purified using the Agencourt AMPure XP from Beckman Coulter and ligated to adaptors of NEBNext Multiplex Oligos for Illumina. Finally  the Q5 Hot Start HiFi PCR Master Mix was used for PCR enrichment of the adaptor ligated DNA. The concentration and quality of the constructed sequencing libraries were measured by using the Agilent High Sensitivity DNA Kit and a Bioanalyzer 2100 from Agilent Technologies. The libraries were submitted to 51 bp single end high throughput sequencing by the Center for Advanced Technology CAT of the University of California  San Francisco using Hiseq 3000.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP495638", null, null, "wt-cs-3_S37_L004_R1_001.fastq.gz wt-cs-3_S37_L004_R2_001.fastq.gz", "fastq fastq", 7766755500.0, 25889185.0, "wt cs 3 S37 L004 R1 001.fastq.gz", "0:150 1:150", "A:2066456864;C:1808454260;G:1837135016;T:2054303347;N:406013", 150, 150, null, null, 2066456864, 1808454260, 1837135016, 2054303347, 406013, "SRX23967982", "SRS20767213", "SRA1825819", "Chinese Academy of Sciences|Institute of Hydrobiology", "Chinese Academy of Sciences", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "nebnext", "bulk", "unknown", "unknown", null, "China", "2024-03-16", "Larval", "Larval", "Trunk", "Surface Structure"], [31477, "SRR28362825", "SRX23967981", "SRS20767212", "SRP495638", "PRJNA1088730", "Effects of noxo1a deficiency on gene expression in zebrafish larvae upon exposure to cold warm stress", "PRJNA1088730", "Other", "Exposure of fish to cold warm stress was reported to elicit ROS generation and subsequent tissue damage. On the other hand  ROS signaling is essential for many physiological functions of the organism. As a NADPH oxidase NOX organizer  deficiency of Noxo1a is expected to decrease the content of hydrogen peroxide in fish tissue upon exposure to cold warm stress. In this study  the effect on Noxo1a deficiency on gene expression in zebrafish larvae under cold warm stress was characterized by RNA sequencing.", null, null, null, "WT cs#2", "WT cs#2", null, "strain:AB strain|dev stage:Larvae|collection date:2023 03 05|geo loc name:China: Wuhan|sex:not determined|tissue:Whole body|genotype:Wild type|treatment:Exposed to 10 \u00b0C for 12 h|replicate:replicate = biological replicate 2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "WT cs#2", "WT cs#2", "WT cs#2", "One microgram total RNA from each sample was used as the beginning material for sequencing library construction. Each treatment included 4 biological replicates. The NEBNext rRNA Depletion Kit was used for rRNA depletion. post rRNA depletion  Agencourt RNAClean XP Beads from Beckman Coulter were used for RNA purification. Then  the NEBNext Ultra Directional RNA Library Prep Kit for Illumina was used for RNA fragmentation  first and second strand cDNA synthesis  double stranded cDNA end repair. Double strand cDNAs were purified using the Agencourt AMPure XP from Beckman Coulter and ligated to adaptors of NEBNext Multiplex Oligos for Illumina. Finally  the Q5 Hot Start HiFi PCR Master Mix was used for PCR enrichment of the adaptor ligated DNA. The concentration and quality of the constructed sequencing libraries were measured by using the Agilent High Sensitivity DNA Kit and a Bioanalyzer 2100 from Agilent Technologies. 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On the other hand  ROS signaling is essential for many physiological functions of the organism. As a NADPH oxidase NOX organizer  deficiency of Noxo1a is expected to decrease the content of hydrogen peroxide in fish tissue upon exposure to cold warm stress. In this study  the effect on Noxo1a deficiency on gene expression in zebrafish larvae under cold warm stress was characterized by RNA sequencing.", null, null, null, "WT cs#1", "WT cs#1", null, "strain:AB strain|dev stage:Larvae|collection date:2023 03 05|geo loc name:China: Wuhan|sex:not determined|tissue:Whole body|genotype:Wild type|treatment:Exposed to 10 \u00b0C for 12 h|replicate:replicate = biological replicate 1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "WT cs#1", "WT cs#1", "WT cs#1", "One microgram total RNA from each sample was used as the beginning material for sequencing library construction. Each treatment included 4 biological replicates. 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On the other hand  ROS signaling is essential for many physiological functions of the organism. As a NADPH oxidase NOX organizer  deficiency of Noxo1a is expected to decrease the content of hydrogen peroxide in fish tissue upon exposure to cold warm stress. In this study  the effect on Noxo1a deficiency on gene expression in zebrafish larvae under cold warm stress was characterized by RNA sequencing.", null, null, null, "WT ctrl#4", "WT ctrl#4", null, "strain:AB strain|dev stage:Larvae|collection date:2023 03 05|geo loc name:China: Wuhan|sex:not determined|tissue:Whole body|genotype:Wild type|treatment:Collected at 96 hpf|replicate:replicate = biological replicate 4|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "WT ctrl#4", "WT ctrl#4", "WT ctrl#4", "One microgram total RNA from each sample was used as the beginning material for sequencing library construction. Each treatment included 4 biological replicates. The NEBNext rRNA Depletion Kit was used for rRNA depletion. post rRNA depletion  Agencourt RNAClean XP Beads from Beckman Coulter were used for RNA purification. Then  the NEBNext Ultra Directional RNA Library Prep Kit for Illumina was used for RNA fragmentation  first and second strand cDNA synthesis  double stranded cDNA end repair. Double strand cDNAs were purified using the Agencourt AMPure XP from Beckman Coulter and ligated to adaptors of NEBNext Multiplex Oligos for Illumina. Finally  the Q5 Hot Start HiFi PCR Master Mix was used for PCR enrichment of the adaptor ligated DNA. The concentration and quality of the constructed sequencing libraries were measured by using the Agilent High Sensitivity DNA Kit and a Bioanalyzer 2100 from Agilent Technologies. The libraries were submitted to 51 bp single end high throughput sequencing by the Center for Advanced Technology CAT of the University of California  San Francisco using Hiseq 3000.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP495638", null, null, "wt-ctrl-4_S20_L004_R1_001.fastq.gz wt-ctrl-4_S20_L004_R2_001.fastq.gz", "fastq fastq", 6576597600.0, 21921992.0, "wt ctrl 4 S20 L004 R1 001.fastq.gz", "0:150 1:150", "A:1706071185;C:1570838977;G:1609917484;T:1689461796;N:308158", 150, 150, null, null, 1706071185, 1570838977, 1609917484, 1689461796, 308158, "SRX23967979", "SRS20767210", "SRA1825819", "Chinese Academy of Sciences|Institute of Hydrobiology", "Chinese Academy of Sciences", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "nebnext", "bulk", "unknown", "unknown", null, "China", "2024-03-16", "Larval", 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