rowid,run.accession,experiment.accession,sample.accession,study.accession,bioproject,study.title,study.alias,study.type,study.abstract,study.attributes,study.PMIDs,sample.description,sample.title,sample.alias,sample.centername,sample.attributes,GEOsample.title,GEOsample.dataprocessing,GEOsample.source,GEOsample.treatmentprotocol,GEOsample.extractprotocol,GEOsample.growthprotocol,GEOsample.characteristics,GEOsample.accession,experiment.title,experiment.alias,experiment.library_name,experiment.design_description,experiment.library_construction_protocol,experiment.attributes,experiment.library_strategy,experiment.library_source,experiment.library_selection,experiment.library_layout,experiment.platform,experiment.instrument_model,experiment.spot_descriptor,experiment.study_ref,run.title,run.attributes,run.filename,run.semantic_name,run.total_bases,run.total_spots,run.alias,run.read_lengths,run.base_counts,run.r1_length,run.r2_length,run.r3_length,run.r4_length,run.Acount,run.Ccount,run.Gcount,run.Tcount,run.Ncount,run.experiment,run.pool_member,submission.accession,submission.srasource,submission.bioprojectsource,seqdetective.n_mates,seqdetective.mapping_rate.mate1,seqdetective.mapping_rate.mate2,seqdetective.nofeature_rate.mate1,seqdetective.nofeature_rate.mate2,seqdetective.sparsity.mate1,seqdetective.sparsity.mate2,seqdetective.pos_strand_rate.mate1,seqdetective.pos_strand_rate.mate2,seqdetective.readlen.mate1,seqdetective.readlen.mate2,seqdetective.judgement.mate1,seqdetective.judgement.mate2,seqdetective.judgement.reason,platform_family,instrument_generation,read_bias,selection_class,prep_kit,sc_or_bulk,tech_class,technology,tech_variant,submission.bioprojectsource.country,earliest_date,devstage_curation,devstage_curation_coarse,tissue_curation,tissue_curation_coarse
35,DRR408239,DRX393845,DRS407003,DRP012035,PRJDB14274,Zebrafish Gut RNA seq.,DRP012035,Transcriptome Analysis,A project to find differential expressed genes between larval and adult zebrafish gut. We dissected guts of wild type AB line  and prepared three duplicates for each of larval and adult gut. Libraries for NGS are prepared using illumina TruSeq standard mRNA sample prep kit.,,,zebrafish wild type AB larval gut replicate 3,zebrafish larval gut replicate 3,SAMD00529459,,sample name:zebrafish larval gut replicate 3|biological replicate:larval 3|strain:AB,,,,,,,,,Illumina HiSeq 1500 sequencing of SAMD00529459,DRX393845,AR012 gut 5  5 dpf 6 dpf larvae,1,1,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 1500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>126</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP012035,Illumina HiSeq 1500 sequencing of SAMD00529459,,,,3463982046.0,27491921.0,DRR408239,0:126 1:0,A:842552557;C:849757648;G:837664725;T:933942026;N:65090,126,0,,,842552557,849757648,837664725,933942026,65090,DRX393845,DRS407003,DRA014885,"NIBB|NIBB core research facilities, National Institute for Basic Biology",University of Hyogo,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,Japan,2024-09-20,Larval,Larval,Gut,Digestive System
36,DRR408238,DRX393844,DRS407002,DRP012035,PRJDB14274,Zebrafish Gut RNA seq.,DRP012035,Transcriptome Analysis,A project to find differential expressed genes between larval and adult zebrafish gut. We dissected guts of wild type AB line  and prepared three duplicates for each of larval and adult gut. Libraries for NGS are prepared using illumina TruSeq standard mRNA sample prep kit.,,,zebrafish wild type AB larval gut replicate 2,zebrafish larval gut replicate 2,SAMD00529458,,sample name:zebrafish larval gut replicate 2|biological replicate:larval 2|strain:AB,,,,,,,,,Illumina HiSeq 1500 sequencing of SAMD00529458,DRX393844,AR005 gut 3  5 dpf 6 dpf larvae,1,1,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 1500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>126</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP012035,Illumina HiSeq 1500 sequencing of SAMD00529458,,,,3782320416.0,30018416.0,DRR408238,0:126 1:0,A:930337206;C:920645770;G:906559955;T:1024704277;N:73208,126,0,,,930337206,920645770,906559955,1024704277,73208,DRX393844,DRS407002,DRA014885,"NIBB|NIBB core research facilities, National Institute for Basic Biology",University of Hyogo,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,Japan,2024-09-20,Larval,Larval,Gut,Digestive System
37,DRR408237,DRX393843,DRS407001,DRP012035,PRJDB14274,Zebrafish Gut RNA seq.,DRP012035,Transcriptome Analysis,A project to find differential expressed genes between larval and adult zebrafish gut. We dissected guts of wild type AB line  and prepared three duplicates for each of larval and adult gut. Libraries for NGS are prepared using illumina TruSeq standard mRNA sample prep kit.,,,zebrafish wild type AB larval gut replicate 1,zebrafish larval gut replicate 1,SAMD00529457,,sample name:zebrafish larval gut replicate 1|biological replicate:larval 1|strain:AB,,,,,,,,,Illumina HiSeq 1500 sequencing of SAMD00529457,DRX393843,AR002 gut 1  5 dpf 6 dpf larvae,1,1,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 1500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>126</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP012035,Illumina HiSeq 1500 sequencing of SAMD00529457,,,,3606885828.0,28626078.0,DRR408237,0:126 1:0,A:879148446;C:885673723;G:870330963;T:971663212;N:69484,126,0,,,879148446,885673723,870330963,971663212,69484,DRX393843,DRS407001,DRA014885,"NIBB|NIBB core research facilities, National Institute for Basic Biology",University of Hyogo,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,Japan,2024-09-20,Larval,Larval,Gut,Digestive System
9331,ERR2862354,ERX2868592,ERS2866329,ERP111743,PRJEB29441,Receptor Tyrosine Kinase pathway activation is sufficient to trigger chordoma in zebrafish,E-MTAB-7349,Transcriptome Analysis,Oncogenic transformation of individual cell fates by developmental signaling cascades and transcription factors triggers diverse cancer types. Chordoma is a rare  aggressive tumor arising from transformed notochord remnants. Various potentially oncogenic factors have been found deregulated in chordoma and its metastases  yet clear causation remains uncertain. In particular  expression of the notochord controlling transcription factor Brachyury is hypothesized as key molecular driver in chordoma formation  yet an in vivo model to causally test its oncogenic potential in the notochord is missing. Here  we apply a zebrafish model of chordoma onset to identify the notochord transforming potential of tumor implicated candidate genes in vivo. We find that overexpression of human and zebrafish Brachyury  including a version with augmented transcriptional activity  is insufficient to initiate notochord hyperplasia in vivo. In contrast  the repeatedly chordoma implicated receptor tyrosine kinase RTK genes EGFR and KDR/VEGFR2 are sufficient to transform developmental notochord cells  akin to direct activation of Ras. Analysis of transcriptome and sub cellular organization from transformed notochords suggests that aberrant activation of RTK/Ras signaling attenuates processes required for the differentiation of notochord cells. Taken together  our results provide first in vivo indication for a lack of tumor initiating potential of Brachyury expression in the notochord  and suggest activated RTK signaling as potent hyperplasia initiating event in chordoma.,ENA FIRST PUBLIC:2018 12 01|ENA LAST UPDATE:2018 10 30,,Protocols: 8 dpf wildtype and Tgtwhh:Gal4;TgUAS:EGFP HRASV12 were euthanized with 3% Tricaine methanesulfonate Sigma. Embryos were decapitated and incubated in Tripsin EDTA Sigma for 30 minutes to facilitate tissue dissociation. Notochords were then dissected using tungsten needles and immediately transferred to Trizol LS Ambion. We isolated 30 50 notochords per replicate  with a total of 3 replicates per condition 3x wildtype  3x HRASV12. Notochord RNA was extracted following the manufacturer's protocol using Trizol LS. RNA seq libraries were constructed using the Truseq stranded total RNA kit.,TUC,SAMEA5055152,UZH,ENA FIRST PUBLIC:2018 12 01T17:03:21Z|ENA LAST UPDATE:2018 10 30T13:30:13Z|External Id:SAMEA5055152|INSDC center name:UZH|INSDC first public:2018 12 01T17:03:21Z|INSDC last update:2018 10 30T13:30:13Z|INSDC status:public|Submitter Id:E MTAB 7349:TUC|age:8|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:wild type genotype|individual:mixed pool of 30 to 50 embryos|organism part:notochord|sample name:E MTAB 7349:TUC|scientific name:Danio rerio|sex:mixed,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Receptor Tyrosine Kinase pathway activation is sufficient to trigger chordoma in zebrafish,E MTAB 7349:TUC p,TUC p,Receptor Tyrosine Kinase pathway activation is sufficient to trigger chordoma in zebrafish,8 dpf wildtype and Tgtwhh:Gal4;TgUAS:EGFP HRASV12 were euthanized with 3% Tricaine methanesulfonate Sigma. Embryos were decapitated and incubated in Tripsin EDTA Sigma for 30 minutes to facilitate tissue dissociation. Notochords were then dissected using tungsten needles and immediately transferred to Trizol LS Ambion. We isolated 30 50 notochords per replicate  with a total of 3 replicates per condition 3x wildtype  3x HRASV12. Notochord RNA was extracted following the manufacturer's protocol using Trizol LS. RNA seq libraries were constructed using the Truseq stranded total RNA kit.,Experimental Factor: genotype:wild type genotype,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP111743,Illumina HiSeq 2500 paired end sequencing; Receptor Tyrosine Kinase pathway activation is sufficient to trigger chordoma in zebrafish,ENA FIRST PUBLIC:2018 12 01|ENA LAST UPDATE:2018 11 16,AGCGATAG_AGGCTATA__160520_I127_FCH732GBBXX_L8_CDKPEI160513002_1.fq.gz AGCGATAG_AGGCTATA__160520_I127_FCH732GBBXX_L8_CDKPEI160513002_2.fq.gz,fastq fastq,12890102400.0,64450512.0,E MTAB 7349:AGCGATAG AGGCTATA  160520 I127 FCH732GBBXX L8 CDKPEI160513002 ,0:100 1:100,A:3347844573;C:3078635366;G:3118813009;T:3343385073;N:1424379,100,100,,,3347844573,3078635366,3118813009,3343385073,1424379,ERX2868592,ERS2866329,ERA1640550,European Nucleotide Archive,European Nucleotide Archive,2,0.89165,0.8896,0.26768,0.26518,0.75142,0.75459,0.60855,0.6105,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,Unknown,2018-10-30,Larval,Larval,Brain,Nervous System
9332,ERR2862353,ERX2868591,ERS2866328,ERP111743,PRJEB29441,Receptor Tyrosine Kinase pathway activation is sufficient to trigger chordoma in zebrafish,E-MTAB-7349,Transcriptome Analysis,Oncogenic transformation of individual cell fates by developmental signaling cascades and transcription factors triggers diverse cancer types. Chordoma is a rare  aggressive tumor arising from transformed notochord remnants. Various potentially oncogenic factors have been found deregulated in chordoma and its metastases  yet clear causation remains uncertain. In particular  expression of the notochord controlling transcription factor Brachyury is hypothesized as key molecular driver in chordoma formation  yet an in vivo model to causally test its oncogenic potential in the notochord is missing. Here  we apply a zebrafish model of chordoma onset to identify the notochord transforming potential of tumor implicated candidate genes in vivo. We find that overexpression of human and zebrafish Brachyury  including a version with augmented transcriptional activity  is insufficient to initiate notochord hyperplasia in vivo. In contrast  the repeatedly chordoma implicated receptor tyrosine kinase RTK genes EGFR and KDR/VEGFR2 are sufficient to transform developmental notochord cells  akin to direct activation of Ras. Analysis of transcriptome and sub cellular organization from transformed notochords suggests that aberrant activation of RTK/Ras signaling attenuates processes required for the differentiation of notochord cells. Taken together  our results provide first in vivo indication for a lack of tumor initiating potential of Brachyury expression in the notochord  and suggest activated RTK signaling as potent hyperplasia initiating event in chordoma.,ENA FIRST PUBLIC:2018 12 01|ENA LAST UPDATE:2018 10 30,,Protocols: 8 dpf wildtype and Tgtwhh:Gal4;TgUAS:EGFP HRASV12 were euthanized with 3% Tricaine methanesulfonate Sigma. Embryos were decapitated and incubated in Tripsin EDTA Sigma for 30 minutes to facilitate tissue dissociation. Notochords were then dissected using tungsten needles and immediately transferred to Trizol LS Ambion. We isolated 30 50 notochords per replicate  with a total of 3 replicates per condition 3x wildtype  3x HRASV12. Notochord RNA was extracted following the manufacturer's protocol using Trizol LS. RNA seq libraries were constructed using the Truseq stranded total RNA kit.,TUB,SAMEA5055151,UZH,ENA FIRST PUBLIC:2018 12 01T17:03:21Z|ENA LAST UPDATE:2018 10 30T13:30:13Z|External Id:SAMEA5055151|INSDC center name:UZH|INSDC first public:2018 12 01T17:03:21Z|INSDC last update:2018 10 30T13:30:13Z|INSDC status:public|Submitter Id:E MTAB 7349:TUB|age:8|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:wild type genotype|individual:mixed pool of 30 to 50 embryos|organism part:notochord|sample name:E MTAB 7349:TUB|scientific name:Danio rerio|sex:mixed,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Receptor Tyrosine Kinase pathway activation is sufficient to trigger chordoma in zebrafish,E MTAB 7349:TUB p,TUB p,Receptor Tyrosine Kinase pathway activation is sufficient to trigger chordoma in zebrafish,8 dpf wildtype and Tgtwhh:Gal4;TgUAS:EGFP HRASV12 were euthanized with 3% Tricaine methanesulfonate Sigma. Embryos were decapitated and incubated in Tripsin EDTA Sigma for 30 minutes to facilitate tissue dissociation. Notochords were then dissected using tungsten needles and immediately transferred to Trizol LS Ambion. We isolated 30 50 notochords per replicate  with a total of 3 replicates per condition 3x wildtype  3x HRASV12. Notochord RNA was extracted following the manufacturer's protocol using Trizol LS. RNA seq libraries were constructed using the Truseq stranded total RNA kit.,Experimental Factor: genotype:wild type genotype,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP111743,Illumina HiSeq 2500 paired end sequencing; Receptor Tyrosine Kinase pathway activation is sufficient to trigger chordoma in zebrafish,ENA FIRST PUBLIC:2018 12 01|ENA LAST UPDATE:2018 11 16,TCTCGCGC_AGGCTATA__160520_I127_FCH732GBBXX_L8_CDKPEI160513002_2.fq.gz TCTCGCGC_AGGCTATA__160520_I127_FCH732GBBXX_L8_CDKPEI160513002_1.fq.gz,fastq fastq,15345882200.0,76729411.0,E MTAB 7349:TCTCGCGC AGGCTATA  160520 I127 FCH732GBBXX L8 CDKPEI160513002 ,0:100 1:100,A:4257362303;C:3394893224;G:3451042837;T:4240872487;N:1711349,100,100,,,4257362303,3394893224,3451042837,4240872487,1711349,ERX2868591,ERS2866328,ERA1640550,European Nucleotide Archive,European Nucleotide Archive,2,0.86888,0.86735,0.45025,0.44476,0.72036,0.72529,0.56048,0.56274,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,Unknown,2018-10-30,Larval,Larval,Brain,Nervous System
9333,ERR2862352,ERX2868590,ERS2866327,ERP111743,PRJEB29441,Receptor Tyrosine Kinase pathway activation is sufficient to trigger chordoma in zebrafish,E-MTAB-7349,Transcriptome Analysis,Oncogenic transformation of individual cell fates by developmental signaling cascades and transcription factors triggers diverse cancer types. Chordoma is a rare  aggressive tumor arising from transformed notochord remnants. Various potentially oncogenic factors have been found deregulated in chordoma and its metastases  yet clear causation remains uncertain. In particular  expression of the notochord controlling transcription factor Brachyury is hypothesized as key molecular driver in chordoma formation  yet an in vivo model to causally test its oncogenic potential in the notochord is missing. Here  we apply a zebrafish model of chordoma onset to identify the notochord transforming potential of tumor implicated candidate genes in vivo. We find that overexpression of human and zebrafish Brachyury  including a version with augmented transcriptional activity  is insufficient to initiate notochord hyperplasia in vivo. In contrast  the repeatedly chordoma implicated receptor tyrosine kinase RTK genes EGFR and KDR/VEGFR2 are sufficient to transform developmental notochord cells  akin to direct activation of Ras. Analysis of transcriptome and sub cellular organization from transformed notochords suggests that aberrant activation of RTK/Ras signaling attenuates processes required for the differentiation of notochord cells. Taken together  our results provide first in vivo indication for a lack of tumor initiating potential of Brachyury expression in the notochord  and suggest activated RTK signaling as potent hyperplasia initiating event in chordoma.,ENA FIRST PUBLIC:2018 12 01|ENA LAST UPDATE:2018 10 30,,Protocols: 8 dpf wildtype and Tgtwhh:Gal4;TgUAS:EGFP HRASV12 were euthanized with 3% Tricaine methanesulfonate Sigma. Embryos were decapitated and incubated in Tripsin EDTA Sigma for 30 minutes to facilitate tissue dissociation. Notochords were then dissected using tungsten needles and immediately transferred to Trizol LS Ambion. We isolated 30 50 notochords per replicate  with a total of 3 replicates per condition 3x wildtype  3x HRASV12. Notochord RNA was extracted following the manufacturer's protocol using Trizol LS. RNA seq libraries were constructed using the Truseq stranded total RNA kit.,TUA,SAMEA5055150,UZH,ENA FIRST PUBLIC:2018 12 01T17:03:21Z|ENA LAST UPDATE:2018 10 30T13:30:13Z|External Id:SAMEA5055150|INSDC center name:UZH|INSDC first public:2018 12 01T17:03:21Z|INSDC last update:2018 10 30T13:30:13Z|INSDC status:public|Submitter Id:E MTAB 7349:TUA|age:8|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:wild type genotype|individual:mixed pool of 30 to 50 embryos|organism part:notochord|sample name:E MTAB 7349:TUA|scientific name:Danio rerio|sex:mixed,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Receptor Tyrosine Kinase pathway activation is sufficient to trigger chordoma in zebrafish,E MTAB 7349:TUA p,TUA p,Receptor Tyrosine Kinase pathway activation is sufficient to trigger chordoma in zebrafish,8 dpf wildtype and Tgtwhh:Gal4;TgUAS:EGFP HRASV12 were euthanized with 3% Tricaine methanesulfonate Sigma. Embryos were decapitated and incubated in Tripsin EDTA Sigma for 30 minutes to facilitate tissue dissociation. Notochords were then dissected using tungsten needles and immediately transferred to Trizol LS Ambion. We isolated 30 50 notochords per replicate  with a total of 3 replicates per condition 3x wildtype  3x HRASV12. Notochord RNA was extracted following the manufacturer's protocol using Trizol LS. RNA seq libraries were constructed using the Truseq stranded total RNA kit.,Experimental Factor: genotype:wild type genotype,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP111743,Illumina HiSeq 2500 paired end sequencing; Receptor Tyrosine Kinase pathway activation is sufficient to trigger chordoma in zebrafish,ENA FIRST PUBLIC:2018 12 01|ENA LAST UPDATE:2018 11 16,TCCGCGAA_AGGCTATA__160520_I127_FCH732GBBXX_L8_CDKPEI160513002_1.fq.gz TCCGCGAA_AGGCTATA__160520_I127_FCH732GBBXX_L8_CDKPEI160513002_2.fq.gz,fastq fastq,11985547000.0,59927735.0,E MTAB 7349:TCCGCGAA AGGCTATA  160520 I127 FCH732GBBXX L8 CDKPEI160513002 ,0:100 1:100,A:3239652711;C:2732996991;G:2737809176;T:3273773368;N:1314754,100,100,,,3239652711,2732996991,2737809176,3273773368,1314754,ERX2868590,ERS2866327,ERA1640550,European Nucleotide Archive,European Nucleotide Archive,2,0.91524,0.91585,0.32418,0.32053,0.72616,0.72671,0.59362,0.42478,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,Unknown,2018-10-30,Larval,Larval,Brain,Nervous System
9334,ERR2862351,ERX2868589,ERS2866326,ERP111743,PRJEB29441,Receptor Tyrosine Kinase pathway activation is sufficient to trigger chordoma in zebrafish,E-MTAB-7349,Transcriptome Analysis,Oncogenic transformation of individual cell fates by developmental signaling cascades and transcription factors triggers diverse cancer types. Chordoma is a rare  aggressive tumor arising from transformed notochord remnants. Various potentially oncogenic factors have been found deregulated in chordoma and its metastases  yet clear causation remains uncertain. In particular  expression of the notochord controlling transcription factor Brachyury is hypothesized as key molecular driver in chordoma formation  yet an in vivo model to causally test its oncogenic potential in the notochord is missing. Here  we apply a zebrafish model of chordoma onset to identify the notochord transforming potential of tumor implicated candidate genes in vivo. We find that overexpression of human and zebrafish Brachyury  including a version with augmented transcriptional activity  is insufficient to initiate notochord hyperplasia in vivo. In contrast  the repeatedly chordoma implicated receptor tyrosine kinase RTK genes EGFR and KDR/VEGFR2 are sufficient to transform developmental notochord cells  akin to direct activation of Ras. Analysis of transcriptome and sub cellular organization from transformed notochords suggests that aberrant activation of RTK/Ras signaling attenuates processes required for the differentiation of notochord cells. Taken together  our results provide first in vivo indication for a lack of tumor initiating potential of Brachyury expression in the notochord  and suggest activated RTK signaling as potent hyperplasia initiating event in chordoma.,ENA FIRST PUBLIC:2018 12 01|ENA LAST UPDATE:2018 10 30,,Protocols: 8 dpf wildtype and Tgtwhh:Gal4;TgUAS:EGFP HRASV12 were euthanized with 3% Tricaine methanesulfonate Sigma. Embryos were decapitated and incubated in Tripsin EDTA Sigma for 30 minutes to facilitate tissue dissociation. Notochords were then dissected using tungsten needles and immediately transferred to Trizol LS Ambion. We isolated 30 50 notochords per replicate  with a total of 3 replicates per condition 3x wildtype  3x HRASV12. Notochord RNA was extracted following the manufacturer's protocol using Trizol LS. RNA seq libraries were constructed using the Truseq stranded total RNA kit.,HRASC,SAMEA5055149,UZH,ENA FIRST PUBLIC:2018 12 01T17:03:21Z|ENA LAST UPDATE:2018 10 30T13:30:13Z|External Id:SAMEA5055149|INSDC center name:UZH|INSDC first public:2018 12 01T17:03:21Z|INSDC last update:2018 10 30T13:30:13Z|INSDC status:public|Submitter Id:E MTAB 7349:HRASC|age:8|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:Tgtwhh:Gal4;TgUAS:EGFP HRASV12|individual:mixed pool of 30 to 50 embryos|organism part:notochord|sample name:E MTAB 7349:HRASC|scientific name:Danio rerio|sex:mixed,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Receptor Tyrosine Kinase pathway activation is sufficient to trigger chordoma in zebrafish,E MTAB 7349:HRASC p,HRASC p,Receptor Tyrosine Kinase pathway activation is sufficient to trigger chordoma in zebrafish,8 dpf wildtype and Tgtwhh:Gal4;TgUAS:EGFP HRASV12 were euthanized with 3% Tricaine methanesulfonate Sigma. Embryos were decapitated and incubated in Tripsin EDTA Sigma for 30 minutes to facilitate tissue dissociation. Notochords were then dissected using tungsten needles and immediately transferred to Trizol LS Ambion. We isolated 30 50 notochords per replicate  with a total of 3 replicates per condition 3x wildtype  3x HRASV12. Notochord RNA was extracted following the manufacturer's protocol using Trizol LS. RNA seq libraries were constructed using the Truseq stranded total RNA kit.,Experimental Factor: genotype:Tgtwhh:Gal4;TgUAS:EGFP HRASV12,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP111743,Illumina HiSeq 2500 paired end sequencing; Receptor Tyrosine Kinase pathway activation is sufficient to trigger chordoma in zebrafish,ENA FIRST PUBLIC:2018 12 01|ENA LAST UPDATE:2018 11 16,CGGCTATG_GTCAGTAC__160520_I127_FCH732GBBXX_L8_CDKPEI160513002_1.fq.gz CGGCTATG_GTCAGTAC__160520_I127_FCH732GBBXX_L8_CDKPEI160513002_2.fq.gz,fastq fastq,11297151800.0,56485759.0,E MTAB 7349:CGGCTATG GTCAGTAC  160520 I127 FCH732GBBXX L8 CDKPEI160513002 ,0:100 1:100,A:3202944476;C:2429970659;G:2461948398;T:3201079699;N:1208568,100,100,,,3202944476,2429970659,2461948398,3201079699,1208568,ERX2868589,ERS2866326,ERA1640550,European Nucleotide Archive,European Nucleotide Archive,2,0.89842,0.86269,0.32455,0.30708,0.74245,0.75191,0.7454,0.74185,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,Unknown,2018-10-30,Larval,Larval,Brain,Nervous System
9335,ERR2862350,ERX2868588,ERS2866325,ERP111743,PRJEB29441,Receptor Tyrosine Kinase pathway activation is sufficient to trigger chordoma in zebrafish,E-MTAB-7349,Transcriptome Analysis,Oncogenic transformation of individual cell fates by developmental signaling cascades and transcription factors triggers diverse cancer types. Chordoma is a rare  aggressive tumor arising from transformed notochord remnants. Various potentially oncogenic factors have been found deregulated in chordoma and its metastases  yet clear causation remains uncertain. In particular  expression of the notochord controlling transcription factor Brachyury is hypothesized as key molecular driver in chordoma formation  yet an in vivo model to causally test its oncogenic potential in the notochord is missing. Here  we apply a zebrafish model of chordoma onset to identify the notochord transforming potential of tumor implicated candidate genes in vivo. We find that overexpression of human and zebrafish Brachyury  including a version with augmented transcriptional activity  is insufficient to initiate notochord hyperplasia in vivo. In contrast  the repeatedly chordoma implicated receptor tyrosine kinase RTK genes EGFR and KDR/VEGFR2 are sufficient to transform developmental notochord cells  akin to direct activation of Ras. Analysis of transcriptome and sub cellular organization from transformed notochords suggests that aberrant activation of RTK/Ras signaling attenuates processes required for the differentiation of notochord cells. Taken together  our results provide first in vivo indication for a lack of tumor initiating potential of Brachyury expression in the notochord  and suggest activated RTK signaling as potent hyperplasia initiating event in chordoma.,ENA FIRST PUBLIC:2018 12 01|ENA LAST UPDATE:2018 10 30,,Protocols: 8 dpf wildtype and Tgtwhh:Gal4;TgUAS:EGFP HRASV12 were euthanized with 3% Tricaine methanesulfonate Sigma. Embryos were decapitated and incubated in Tripsin EDTA Sigma for 30 minutes to facilitate tissue dissociation. Notochords were then dissected using tungsten needles and immediately transferred to Trizol LS Ambion. We isolated 30 50 notochords per replicate  with a total of 3 replicates per condition 3x wildtype  3x HRASV12. Notochord RNA was extracted following the manufacturer's protocol using Trizol LS. RNA seq libraries were constructed using the Truseq stranded total RNA kit.,HRASB 1A,SAMEA5055148,UZH,ENA FIRST PUBLIC:2018 12 01T17:03:21Z|ENA LAST UPDATE:2018 10 30T13:30:13Z|External Id:SAMEA5055148|INSDC center name:UZH|INSDC first public:2018 12 01T17:03:21Z|INSDC last update:2018 10 30T13:30:13Z|INSDC status:public|Submitter Id:E MTAB 7349:HRASB 1A|age:8|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:Tgtwhh:Gal4;TgUAS:EGFP HRASV12|individual:mixed pool of 30 to 50 embryos|organism part:notochord|sample name:E MTAB 7349:HRASB 1A|scientific name:Danio rerio|sex:mixed,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Receptor Tyrosine Kinase pathway activation is sufficient to trigger chordoma in zebrafish,E MTAB 7349:HRASB 1A p,HRASB 1A p,Receptor Tyrosine Kinase pathway activation is sufficient to trigger chordoma in zebrafish,8 dpf wildtype and Tgtwhh:Gal4;TgUAS:EGFP HRASV12 were euthanized with 3% Tricaine methanesulfonate Sigma. Embryos were decapitated and incubated in Tripsin EDTA Sigma for 30 minutes to facilitate tissue dissociation. Notochords were then dissected using tungsten needles and immediately transferred to Trizol LS Ambion. We isolated 30 50 notochords per replicate  with a total of 3 replicates per condition 3x wildtype  3x HRASV12. Notochord RNA was extracted following the manufacturer's protocol using Trizol LS. RNA seq libraries were constructed using the Truseq stranded total RNA kit.,Experimental Factor: genotype:Tgtwhh:Gal4;TgUAS:EGFP HRASV12,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP111743,Illumina HiSeq 2500 paired end sequencing; Receptor Tyrosine Kinase pathway activation is sufficient to trigger chordoma in zebrafish,ENA FIRST PUBLIC:2018 12 01|ENA LAST UPDATE:2018 11 16,TCTCGCGC_GTCAGTAC__160520_I127_FCH732GBBXX_L8_CDKPEI160513002_1.fq.gz TCTCGCGC_GTCAGTAC__160520_I127_FCH732GBBXX_L8_CDKPEI160513002_2.fq.gz,fastq fastq,13035635000.0,65178175.0,E MTAB 7349:TCTCGCGC GTCAGTAC  160520 I127 FCH732GBBXX L8 CDKPEI160513002 ,0:100 1:100,A:3518767071;C:2991842048;G:3005014068;T:3518541297;N:1470516,100,100,,,3518767071,2991842048,3005014068,3518541297,1470516,ERX2868588,ERS2866325,ERA1640550,European Nucleotide Archive,European Nucleotide Archive,2,0.89434,0.89384,0.28234,0.28093,0.7274,0.72813,0.6198,0.62424,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,Unknown,2018-10-30,Larval,Larval,Brain,Nervous System
9336,ERR2862349,ERX2868587,ERS2866324,ERP111743,PRJEB29441,Receptor Tyrosine Kinase pathway activation is sufficient to trigger chordoma in zebrafish,E-MTAB-7349,Transcriptome Analysis,Oncogenic transformation of individual cell fates by developmental signaling cascades and transcription factors triggers diverse cancer types. Chordoma is a rare  aggressive tumor arising from transformed notochord remnants. Various potentially oncogenic factors have been found deregulated in chordoma and its metastases  yet clear causation remains uncertain. In particular  expression of the notochord controlling transcription factor Brachyury is hypothesized as key molecular driver in chordoma formation  yet an in vivo model to causally test its oncogenic potential in the notochord is missing. Here  we apply a zebrafish model of chordoma onset to identify the notochord transforming potential of tumor implicated candidate genes in vivo. We find that overexpression of human and zebrafish Brachyury  including a version with augmented transcriptional activity  is insufficient to initiate notochord hyperplasia in vivo. In contrast  the repeatedly chordoma implicated receptor tyrosine kinase RTK genes EGFR and KDR/VEGFR2 are sufficient to transform developmental notochord cells  akin to direct activation of Ras. Analysis of transcriptome and sub cellular organization from transformed notochords suggests that aberrant activation of RTK/Ras signaling attenuates processes required for the differentiation of notochord cells. Taken together  our results provide first in vivo indication for a lack of tumor initiating potential of Brachyury expression in the notochord  and suggest activated RTK signaling as potent hyperplasia initiating event in chordoma.,ENA FIRST PUBLIC:2018 12 01|ENA LAST UPDATE:2018 10 30,,Protocols: 8 dpf wildtype and Tgtwhh:Gal4;TgUAS:EGFP HRASV12 were euthanized with 3% Tricaine methanesulfonate Sigma. Embryos were decapitated and incubated in Tripsin EDTA Sigma for 30 minutes to facilitate tissue dissociation. Notochords were then dissected using tungsten needles and immediately transferred to Trizol LS Ambion. We isolated 30 50 notochords per replicate  with a total of 3 replicates per condition 3x wildtype  3x HRASV12. Notochord RNA was extracted following the manufacturer's protocol using Trizol LS. RNA seq libraries were constructed using the Truseq stranded total RNA kit.,2A,SAMEA5055147,UZH,ENA FIRST PUBLIC:2018 12 01T17:03:21Z|ENA LAST UPDATE:2018 10 30T13:30:13Z|External Id:SAMEA5055147|INSDC center name:UZH|INSDC first public:2018 12 01T17:03:21Z|INSDC last update:2018 10 30T13:30:13Z|INSDC status:public|Submitter Id:E MTAB 7349:2A|age:8|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:Tgtwhh:Gal4;TgUAS:EGFP HRASV12|individual:mixed pool of 30 to 50 embryos|organism part:notochord|sample name:E MTAB 7349:2A|scientific name:Danio rerio|sex:mixed,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Receptor Tyrosine Kinase pathway activation is sufficient to trigger chordoma in zebrafish,E MTAB 7349:2A p,2A p,Receptor Tyrosine Kinase pathway activation is sufficient to trigger chordoma in zebrafish,8 dpf wildtype and Tgtwhh:Gal4;TgUAS:EGFP HRASV12 were euthanized with 3% Tricaine methanesulfonate Sigma. Embryos were decapitated and incubated in Tripsin EDTA Sigma for 30 minutes to facilitate tissue dissociation. Notochords were then dissected using tungsten needles and immediately transferred to Trizol LS Ambion. We isolated 30 50 notochords per replicate  with a total of 3 replicates per condition 3x wildtype  3x HRASV12. Notochord RNA was extracted following the manufacturer's protocol using Trizol LS. RNA seq libraries were constructed using the Truseq stranded total RNA kit.,Experimental Factor: genotype:Tgtwhh:Gal4;TgUAS:EGFP HRASV12,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP111743,Illumina HiSeq 2500 paired end sequencing; Receptor Tyrosine Kinase pathway activation is sufficient to trigger chordoma in zebrafish,ENA FIRST PUBLIC:2018 12 01|ENA LAST UPDATE:2018 11 16,TCCGCGAA_GTCAGTAC__160520_I127_FCH732GBBXX_L8_CDKPEI160513002_2.fq.gz TCCGCGAA_GTCAGTAC__160520_I127_FCH732GBBXX_L8_CDKPEI160513002_1.fq.gz,fastq fastq,11671772800.0,58358864.0,E MTAB 7349:TCCGCGAA GTCAGTAC  160520 I127 FCH732GBBXX L8 CDKPEI160513002 ,0:100 1:100,A:3164806186;C:2661342106;G:2677258036;T:3167072669;N:1293803,100,100,,,3164806186,2661342106,2677258036,3167072669,1293803,ERX2868587,ERS2866324,ERA1640550,European Nucleotide Archive,European Nucleotide Archive,2,0.89879,0.89878,0.28162,0.28061,0.73212,0.73452,0.59632,0.60115,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,Unknown,2018-10-30,Larval,Larval,Brain,Nervous System
9711,ERR3366000,ERX3390288,ERS3506636,ERP115705,PRJEB32960,RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type,E-MTAB-8029,Transcriptome Analysis,RNA was extracted from 5 dpf embyros with and without xxx c.386C>T p.Ser129Phe variant in wdr37. Three independent RNA samples were prepared with each sample containing RNA from five individual embryos.,ENA FIRST PUBLIC:2019 07 19|ENA LAST UPDATE:2019 06 10,,Protocols: Five dpf zebrafish embryos were genotyped. Three independent RNA samples were prepared for both WT and mutant with 5 embryos pooled for each sample. RNA samples were prepared using Direct zol™ RNA MiniPrep kit Zymo Research. TruSeq RNA Sample Prep Kit v2 was used with protocol TruSeq RNA Sample Preparation v2 Guide  Part # 15026495 Rev. F.,WT 5dpf whole 3,SAMEA5702979,Medical College of Wisconsin,ENA FIRST PUBLIC:2019 07 19T04:04:05Z|ENA LAST UPDATE:2019 06 10T11:46:52Z|External Id:SAMEA5702979|INSDC center name:Medical College of Wisconsin|INSDC first public:2019 07 19T04:04:05Z|INSDC last update:2019 06 10T11:46:52Z|INSDC status:public|Submitter Id:E MTAB 8029:WT 5dpf whole 3|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 5|genotype:wild type genotype|individual:mixed pool of 5 embryos|organism part:whole organism|sample name:E MTAB 8029:WT 5dpf whole 3|scientific name:Danio rerio,,,,,,,,,HiSeq X Ten paired end sequencing; RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type,E MTAB 8029:WT 5dpf whole 3 p,WT 5dpf whole 3 p,RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type,Five dpf zebrafish embryos were genotyped. Three independent RNA samples were prepared for both WT and mutant with 5 embryos pooled for each sample. RNA samples were prepared using Direct zol™ RNA MiniPrep kit Zymo Research.  TruSeq RNA Sample Prep Kit v2 was used with protocol TruSeq RNA Sample Preparation v2 Guide  Part # 15026495 Rev. F.,Experimental Factor: genotype:wild type genotype,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq X Ten,,ERP115705,HiSeq X Ten paired end sequencing; RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type,ENA FIRST PUBLIC:2019 07 19|ENA LAST UPDATE:2019 06 10|instrument model:HiSeq X Ten,WT-5dpf-whole-3_1.fastq.gz WT-5dpf-whole-3_2.fastq.gz,fastq fastq,7638506536.0,25293068.0,E MTAB 8029:WT 5dpf whole 3 ,0:151 1:151,A:2033085216;C:1787203019;G:1834311569;T:1982924179;N:982553,151,151,,,2033085216,1787203019,1834311569,1982924179,982553,ERX3390288,ERS3506636,ERA1993466,European Nucleotide Archive,European Nucleotide Archive,2,0.92943,0.93349,0.06443,0.06476,0.67008,0.68489,0.45244,0.47512,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,Unknown,2019-06-10,Larval,Larval,Whole Organism,All anatomical structures
9712,ERR3365999,ERX3390287,ERS3506635,ERP115705,PRJEB32960,RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type,E-MTAB-8029,Transcriptome Analysis,RNA was extracted from 5 dpf embyros with and without xxx c.386C>T p.Ser129Phe variant in wdr37. Three independent RNA samples were prepared with each sample containing RNA from five individual embryos.,ENA FIRST PUBLIC:2019 07 19|ENA LAST UPDATE:2019 06 10,,Protocols: Five dpf zebrafish embryos were genotyped. Three independent RNA samples were prepared for both WT and mutant with 5 embryos pooled for each sample. RNA samples were prepared using Direct zol™ RNA MiniPrep kit Zymo Research. TruSeq RNA Sample Prep Kit v2 was used with protocol TruSeq RNA Sample Preparation v2 Guide  Part # 15026495 Rev. F.,WT 5dpf whole 2,SAMEA5702978,Medical College of Wisconsin,ENA FIRST PUBLIC:2019 07 19T04:04:05Z|ENA LAST UPDATE:2019 06 10T11:46:52Z|External Id:SAMEA5702978|INSDC center name:Medical College of Wisconsin|INSDC first public:2019 07 19T04:04:05Z|INSDC last update:2019 06 10T11:46:52Z|INSDC status:public|Submitter Id:E MTAB 8029:WT 5dpf whole 2|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 5|genotype:wild type genotype|individual:mixed pool of 5 embryos|organism part:whole organism|sample name:E MTAB 8029:WT 5dpf whole 2|scientific name:Danio rerio,,,,,,,,,HiSeq X Ten paired end sequencing; RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type,E MTAB 8029:WT 5dpf whole 2 p,WT 5dpf whole 2 p,RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type,Five dpf zebrafish embryos were genotyped. Three independent RNA samples were prepared for both WT and mutant with 5 embryos pooled for each sample. RNA samples were prepared using Direct zol™ RNA MiniPrep kit Zymo Research.  TruSeq RNA Sample Prep Kit v2 was used with protocol TruSeq RNA Sample Preparation v2 Guide  Part # 15026495 Rev. F.,Experimental Factor: genotype:wild type genotype,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq X Ten,,ERP115705,HiSeq X Ten paired end sequencing; RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type,ENA FIRST PUBLIC:2019 07 19|ENA LAST UPDATE:2019 06 10|instrument model:HiSeq X Ten,WT-5dpf--whole-2_1.fastq.gz WT-5dpf--whole-2_2.fastq.gz,fastq fastq,8029356446.0,26587273.0,E MTAB 8029:WT 5dpf  whole 2 ,0:151 1:151,A:2111720421;C:1902949602;G:1956400199;T:2057162414;N:1123810,151,151,,,2111720421,1902949602,1956400199,2057162414,1123810,ERX3390287,ERS3506635,ERA1993466,European Nucleotide Archive,European Nucleotide Archive,2,0.93664,0.9394,0.06211,0.06234,0.67036,0.68416,0.44709,0.4713,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,Unknown,2019-06-10,Larval,Larval,Whole Organism,All anatomical structures
9713,ERR3365998,ERX3390286,ERS3506634,ERP115705,PRJEB32960,RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type,E-MTAB-8029,Transcriptome Analysis,RNA was extracted from 5 dpf embyros with and without xxx c.386C>T p.Ser129Phe variant in wdr37. Three independent RNA samples were prepared with each sample containing RNA from five individual embryos.,ENA FIRST PUBLIC:2019 07 19|ENA LAST UPDATE:2019 06 10,,Protocols: Five dpf zebrafish embryos were genotyped. Three independent RNA samples were prepared for both WT and mutant with 5 embryos pooled for each sample. RNA samples were prepared using Direct zol™ RNA MiniPrep kit Zymo Research. TruSeq RNA Sample Prep Kit v2 was used with protocol TruSeq RNA Sample Preparation v2 Guide  Part # 15026495 Rev. F.,WT 5dpf whole 1,SAMEA5702977,Medical College of Wisconsin,ENA FIRST PUBLIC:2019 07 19T04:04:05Z|ENA LAST UPDATE:2019 06 10T11:46:52Z|External Id:SAMEA5702977|INSDC center name:Medical College of Wisconsin|INSDC first public:2019 07 19T04:04:05Z|INSDC last update:2019 06 10T11:46:52Z|INSDC status:public|Submitter Id:E MTAB 8029:WT 5dpf whole 1|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 5|genotype:wild type genotype|individual:mixed pool of 5 embryos|organism part:whole organism|sample name:E MTAB 8029:WT 5dpf whole 1|scientific name:Danio rerio,,,,,,,,,HiSeq X Ten paired end sequencing; RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type,E MTAB 8029:WT 5dpf whole 1 p,WT 5dpf whole 1 p,RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type,Five dpf zebrafish embryos were genotyped. Three independent RNA samples were prepared for both WT and mutant with 5 embryos pooled for each sample. RNA samples were prepared using Direct zol™ RNA MiniPrep kit Zymo Research.  TruSeq RNA Sample Prep Kit v2 was used with protocol TruSeq RNA Sample Preparation v2 Guide  Part # 15026495 Rev. F.,Experimental Factor: genotype:wild type genotype,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq X Ten,,ERP115705,HiSeq X Ten paired end sequencing; RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type,ENA FIRST PUBLIC:2019 07 19|ENA LAST UPDATE:2019 06 10|instrument model:HiSeq X Ten,WT-5dpf-whole-1_1.fastq.gz WT-5dpf-whole-1_2.fastq.gz,fastq fastq,7581314682.0,25103691.0,E MTAB 8029:WT 5dpf whole 1 ,0:151 1:151,A:2028089715;C:1768357820;G:1809746152;T:1974047455;N:1073540,151,151,,,2028089715,1768357820,1809746152,1974047455,1073540,ERX3390286,ERS3506634,ERA1993466,European Nucleotide Archive,European Nucleotide Archive,2,0.92712,0.93122,0.06876,0.06853,0.66464,0.67537,0.46592,0.47176,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,Unknown,2019-06-10,Larval,Larval,Whole Organism,All anatomical structures
9714,ERR3365997,ERX3390285,ERS3506633,ERP115705,PRJEB32960,RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type,E-MTAB-8029,Transcriptome Analysis,RNA was extracted from 5 dpf embyros with and without xxx c.386C>T p.Ser129Phe variant in wdr37. Three independent RNA samples were prepared with each sample containing RNA from five individual embryos.,ENA FIRST PUBLIC:2019 07 19|ENA LAST UPDATE:2019 06 10,,Protocols: Five dpf zebrafish embryos were genotyped. Three independent RNA samples were prepared for both WT and mutant with 5 embryos pooled for each sample. RNA samples were prepared using Direct zol™ RNA MiniPrep kit Zymo Research. TruSeq RNA Sample Prep Kit v2 was used with protocol TruSeq RNA Sample Preparation v2 Guide  Part # 15026495 Rev. F.,c386C T het 5dpf whl2,SAMEA5702976,Medical College of Wisconsin,ENA FIRST PUBLIC:2019 07 19T04:04:05Z|ENA LAST UPDATE:2019 06 10T11:46:52Z|External Id:SAMEA5702976|INSDC center name:Medical College of Wisconsin|INSDC first public:2019 07 19T04:04:05Z|INSDC last update:2019 06 10T11:46:52Z|INSDC status:public|Submitter Id:E MTAB 8029:c386C T het 5dpf whl2|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 5|genotype:wdr37 mutant c.386C>T p.Ser129Phe|individual:mixed pool of 5 embryos|organism part:whole organism|sample name:E MTAB 8029:c386C T het 5dpf whl2|scientific name:Danio rerio,,,,,,,,,HiSeq X Ten paired end sequencing; RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type,E MTAB 8029:c386C T het 5dpf whl2 p,c386C T het 5dpf whl2 p,RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type,Five dpf zebrafish embryos were genotyped. Three independent RNA samples were prepared for both WT and mutant with 5 embryos pooled for each sample. RNA samples were prepared using Direct zol™ RNA MiniPrep kit Zymo Research.  TruSeq RNA Sample Prep Kit v2 was used with protocol TruSeq RNA Sample Preparation v2 Guide  Part # 15026495 Rev. F.,Experimental Factor: genotype:wdr37 mutant c.386C>T p.Ser129Phe,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq X Ten,,ERP115705,HiSeq X Ten paired end sequencing; RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type,ENA FIRST PUBLIC:2019 07 19|ENA LAST UPDATE:2019 06 10|instrument model:HiSeq X Ten,c386C-T-het-5dpf-whl-2_1.fastq.gz c386C-T-het-5dpf-whl-2_2.fastq.gz,fastq fastq,7431512716.0,24607658.0,E MTAB 8029:c386C T het 5dpf whl 2 ,0:151 1:151,A:1981584337;C:1740735155;G:1776201259;T:1931922393;N:1069572,151,151,,,1981584337,1740735155,1776201259,1931922393,1069572,ERX3390285,ERS3506633,ERA1993466,European Nucleotide Archive,European Nucleotide Archive,2,0.92957,0.933,0.0653,0.06445,0.66967,0.6788,0.46228,0.46392,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,Unknown,2019-06-10,Larval,Larval,Whole Organism,All anatomical structures
9715,ERR3365996,ERX3390284,ERS3506632,ERP115705,PRJEB32960,RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type,E-MTAB-8029,Transcriptome Analysis,RNA was extracted from 5 dpf embyros with and without xxx c.386C>T p.Ser129Phe variant in wdr37. Three independent RNA samples were prepared with each sample containing RNA from five individual embryos.,ENA FIRST PUBLIC:2019 07 19|ENA LAST UPDATE:2019 06 10,,Protocols: Five dpf zebrafish embryos were genotyped. Three independent RNA samples were prepared for both WT and mutant with 5 embryos pooled for each sample. RNA samples were prepared using Direct zol™ RNA MiniPrep kit Zymo Research. TruSeq RNA Sample Prep Kit v2 was used with protocol TruSeq RNA Sample Preparation v2 Guide  Part # 15026495 Rev. F.,c386C T het 5dpf whl1,SAMEA5702975,Medical College of Wisconsin,ENA FIRST PUBLIC:2019 07 19T04:04:05Z|ENA LAST UPDATE:2019 06 10T11:46:52Z|External Id:SAMEA5702975|INSDC center name:Medical College of Wisconsin|INSDC first public:2019 07 19T04:04:05Z|INSDC last update:2019 06 10T11:46:52Z|INSDC status:public|Submitter Id:E MTAB 8029:c386C T het 5dpf whl1|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 5|genotype:wdr37 mutant c.386C>T p.Ser129Phe|individual:mixed pool of 5 embryos|organism part:whole organism|sample name:E MTAB 8029:c386C T het 5dpf whl1|scientific name:Danio rerio,,,,,,,,,HiSeq X Ten paired end sequencing; RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type,E MTAB 8029:c386C T het 5dpf whl1 p,c386C T het 5dpf whl1 p,RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type,Five dpf zebrafish embryos were genotyped. Three independent RNA samples were prepared for both WT and mutant with 5 embryos pooled for each sample. RNA samples were prepared using Direct zol™ RNA MiniPrep kit Zymo Research.  TruSeq RNA Sample Prep Kit v2 was used with protocol TruSeq RNA Sample Preparation v2 Guide  Part # 15026495 Rev. F.,Experimental Factor: genotype:wdr37 mutant c.386C>T p.Ser129Phe,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq X Ten,,ERP115705,HiSeq X Ten paired end sequencing; RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type,ENA FIRST PUBLIC:2019 07 19|ENA LAST UPDATE:2019 06 10|instrument model:HiSeq X Ten,c386C-T-het-5dpf-whl-1_1.fastq.gz c386C-T-het-5dpf-whl-1_2.fastq.gz,fastq fastq,7350140024.0,24338212.0,E MTAB 8029:c386C T het 5dpf whl 1 ,0:151 1:151,A:1930881649;C:1748604586;G:1790297791;T:1879354724;N:1001274,151,151,,,1930881649,1748604586,1790297791,1879354724,1001274,ERX3390284,ERS3506632,ERA1993466,European Nucleotide Archive,European Nucleotide Archive,2,0.93663,0.9384,0.05835,0.05828,0.66557,0.67588,0.467,0.46407,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,Unknown,2019-06-10,Larval,Larval,Whole Organism,All anatomical structures
9716,ERR3365995,ERX3390283,ERS3506631,ERP115705,PRJEB32960,RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type,E-MTAB-8029,Transcriptome Analysis,RNA was extracted from 5 dpf embyros with and without xxx c.386C>T p.Ser129Phe variant in wdr37. Three independent RNA samples were prepared with each sample containing RNA from five individual embryos.,ENA FIRST PUBLIC:2019 07 19|ENA LAST UPDATE:2019 06 10,,Protocols: Five dpf zebrafish embryos were genotyped. Three independent RNA samples were prepared for both WT and mutant with 5 embryos pooled for each sample. RNA samples were prepared using Direct zol™ RNA MiniPrep kit Zymo Research. TruSeq RNA Sample Prep Kit v2 was used with protocol TruSeq RNA Sample Preparation v2 Guide  Part # 15026495 Rev. F.,c.386C T het 5dpf whl3,SAMEA5702974,Medical College of Wisconsin,ENA FIRST PUBLIC:2019 07 19T04:04:05Z|ENA LAST UPDATE:2019 06 10T11:46:52Z|External Id:SAMEA5702974|INSDC center name:Medical College of Wisconsin|INSDC first public:2019 07 19T04:04:05Z|INSDC last update:2019 06 10T11:46:52Z|INSDC status:public|Submitter Id:E MTAB 8029:c.386C T het 5dpf whl3|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 5|genotype:wdr37 mutant c.386C>T p.Ser129Phe|individual:mixed pool of 5 embryos|organism part:whole organism|sample name:E MTAB 8029:c.386C T het 5dpf whl3|scientific name:Danio rerio,,,,,,,,,HiSeq X Ten paired end sequencing; RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type,E MTAB 8029:c.386C T het 5dpf whl3 p,c.386C T het 5dpf whl3 p,RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type,Five dpf zebrafish embryos were genotyped. Three independent RNA samples were prepared for both WT and mutant with 5 embryos pooled for each sample. RNA samples were prepared using Direct zol™ RNA MiniPrep kit Zymo Research.  TruSeq RNA Sample Prep Kit v2 was used with protocol TruSeq RNA Sample Preparation v2 Guide  Part # 15026495 Rev. F.,Experimental Factor: genotype:wdr37 mutant c.386C>T p.Ser129Phe,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq X Ten,,ERP115705,HiSeq X Ten paired end sequencing; RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type,ENA FIRST PUBLIC:2019 07 19|ENA LAST UPDATE:2019 06 12|instrument model:HiSeq X Ten,c386C-T-het-5dpf-whl-3_1.fastq.gz c386C-T-het-5dpf-whl-3_2.fastq.gz,fastq fastq,6059681642.0,20065171.0,E MTAB 8029:c386C T het 5dpf whl 3 ,0:151 1:151,A:1604034432;C:1423963595;G:1467519505;T:1563303018;N:861092,151,151,,,1604034432,1423963595,1467519505,1563303018,861092,ERX3390283,ERS3506631,ERA1993466,European Nucleotide Archive,European Nucleotide Archive,2,0.93301,0.9374,0.0658,0.06581,0.66681,0.68503,0.46139,0.47743,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,Unknown,2019-06-10,Larval,Larval,Whole Organism,All anatomical structures
10374,ERR8058375,ERX7625096,ERS10119356,ERP134902,PRJEB50332,RNA seq pf zebrafish embryos treated with drugs of abuse  morphine and cocaine,E-MTAB-11346,Transcriptome Analysis,To determine the transcriptomic changes elicted by drugs of abuse  zebrafish embryos were exposed to 10uM morphine from xxx hpf ttwo xxx hpf. Embryos were euthanized and deep frozen with N2l. RNA was extracted and an RNA seq assay was performed with Illumina Platform,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,,Protocols: At 72 hpf embryos were sacrificed by cold exposure  incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs  medium was removed and they were frozen in N2l. Tissue was stored at  80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific  the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm  and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented  reverse transcrided using random hexamers  three prime and five prime adapters were attached and library was amplified by PCR,Morphine 3,SAMEA12512752,"Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.",ENA FIRST PUBLIC:2022 12 31|ENA LAST UPDATE:2022 12 31|External Id:SAMEA12512752|INSDC center alias:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca  Spain.|INSDC center name:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca  Spain.|INSDC first public:2022 12 31T00:57:45Z|INSDC last update:2022 12 31T00:57:45Z|INSDC status:public|Submitter Id:E MTAB 11346:Morphine 3|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|developmental stage:72|genotype:wild type genotype|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11346:Morphine 3|strain:AB,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse  morphine and cocaine,E MTAB 11346:Morphine 3 p,Morphine 3 p,RNA seq pf zebrafish embryos treated with drugs of abuse  morphine and cocaine,At 72 hpf embryos were sacrificed by cold exposure  incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs  medium was removed and they were frozen in N2l. Tissue was stored at  80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific  the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm  and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™  RNA was fragmented  reverse transcrided using random hexamers  three prime and five prime adapters were attached and library was amplified by PCR,Experimental Factor: compound:morphine|Experimental Factor: dose:10,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP134902,Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse  morphine and cocaine,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,NG-10331_4M_lib138515_4790_6_1.fastq.gz NG-10331_4M_lib138515_4790_6_2.fastq.gz,fastq fastq,11175776640.0,44348320.0,E MTAB 11346:NG 10331 4M lib138515 4790 6 ,0:126 1:126,A:3058552548;C:2537121022;G:2531362154;T:3047376587;N:1364329,126,126,,,3058552548,2537121022,2531362154,3047376587,1364329,ERX7625096,ERS10119356,ERA8439547,"Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive","Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive",2,0.93345,0.93836,0.09826,0.09482,0.69497,0.69968,0.46885,0.46966,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Spain,2022-12-31,Larval,Larval,Whole Organism,All anatomical structures
10375,ERR8058374,ERX7625095,ERS10119355,ERP134902,PRJEB50332,RNA seq pf zebrafish embryos treated with drugs of abuse  morphine and cocaine,E-MTAB-11346,Transcriptome Analysis,To determine the transcriptomic changes elicted by drugs of abuse  zebrafish embryos were exposed to 10uM morphine from xxx hpf ttwo xxx hpf. Embryos were euthanized and deep frozen with N2l. RNA was extracted and an RNA seq assay was performed with Illumina Platform,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,,Protocols: At 72 hpf embryos were sacrificed by cold exposure  incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs  medium was removed and they were frozen in N2l. Tissue was stored at  80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific  the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm  and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented  reverse transcrided using random hexamers  three prime and five prime adapters were attached and library was amplified by PCR,Morphine 2,SAMEA12512751,"Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.",ENA FIRST PUBLIC:2022 12 31|ENA LAST UPDATE:2022 12 31|External Id:SAMEA12512751|INSDC center alias:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca  Spain.|INSDC center name:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca  Spain.|INSDC first public:2022 12 31T00:57:45Z|INSDC last update:2022 12 31T00:57:45Z|INSDC status:public|Submitter Id:E MTAB 11346:Morphine 2|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|developmental stage:72|genotype:wild type genotype|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11346:Morphine 2|strain:AB,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse  morphine and cocaine,E MTAB 11346:Morphine 2 p,Morphine 2 p,RNA seq pf zebrafish embryos treated with drugs of abuse  morphine and cocaine,At 72 hpf embryos were sacrificed by cold exposure  incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs  medium was removed and they were frozen in N2l. Tissue was stored at  80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific  the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm  and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™  RNA was fragmented  reverse transcrided using random hexamers  three prime and five prime adapters were attached and library was amplified by PCR,Experimental Factor: compound:morphine|Experimental Factor: dose:10,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP134902,Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse  morphine and cocaine,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,NG-10331_3M_lib138512_4790_5_1.fastq.gz NG-10331_3M_lib138512_4790_5_2.fastq.gz,fastq fastq,10428424776.0,41382638.0,E MTAB 11346:NG 10331 3M lib138512 4790 5 ,0:126 1:126,A:2840226558;C:2379827926;G:2389813154;T:2817428937;N:1128201,126,126,,,2840226558,2379827926,2389813154,2817428937,1128201,ERX7625095,ERS10119355,ERA8439547,"Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive","Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive",2,0.94204,0.9476,0.09827,0.09565,0.7008,0.70483,0.47435,0.47651,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Spain,2022-12-31,Larval,Larval,Whole Organism,All anatomical structures
10376,ERR8058373,ERX7625094,ERS10119354,ERP134902,PRJEB50332,RNA seq pf zebrafish embryos treated with drugs of abuse  morphine and cocaine,E-MTAB-11346,Transcriptome Analysis,To determine the transcriptomic changes elicted by drugs of abuse  zebrafish embryos were exposed to 10uM morphine from xxx hpf ttwo xxx hpf. Embryos were euthanized and deep frozen with N2l. RNA was extracted and an RNA seq assay was performed with Illumina Platform,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,,Protocols: At 72 hpf embryos were sacrificed by cold exposure  incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs  medium was removed and they were frozen in N2l. Tissue was stored at  80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific  the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm  and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented  reverse transcrided using random hexamers  three prime and five prime adapters were attached and library was amplified by PCR,Morphine 1,SAMEA12512750,"Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.",ENA FIRST PUBLIC:2022 12 31|ENA LAST UPDATE:2022 12 31|External Id:SAMEA12512750|INSDC center alias:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca  Spain.|INSDC center name:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca  Spain.|INSDC first public:2022 12 31T00:57:45Z|INSDC last update:2022 12 31T00:57:45Z|INSDC status:public|Submitter Id:E MTAB 11346:Morphine 1|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|developmental stage:72|genotype:wild type genotype|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11346:Morphine 1|strain:AB,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse  morphine and cocaine,E MTAB 11346:Morphine 1 p,Morphine 1 p,RNA seq pf zebrafish embryos treated with drugs of abuse  morphine and cocaine,At 72 hpf embryos were sacrificed by cold exposure  incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs  medium was removed and they were frozen in N2l. Tissue was stored at  80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific  the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm  and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™  RNA was fragmented  reverse transcrided using random hexamers  three prime and five prime adapters were attached and library was amplified by PCR,Experimental Factor: compound:morphine|Experimental Factor: dose:10,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP134902,Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse  morphine and cocaine,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,NG-10331_2M_lib138509_4790_5_1.fastq.gz NG-10331_2M_lib138509_4790_5_2.fastq.gz,fastq fastq,13158093312.0,52214656.0,E MTAB 11346:NG 10331 2M lib138509 4790 5 ,0:126 1:126,A:3613282182;C:2969954628;G:2964948806;T:3608471124;N:1436572,126,126,,,3613282182,2969954628,2964948806,3608471124,1436572,ERX7625094,ERS10119354,ERA8439547,"Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive","Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive",2,0.93755,0.93735,0.11204,0.10849,0.67838,0.68335,0.45142,0.46509,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Spain,2022-12-31,Larval,Larval,Whole Organism,All anatomical structures
10377,ERR8058372,ERX7625093,ERS10119353,ERP134902,PRJEB50332,RNA seq pf zebrafish embryos treated with drugs of abuse  morphine and cocaine,E-MTAB-11346,Transcriptome Analysis,To determine the transcriptomic changes elicted by drugs of abuse  zebrafish embryos were exposed to 10uM morphine from xxx hpf ttwo xxx hpf. Embryos were euthanized and deep frozen with N2l. RNA was extracted and an RNA seq assay was performed with Illumina Platform,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,,Protocols: At 72 hpf embryos were sacrificed by cold exposure  incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs  medium was removed and they were frozen in N2l. Tissue was stored at  80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific  the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm  and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented  reverse transcrided using random hexamers  three prime and five prime adapters were attached and library was amplified by PCR,Control 3,SAMEA12512749,"Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.",ENA FIRST PUBLIC:2022 12 31|ENA LAST UPDATE:2022 12 31|External Id:SAMEA12512749|INSDC center alias:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca  Spain.|INSDC center name:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca  Spain.|INSDC first public:2022 12 31T00:57:45Z|INSDC last update:2022 12 31T00:57:45Z|INSDC status:public|Submitter Id:E MTAB 11346:Control 3|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|developmental stage:72|genotype:wild type genotype|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11346:Control 3|strain:AB,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse  morphine and cocaine,E MTAB 11346:Control 3 p,Control 3 p,RNA seq pf zebrafish embryos treated with drugs of abuse  morphine and cocaine,At 72 hpf embryos were sacrificed by cold exposure  incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs  medium was removed and they were frozen in N2l. Tissue was stored at  80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific  the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm  and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™  RNA was fragmented  reverse transcrided using random hexamers  three prime and five prime adapters were attached and library was amplified by PCR,Experimental Factor: compound:n1,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP134902,Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse  morphine and cocaine,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,NG-10331_4C_lib138514_4790_6_1.fastq.gz NG-10331_4C_lib138514_4790_6_2.fastq.gz,fastq fastq,14106514968.0,55978234.0,E MTAB 11346:NG 10331 4C lib138514 4790 6 ,0:126 1:126,A:3862641975;C:3195634147;G:3187866318;T:3858673135;N:1699393,126,126,,,3862641975,3195634147,3187866318,3858673135,1699393,ERX7625093,ERS10119353,ERA8439547,"Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive","Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive",2,0.93657,0.93813,0.09783,0.09438,0.68925,0.69605,0.4741,0.47037,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Spain,2022-12-31,Larval,Larval,Whole Organism,All anatomical structures
10378,ERR8058371,ERX7625092,ERS10119352,ERP134902,PRJEB50332,RNA seq pf zebrafish embryos treated with drugs of abuse  morphine and cocaine,E-MTAB-11346,Transcriptome Analysis,To determine the transcriptomic changes elicted by drugs of abuse  zebrafish embryos were exposed to 10uM morphine from xxx hpf ttwo xxx hpf. Embryos were euthanized and deep frozen with N2l. RNA was extracted and an RNA seq assay was performed with Illumina Platform,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,,Protocols: At 72 hpf embryos were sacrificed by cold exposure  incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs  medium was removed and they were frozen in N2l. Tissue was stored at  80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific  the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm  and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented  reverse transcrided using random hexamers  three prime and five prime adapters were attached and library was amplified by PCR,Control 2,SAMEA12512748,"Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.",ENA FIRST PUBLIC:2022 12 31|ENA LAST UPDATE:2022 12 31|External Id:SAMEA12512748|INSDC center alias:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca  Spain.|INSDC center name:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca  Spain.|INSDC first public:2022 12 31T00:57:45Z|INSDC last update:2022 12 31T00:57:45Z|INSDC status:public|Submitter Id:E MTAB 11346:Control 2|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|developmental stage:72|genotype:wild type genotype|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11346:Control 2|strain:AB,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse  morphine and cocaine,E MTAB 11346:Control 2 p,Control 2 p,RNA seq pf zebrafish embryos treated with drugs of abuse  morphine and cocaine,At 72 hpf embryos were sacrificed by cold exposure  incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs  medium was removed and they were frozen in N2l. Tissue was stored at  80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific  the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm  and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™  RNA was fragmented  reverse transcrided using random hexamers  three prime and five prime adapters were attached and library was amplified by PCR,Experimental Factor: compound:n1,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP134902,Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse  morphine and cocaine,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,NG-10331_3C_lib138511_4790_5_1.fastq.gz NG-10331_3C_lib138511_4790_5_2.fastq.gz,fastq fastq,8889952680.0,35277590.0,E MTAB 11346:NG 10331 3C lib138511 4790 5 ,0:126 1:126,A:2424658667;C:2024699093;G:2023098669;T:2416527349;N:968902,126,126,,,2424658667,2024699093,2023098669,2416527349,968902,ERX7625092,ERS10119352,ERA8439547,"Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive","Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive",2,0.94168,0.94149,0.09632,0.09404,0.68996,0.69672,0.46007,0.47123,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Spain,2022-12-31,Larval,Larval,Whole Organism,All anatomical structures
10379,ERR8058370,ERX7625091,ERS10119351,ERP134902,PRJEB50332,RNA seq pf zebrafish embryos treated with drugs of abuse  morphine and cocaine,E-MTAB-11346,Transcriptome Analysis,To determine the transcriptomic changes elicted by drugs of abuse  zebrafish embryos were exposed to 10uM morphine from xxx hpf ttwo xxx hpf. Embryos were euthanized and deep frozen with N2l. RNA was extracted and an RNA seq assay was performed with Illumina Platform,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,,Protocols: At 72 hpf embryos were sacrificed by cold exposure  incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs  medium was removed and they were frozen in N2l. Tissue was stored at  80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific  the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm  and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented  reverse transcrided using random hexamers  three prime and five prime adapters were attached and library was amplified by PCR,Control 1,SAMEA12512747,"Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.",ENA FIRST PUBLIC:2022 12 31|ENA LAST UPDATE:2022 12 31|External Id:SAMEA12512747|INSDC center alias:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca  Spain.|INSDC center name:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca  Spain.|INSDC first public:2022 12 31T00:57:45Z|INSDC last update:2022 12 31T00:57:45Z|INSDC status:public|Submitter Id:E MTAB 11346:Control 1|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|developmental stage:72|genotype:wild type genotype|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11346:Control 1|strain:AB,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse  morphine and cocaine,E MTAB 11346:Control 1 p,Control 1 p,RNA seq pf zebrafish embryos treated with drugs of abuse  morphine and cocaine,At 72 hpf embryos were sacrificed by cold exposure  incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs  medium was removed and they were frozen in N2l. Tissue was stored at  80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific  the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm  and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™  RNA was fragmented  reverse transcrided using random hexamers  three prime and five prime adapters were attached and library was amplified by PCR,Experimental Factor: compound:n1,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP134902,Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse  morphine and cocaine,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,NG-10331_2C_lib138508_4790_5_1.fastq.gz NG-10331_2C_lib138508_4790_5_2.fastq.gz,fastq fastq,12714421356.0,50454053.0,E MTAB 11346:NG 10331 2C lib138508 4790 5 ,0:126 1:126,A:3470625985;C:2894721473;G:2886656166;T:3461036460;N:1381272,126,126,,,3470625985,2894721473,2886656166,3461036460,1381272,ERX7625091,ERS10119351,ERA8439547,"Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive","Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive",2,0.93951,0.93975,0.10489,0.10173,0.68134,0.68702,0.45337,0.44545,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Spain,2022-12-31,Larval,Larval,Whole Organism,All anatomical structures
10380,ERR8058369,ERX7625090,ERS10119350,ERP134902,PRJEB50332,RNA seq pf zebrafish embryos treated with drugs of abuse  morphine and cocaine,E-MTAB-11346,Transcriptome Analysis,To determine the transcriptomic changes elicted by drugs of abuse  zebrafish embryos were exposed to 10uM morphine from xxx hpf ttwo xxx hpf. Embryos were euthanized and deep frozen with N2l. RNA was extracted and an RNA seq assay was performed with Illumina Platform,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,,Protocols: At 72 hpf embryos were sacrificed by cold exposure  incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs  medium was removed and they were frozen in N2l. Tissue was stored at  80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific  the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm  and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented  reverse transcrided using random hexamers  three prime and five prime adapters were attached and library was amplified by PCR,Cocaine 3,SAMEA12512746,"Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.",ENA FIRST PUBLIC:2022 12 31|ENA LAST UPDATE:2022 12 31|External Id:SAMEA12512746|INSDC center alias:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca  Spain.|INSDC center name:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca  Spain.|INSDC first public:2022 12 31T00:57:45Z|INSDC last update:2022 12 31T00:57:45Z|INSDC status:public|Submitter Id:E MTAB 11346:Cocaine 3|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|developmental stage:72|genotype:wild type genotype|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11346:Cocaine 3|strain:AB,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse  morphine and cocaine,E MTAB 11346:Cocaine 3 p,Cocaine 3 p,RNA seq pf zebrafish embryos treated with drugs of abuse  morphine and cocaine,At 72 hpf embryos were sacrificed by cold exposure  incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs  medium was removed and they were frozen in N2l. Tissue was stored at  80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific  the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm  and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™  RNA was fragmented  reverse transcrided using random hexamers  three prime and five prime adapters were attached and library was amplified by PCR,Experimental Factor: compound:cocaine|Experimental Factor: dose:15,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP134902,Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse  morphine and cocaine,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,NG-10331_4CC_lib138516_4790_6_1.fastq.gz NG-10331_4CC_lib138516_4790_6_2.fastq.gz,fastq fastq,9574359984.0,37993492.0,E MTAB 11346:NG 10331 4CC lib138516 4790 6 ,0:126 1:126,A:2623103101;C:2170327733;G:2166494677;T:2613276955;N:1157518,126,126,,,2623103101,2170327733,2166494677,2613276955,1157518,ERX7625090,ERS10119350,ERA8439547,"Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive","Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive",2,0.9366,0.93856,0.10196,0.09901,0.69018,0.69611,0.46501,0.46917,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Spain,2022-12-31,Larval,Larval,Whole Organism,All anatomical structures
10381,ERR8058368,ERX7625089,ERS10119349,ERP134902,PRJEB50332,RNA seq pf zebrafish embryos treated with drugs of abuse  morphine and cocaine,E-MTAB-11346,Transcriptome Analysis,To determine the transcriptomic changes elicted by drugs of abuse  zebrafish embryos were exposed to 10uM morphine from xxx hpf ttwo xxx hpf. Embryos were euthanized and deep frozen with N2l. RNA was extracted and an RNA seq assay was performed with Illumina Platform,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,,Protocols: At 72 hpf embryos were sacrificed by cold exposure  incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs  medium was removed and they were frozen in N2l. Tissue was stored at  80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific  the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm  and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented  reverse transcrided using random hexamers  three prime and five prime adapters were attached and library was amplified by PCR,Cocaine 2,SAMEA12512745,"Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.",ENA FIRST PUBLIC:2022 12 31|ENA LAST UPDATE:2022 12 31|External Id:SAMEA12512745|INSDC center alias:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca  Spain.|INSDC center name:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca  Spain.|INSDC first public:2022 12 31T00:57:45Z|INSDC last update:2022 12 31T00:57:45Z|INSDC status:public|Submitter Id:E MTAB 11346:Cocaine 2|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|developmental stage:72|genotype:wild type genotype|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11346:Cocaine 2|strain:AB,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse  morphine and cocaine,E MTAB 11346:Cocaine 2 p,Cocaine 2 p,RNA seq pf zebrafish embryos treated with drugs of abuse  morphine and cocaine,At 72 hpf embryos were sacrificed by cold exposure  incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs  medium was removed and they were frozen in N2l. Tissue was stored at  80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific  the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm  and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™  RNA was fragmented  reverse transcrided using random hexamers  three prime and five prime adapters were attached and library was amplified by PCR,Experimental Factor: compound:cocaine|Experimental Factor: dose:15,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP134902,Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse  morphine and cocaine,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,NG-10331_3CC_lib138513_4828_1_1.fastq.gz NG-10331_3CC_lib138513_4828_1_2.fastq.gz,fastq fastq,6977861604.0,27689927.0,E MTAB 11346:NG 10331 3CC lib138513 4828 1 ,0:126 1:126,A:1938593544;C:1560242508;G:1564690065;T:1913028128;N:1307359,126,126,,,1938593544,1560242508,1564690065,1913028128,1307359,ERX7625089,ERS10119349,ERA8439547,"Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive","Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive",2,0.94226,0.9472,0.10354,0.10202,0.69911,0.69891,0.4749,0.47595,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Spain,2022-12-31,Larval,Larval,Whole Organism,All anatomical structures
10382,ERR8058367,ERX7625088,ERS10119348,ERP134902,PRJEB50332,RNA seq pf zebrafish embryos treated with drugs of abuse  morphine and cocaine,E-MTAB-11346,Transcriptome Analysis,To determine the transcriptomic changes elicted by drugs of abuse  zebrafish embryos were exposed to 10uM morphine from xxx hpf ttwo xxx hpf. Embryos were euthanized and deep frozen with N2l. RNA was extracted and an RNA seq assay was performed with Illumina Platform,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,,Protocols: At 72 hpf embryos were sacrificed by cold exposure  incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs  medium was removed and they were frozen in N2l. Tissue was stored at  80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific  the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm  and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented  reverse transcrided using random hexamers  three prime and five prime adapters were attached and library was amplified by PCR,Cocaine 1,SAMEA12512744,"Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.",ENA FIRST PUBLIC:2022 12 31|ENA LAST UPDATE:2022 12 31|External Id:SAMEA12512744|INSDC center alias:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca  Spain.|INSDC center name:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca  Spain.|INSDC first public:2022 12 31T00:57:45Z|INSDC last update:2022 12 31T00:57:45Z|INSDC status:public|Submitter Id:E MTAB 11346:Cocaine 1|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|developmental stage:72|genotype:wild type genotype|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11346:Cocaine 1|strain:AB,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse  morphine and cocaine,E MTAB 11346:Cocaine 1 p,Cocaine 1 p,RNA seq pf zebrafish embryos treated with drugs of abuse  morphine and cocaine,At 72 hpf embryos were sacrificed by cold exposure  incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs  medium was removed and they were frozen in N2l. Tissue was stored at  80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific  the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm  and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™  RNA was fragmented  reverse transcrided using random hexamers  three prime and five prime adapters were attached and library was amplified by PCR,Experimental Factor: compound:cocaine|Experimental Factor: dose:15,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP134902,Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse  morphine and cocaine,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,NG-10331_2CC_lib138510_4790_5_1.fastq.gz NG-10331_2CC_lib138510_4790_5_2.fastq.gz,fastq fastq,13608728532.0,54002891.0,E MTAB 11346:NG 10331 2CC lib138510 4790 5 ,0:126 1:126,A:3713185950;C:3097562409;G:3088976816;T:3707538756;N:1464601,126,126,,,3713185950,3097562409,3088976816,3707538756,1464601,ERX7625088,ERS10119348,ERA8439547,"Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive","Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive",2,0.93921,0.94011,0.104,0.10075,0.68043,0.68523,0.44482,0.4591,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Spain,2022-12-31,Larval,Larval,Whole Organism,All anatomical structures
28383,SRR26319642,SRX22027776,SRS19100884,SRP463771,PRJNA1022139,Danio rerio strain:AB Transcriptome or Gene expression,PRJNA1022139,Other,Effects and Mechanisms of Porphyromonas gingivalis Outer Membrane Vesicles Induced Cardiovascular Injury,,,,,WT 3,,strain:AB|age:larvae|dev stage:48 hpi|collection date:2022 11 06|geo loc name:China:Fujian|sex:not applicable|tissue:Whole body|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio:PBS treated,WT 3,WT 3,PBS treated,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP463771,,,WT_3_1.fq.gz WT_3_2.fq.gz,fastq fastq,6638052600.0,22126842.0,WT 3 1.fq.gz,0:150 1:150,A:1795389898;C:1548955123;G:1524873816;T:1768758791;N:74972,150,150,,,1795389898,1548955123,1524873816,1768758791,74972,SRX22027776,SRS19100884,SRA1727571,"Hospital of Stomatology, Fujian Medical University|Department of Orthodontics","Hospital of Stomatology, Fujian Medical University",2,0.94512,0.94441,0.0675,0.06744,0.69457,0.69353,0.47279,0.46651,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2023-10-11,Larval,Larval,Trunk,Surface Structure
28384,SRR26316552,SRX22024811,SRS19097993,SRP463771,PRJNA1022139,Danio rerio strain:AB Transcriptome or Gene expression,PRJNA1022139,Other,Effects and Mechanisms of Porphyromonas gingivalis Outer Membrane Vesicles Induced Cardiovascular Injury,,,,WT 1,WT 1,,strain:AB|age:larvae|dev stage:48 hpi|collection date:2022 11 06|geo loc name:China:Fujian|sex:not applicable|tissue:Whole body|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio:PBS treated,WT 1,WT 1,PBS treated,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP463771,,,WT_1_1.fq.gz WT_1_2.fq.gz,fastq fastq,6806096700.0,22686989.0,WT 1 1.fq.gz,0:150 1:150,A:1824700900;C:1607509679;G:1583685250;T:1790098957;N:101914,150,150,,,1824700900,1607509679,1583685250,1790098957,101914,SRX22024811,SRS19097993,SRA1727466,"Hospital of Stomatology, Fujian Medical University|Department of Orthodontics","Hospital of Stomatology, Fujian Medical University",2,0.94441,0.94413,0.0633,0.06243,0.69589,0.69603,0.47278,0.46311,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2023-10-11,Larval,Larval,Trunk,Surface Structure
28385,SRR26298124,SRX22006623,SRS19081287,SRP463771,PRJNA1022139,Danio rerio strain:AB Transcriptome or Gene expression,PRJNA1022139,Other,Effects and Mechanisms of Porphyromonas gingivalis Outer Membrane Vesicles Induced Cardiovascular Injury,,,,Pg OMVs 3,Pg OMVs 3,,strain:AB|age:larvae|dev stage:48 hpi|collection date:2022 11 06|geo loc name:China:Fujian|sex:not applicable|tissue:whole body|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio:Pg OMVs treated,Pg OMVs 3,Pg OMVs 3,Pg OMVs treated,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP463771,,,Pgom_3_1.fq.gz Pgom_3_2.fq.gz,fastq fastq,6799556700.0,22665189.0,Pgom 3 1.fq.gz,0:150 1:150,A:1841955583;C:1578686846;G:1566584129;T:1812024582;N:305560,150,150,,,1841955583,1578686846,1566584129,1812024582,305560,SRX22006623,SRS19081287,SRA1726653,"Hospital of Stomatology, Fujian Medical University|Department of Orthodontics","Hospital of Stomatology, Fujian Medical University",2,0.93679,0.93643,0.0705,0.07046,0.69522,0.69572,0.46657,0.46769,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2023-10-09,Larval,Larval,Trunk,Surface Structure
28386,SRR26284600,SRX21993532,SRS19068394,SRP463771,PRJNA1022139,Danio rerio strain:AB Transcriptome or Gene expression,PRJNA1022139,Other,Effects and Mechanisms of Porphyromonas gingivalis Outer Membrane Vesicles Induced Cardiovascular Injury,,,,Pg OMVs 2,Pg OMVs 2,,strain:AB|age:larvae|dev stage:48 hpi|collection date:2022 11 06|geo loc name:China:Fujian|sex:not applicable|tissue:whole body|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio:Pg OMVs treated,Pg OMVs 2,Pg OMVs 2,Pg OMVs treated,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP463771,,,Pgom_2_2.fq.gz Pgom_2_1.fq.gz,fastq fastq,6873087300.0,22910291.0,Pgom 2 1.fq.gz,0:150 1:150,A:1852244290;C:1608380801;G:1593161224;T:1819219541;N:81444,150,150,,,1852244290,1608380801,1593161224,1819219541,81444,SRX21993532,SRS19068394,SRA1726180,"Hospital of Stomatology, Fujian Medical University|Department of Orthodontics","Hospital of Stomatology, Fujian Medical University",2,0.93991,0.93977,0.06917,0.06976,0.68883,0.68931,0.47575,0.45981,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2023-10-06,Larval,Larval,Trunk,Surface Structure
28387,SRR26283523,SRX21992473,SRS19067399,SRP463771,PRJNA1022139,Danio rerio strain:AB Transcriptome or Gene expression,PRJNA1022139,Other,Effects and Mechanisms of Porphyromonas gingivalis Outer Membrane Vesicles Induced Cardiovascular Injury,,,,,WT 2,,strain:AB|age:larvae|dev stage:48 hpi|collection date:2022 11 06|geo loc name:China:Fujian|sex:not applicable|tissue:whole body|BioSampleModel:Model organism or animal,,,,,,,,,not applicable,not applicable,not applicable,wild type,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP463771,,,WT_2_1.fq.gz WT_2_2.fq.gz,fastq fastq,6662879700.0,22209599.0,WT 2 1.fq.gz,0:150 1:150,A:1793163738;C:1560948295;G:1543048656;T:1765563975;N:155036,150,150,,,1793163738,1560948295,1543048656,1765563975,155036,SRX21992473,SRS19067399,SRA1726064,"Hospital of Stomatology, Fujian Medical University|Department of Orthodontics","Hospital of Stomatology, Fujian Medical University",2,0.94479,0.94546,0.06315,0.06307,0.69751,0.69627,0.46332,0.45959,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2023-10-06,Larval,Larval,Trunk,Surface Structure
28388,SRR26213372,SRX21923899,SRS19008410,SRP463771,PRJNA1022139,Danio rerio strain:AB Transcriptome or Gene expression,PRJNA1022139,Other,Effects and Mechanisms of Porphyromonas gingivalis Outer Membrane Vesicles Induced Cardiovascular Injury,,,,Model organism or animal sample from Danio rerio,Pg OMVs 1 a,,strain:AB|dev stage:larvae|collection date:2022 11 06|geo loc name:China:Fujian|sex:not applicable|tissue:whole body|treatment:Pg OMVs injected|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish:48 hpi,Pg OMVs group1a,Pg OMVs group1a,Pg OMVs injected,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP463771,,,Pgom_1_1.fq.gz Pgom_1_2.fq.gz,fastq fastq,6768097800.0,22560326.0,Pgom 1 1.fq.gz,0:150 1:150,A:1807197563;C:1591333381;G:1591884474;T:1777600011;N:82371,150,150,,,1807197563,1591333381,1591884474,1777600011,82371,SRX21923899,SRS19008410,SRA1722765,"Hospital of Stomatology, Fujian Medical University|Department of Orthodontics","Hospital of Stomatology, Fujian Medical University",2,0.93975,0.93898,0.05827,0.05801,0.68521,0.68517,0.46882,0.46802,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2023-09-28,Larval,Larval,Trunk,Surface Structure
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.,,,,WT re#2,WT re#2,,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 °C for 12 h followed by recovery at 28 °C for 6 h|replicate:replicate = biological replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,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.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP495638,,,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,,,1953410192,1717566713,1749971750,1938773172,385473,SRX23967985,SRS20767216,SRA1825819,Chinese Academy of Sciences|Institute of Hydrobiology,Chinese Academy of Sciences,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,nebnext,bulk,unknown,unknown,,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.,,,,WT re#1,WT re#1,,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 °C for 12 h followed by recovery at 28 °C for 6 h|replicate:replicate = biological replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,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.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP495638,,,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,,,1931654450,1711483982,1750280300,1911082544,475024,SRX23967984,SRS20767215,SRA1825819,Chinese Academy of Sciences|Institute of Hydrobiology,Chinese Academy of Sciences,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,nebnext,bulk,unknown,unknown,,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.,,,,WT cs#4,WT cs#4,,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 °C for 12 h|replicate:replicate = biological replicate 4|BioSampleModel:Model organism or animal,,,,,,,,,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.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP495638,,,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,,,1893835105,1654405982,1690442550,1878207126,375537,SRX23967983,SRS20767214,SRA1825819,Chinese Academy of Sciences|Institute of Hydrobiology,Chinese Academy of Sciences,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,nebnext,bulk,unknown,unknown,,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.,,,,WT cs#3,WT cs#3,,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 °C for 12 h|replicate:replicate = biological replicate 3|BioSampleModel:Model organism or animal,,,,,,,,,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.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP495638,,,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,,,2066456864,1808454260,1837135016,2054303347,406013,SRX23967982,SRS20767213,SRA1825819,Chinese Academy of Sciences|Institute of Hydrobiology,Chinese Academy of Sciences,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,nebnext,bulk,unknown,unknown,,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.,,,,WT cs#2,WT cs#2,,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 °C for 12 h|replicate:replicate = biological replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,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. 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.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP495638,,,wt-cs-2_S36_L004_R1_001.fastq.gz wt-cs-2_S36_L004_R2_001.fastq.gz,fastq fastq,7863905100.0,26213017.0,wt cs 2 S36 L004 R1 001.fastq.gz,0:150 1:150,A:2095810379;C:1826144395;G:1861582031;T:2079957538;N:410757,150,150,,,2095810379,1826144395,1861582031,2079957538,410757,SRX23967981,SRS20767212,SRA1825819,Chinese Academy of Sciences|Institute of Hydrobiology,Chinese Academy of Sciences,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,nebnext,bulk,unknown,unknown,,China,2024-03-16,Larval,Larval,Trunk,Surface Structure
31478,SRR28362826,SRX23967980,SRS20767211,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.,,,,WT cs#1,WT cs#1,,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 °C for 12 h|replicate:replicate = biological replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,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. 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.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP495638,,,wt-cs-1_S35_L004_R1_001.fastq.gz wt-cs-1_S35_L004_R2_001.fastq.gz,fastq fastq,6904903200.0,23016344.0,wt cs 1 S35 L004 R1 001.fastq.gz,0:150 1:150,A:1837602528;C:1605156041;G:1638534027;T:1823249554;N:361050,150,150,,,1837602528,1605156041,1638534027,1823249554,361050,SRX23967980,SRS20767211,SRA1825819,Chinese Academy of Sciences|Institute of Hydrobiology,Chinese Academy of Sciences,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,nebnext,bulk,unknown,unknown,,China,2024-03-16,Larval,Larval,Trunk,Surface Structure
31479,SRR28362827,SRX23967979,SRS20767210,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.,,,,WT ctrl#4,WT ctrl#4,,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,,,,,,,,,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.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP495638,,,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,,,1706071185,1570838977,1609917484,1689461796,308158,SRX23967979,SRS20767210,SRA1825819,Chinese Academy of Sciences|Institute of Hydrobiology,Chinese Academy of Sciences,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,nebnext,bulk,unknown,unknown,,China,2024-03-16,Larval,Larval,Trunk,Surface Structure
31480,SRR28362828,SRX23967978,SRS20767209,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.,,,,noxo1a re#4,noxo1a re#4,,strain:AB strain|dev stage:Larvae|collection date:2023 03 05|geo loc name:China: Wuhan|sex:not determined|tissue:Whole body|genotype:noxo1a mutant with indel|treatment:Exposed to 10 °C for 12 h followed by recovery at 28 °C for 6 h|replicate:replicate = biological replicate 4|BioSampleModel:Model organism or animal,,,,,,,,,noxo1a re#4,noxo1a re#4,noxo1a re#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.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP495638,,,noxo1a-re-4_S0_L000_R1_000.fastq.gz noxo1a-re-4_S0_L000_R2_000.fastq.gz,fastq fastq,6288486900.0,20961623.0,noxo1a re 4 S0 L000 R1 000.fastq.gz,0:150 1:150,A:1666277839;C:1470224724;G:1500784713;T:1651119958;N:79666,150,150,,,1666277839,1470224724,1500784713,1651119958,79666,SRX23967978,SRS20767209,SRA1825819,Chinese Academy of Sciences|Institute of Hydrobiology,Chinese Academy of Sciences,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,nebnext,bulk,unknown,unknown,,China,2024-03-16,Larval,Larval,Trunk,Surface Structure
31481,SRR28362830,SRX23967977,SRS20767208,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.,,,,noxo1a re#3,noxo1a re#3,,strain:AB strain|dev stage:Larvae|collection date:2023 03 05|geo loc name:China: Wuhan|sex:not determined|tissue:Whole body|genotype:noxo1a mutant with indel|treatment:Exposed to 10 °C for 12 h followed by recovery at 28 °C for 6 h|replicate:replicate = biological replicate 3|BioSampleModel:Model organism or animal,,,,,,,,,noxo1a re#3,noxo1a re#3,noxo1a re#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.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP495638,,,noxo1a-re-3_S1_L001_R1_001.fastq.gz noxo1a-re-3_S1_L001_R2_001.fastq.gz noxo1a-re-3_S2_L004_R1_001.fastq.gz noxo1a-re-3_S2_L004_R2_001.fastq.gz,fastq fastq fastq fastq,6993336600.0,23311122.0,noxo1a re 3 S1 L001 R1 001.fastq.gz,0:150 1:150,A:1857289544;C:1633216640;G:1660910386;T:1841856529;N:63501,150,150,,,1857289544,1633216640,1660910386,1841856529,63501,SRX23967977,SRS20767208,SRA1825819,Chinese Academy of Sciences|Institute of Hydrobiology,Chinese Academy of Sciences,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,nebnext,bulk,unknown,unknown,,China,2024-03-16,Larval,Larval,Trunk,Surface Structure
31482,SRR28362831,SRX23967976,SRS20767207,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.,,,,noxo1a re#2,noxo1a re#2,,strain:AB strain|dev stage:Larvae|collection date:2023 03 05|geo loc name:China: Wuhan|sex:not determined|tissue:Whole body|genotype:noxo1a mutant with indel|treatment:Exposed to 10 °C for 12 h followed by recovery at 28 °C for 6 h|replicate:replicate = biological replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,noxo1a re#2,noxo1a re#2,noxo1a 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.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP495638,,,noxo1a-re-2_S1_L004_R1_001.fastq.gz noxo1a-re-2_S1_L004_R2_001.fastq.gz,fastq fastq,6021534600.0,20071782.0,noxo1a re 2 S1 L004 R1 001.fastq.gz,0:150 1:150,A:1597183597;C:1408878472;G:1434927510;T:1580500451;N:44570,150,150,,,1597183597,1408878472,1434927510,1580500451,44570,SRX23967976,SRS20767207,SRA1825819,Chinese Academy of Sciences|Institute of Hydrobiology,Chinese Academy of Sciences,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,nebnext,bulk,unknown,unknown,,China,2024-03-16,Larval,Larval,Trunk,Surface Structure
31483,SRR28362832,SRX23967975,SRS20767206,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.,,,,noxo1a re#1,noxo1a re#1,,strain:AB strain|dev stage:Larvae|collection date:2023 03 05|geo loc name:China: Wuhan|sex:not determined|tissue:Whole body|genotype:noxo1a mutant with indel|treatment:Exposed to 10 °C for 12 h followed by recovery at 28 °C for 6 h|replicate:replicate = biological replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,noxo1a re#1,noxo1a re#1,noxo1a 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.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP495638,,,noxo1a-re-1_S44_L004_R1_001.fastq.gz noxo1a-re-1_S44_L004_R2_001.fastq.gz,fastq fastq,6459165300.0,21530551.0,noxo1a re 1 S44 L004 R1 001.fastq.gz,0:150 1:150,A:1704973328;C:1516599476;G:1546419572;T:1690833152;N:339772,150,150,,,1704973328,1516599476,1546419572,1690833152,339772,SRX23967975,SRS20767206,SRA1825819,Chinese Academy of Sciences|Institute of Hydrobiology,Chinese Academy of Sciences,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,nebnext,bulk,unknown,unknown,,China,2024-03-16,Larval,Larval,Trunk,Surface Structure
31484,SRR28362833,SRX23967974,SRS20767205,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.,,,,WT ctrl#3,WT ctrl#3,,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 3|BioSampleModel:Model organism or animal,,,,,,,,,WT ctrl#3,WT ctrl#3,WT ctrl#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.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP495638,,,wt-ctrl-3_S31_L004_R1_001.fastq.gz wt-ctrl-3_S31_L004_R2_001.fastq.gz,fastq fastq,7847308200.0,26157694.0,wt ctrl 3 S31 L004 R1 001.fastq.gz,0:150 1:150,A:2059319370;C:1853070672;G:1895075718;T:2039431518;N:410922,150,150,,,2059319370,1853070672,1895075718,2039431518,410922,SRX23967974,SRS20767205,SRA1825819,Chinese Academy of Sciences|Institute of Hydrobiology,Chinese Academy of Sciences,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,nebnext,bulk,unknown,unknown,,China,2024-03-16,Larval,Larval,Trunk,Surface Structure
31485,SRR28362834,SRX23967973,SRS20767204,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.,,,,noxo1a cs#4,noxo1a cs#4,,strain:AB strain|dev stage:Larvae|collection date:2023 03 05|geo loc name:China: Wuhan|sex:not determined|tissue:Whole body|genotype:noxo1a mutant with indel|treatment:Exposed to 10 °C for 12 h|replicate:replicate = biological replicate 4|BioSampleModel:Model organism or animal,,,,,,,,,noxo1a cs#4,noxo1a cs#4,noxo1a 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.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP495638,,,noxo1a-cs-4_S23_L004_R1_001.fastq.gz noxo1a-cs-4_S23_L004_R2_001.fastq.gz,fastq fastq,6310591800.0,21035306.0,noxo1a cs 4 S23 L004 R1 001.fastq.gz,0:150 1:150,A:1649781865;C:1495677401;G:1531600458;T:1633236277;N:295799,150,150,,,1649781865,1495677401,1531600458,1633236277,295799,SRX23967973,SRS20767204,SRA1825819,Chinese Academy of Sciences|Institute of Hydrobiology,Chinese Academy of Sciences,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,nebnext,bulk,unknown,unknown,,China,2024-03-16,Larval,Larval,Trunk,Surface Structure
31486,SRR28362835,SRX23967972,SRS20767203,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.,,,,noxo1a cs#3,noxo1a cs#3,,strain:AB strain|dev stage:Larvae|collection date:2023 03 05|geo loc name:China: Wuhan|sex:not determined|tissue:Whole body|genotype:noxo1a mutant with indel|treatment:Exposed to 10 °C for 12 h|replicate:replicate = biological replicate 3|BioSampleModel:Model organism or animal,,,,,,,,,noxo1a cs#3,noxo1a cs#3,noxo1a 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.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP495638,,,noxo1a-cs-3_S40_L004_R1_001.fastq.gz noxo1a-cs-3_S40_L004_R2_001.fastq.gz,fastq fastq,6704622300.0,22348741.0,noxo1a cs 3 S40 L004 R1 001.fastq.gz,0:150 1:150,A:1767126555;C:1576232837;G:1610607905;T:1750301837;N:353166,150,150,,,1767126555,1576232837,1610607905,1750301837,353166,SRX23967972,SRS20767203,SRA1825819,Chinese Academy of Sciences|Institute of Hydrobiology,Chinese Academy of Sciences,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,nebnext,bulk,unknown,unknown,,China,2024-03-16,Larval,Larval,Trunk,Surface Structure
31487,SRR28362836,SRX23967971,SRS20767202,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.,,,,noxo1a cs#2,noxo1a cs#2,,strain:AB strain|dev stage:Larvae|collection date:2023 03 05|geo loc name:China: Wuhan|sex:not determined|tissue:Whole body|genotype:noxo1a mutant with indel|treatment:Exposed to 10 °C for 12 h|replicate:replicate = biological replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,noxo1a cs#2,noxo1a cs#2,noxo1a 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. 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.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP495638,,,noxo1a-cs-2_S22_L004_R1_001.fastq.gz noxo1a-cs-2_S22_L004_R2_001.fastq.gz,fastq fastq,6500565900.0,21668553.0,noxo1a cs 2 S22 L004 R1 001.fastq.gz,0:150 1:150,A:1717991417;C:1522293556;G:1558318730;T:1701666138;N:296059,150,150,,,1717991417,1522293556,1558318730,1701666138,296059,SRX23967971,SRS20767202,SRA1825819,Chinese Academy of Sciences|Institute of Hydrobiology,Chinese Academy of Sciences,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,nebnext,bulk,unknown,unknown,,China,2024-03-16,Larval,Larval,Trunk,Surface Structure
31488,SRR28362837,SRX23967970,SRS20767201,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.,,,,noxo1a cs#1,noxo1a cs#1,,strain:AB strain|dev stage:Larvae|collection date:2023 03 05|geo loc name:China: Wuhan|sex:not determined|tissue:Whole body|genotype:noxo1a mutant with indel|treatment:Exposed to 10 °C for 12 h|replicate:replicate = biological replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,noxo1a cs#1,noxo1a cs#1,noxo1a 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. 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.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP495638,,,noxo1a-cs-1_S39_L004_R1_001.fastq.gz noxo1a-cs-1_S39_L004_R2_001.fastq.gz,fastq fastq,6662253600.0,22207512.0,noxo1a cs 1 S39 L004 R1 001.fastq.gz,0:150 1:150,A:1765032411;C:1556260041;G:1592453845;T:1748156183;N:351120,150,150,,,1765032411,1556260041,1592453845,1748156183,351120,SRX23967970,SRS20767201,SRA1825819,Chinese Academy of Sciences|Institute of Hydrobiology,Chinese Academy of Sciences,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,nebnext,bulk,unknown,unknown,,China,2024-03-16,Larval,Larval,Trunk,Surface Structure
31489,SRR28362838,SRX23967969,SRS20767200,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.,,,,noxo1a ctrl#4,noxo1a ctrl#4,,strain:AB strain|dev stage:Larvae|collection date:2023 03 05|geo loc name:China: Wuhan|sex:not determined|tissue:Whole body|genotype:noxo1a mutant with indel|treatment:Collected at 96 hpf|replicate:replicate = biological replicate 4|BioSampleModel:Model organism or animal,,,,,,,,,noxo1a ctrl#4,noxo1a ctrl#4,noxo1a 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.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP495638,,,noxo1a-ctrl-4_S21_L004_R1_001.fastq.gz noxo1a-ctrl-4_S21_L004_R2_001.fastq.gz,fastq fastq,6428415000.0,21428050.0,noxo1a ctrl 4 S21 L004 R1 001.fastq.gz,0:150 1:150,A:1704089785;C:1501936031;G:1530024908;T:1692071168;N:293108,150,150,,,1704089785,1501936031,1530024908,1692071168,293108,SRX23967969,SRS20767200,SRA1825819,Chinese Academy of Sciences|Institute of Hydrobiology,Chinese Academy of Sciences,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,nebnext,bulk,unknown,unknown,,China,2024-03-16,Larval,Larval,Trunk,Surface Structure
31490,SRR28362839,SRX23967968,SRS20767199,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.,,,,noxo1a ctrl#3,noxo1a ctrl#3,,strain:AB strain|dev stage:Larvae|collection date:2023 03 05|geo loc name:China: Wuhan|sex:not determined|tissue:Whole body|genotype:noxo1a mutant with indel|treatment:Collected at 96 hpf|replicate:replicate = biological replicate 3|BioSampleModel:Model organism or animal,,,,,,,,,noxo1a ctrl#3,noxo1a ctrl#3,noxo1a ctrl#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.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP495638,,,noxo1a-ctrl-3_S34_L004_R1_001.fastq.gz noxo1a-ctrl-3_S34_L004_R2_001.fastq.gz,fastq fastq,6988991100.0,23296637.0,noxo1a ctrl 3 S34 L004 R1 001.fastq.gz,0:150 1:150,A:1853131820;C:1633719581;G:1663738566;T:1838036906;N:364227,150,150,,,1853131820,1633719581,1663738566,1838036906,364227,SRX23967968,SRS20767199,SRA1825819,Chinese Academy of Sciences|Institute of Hydrobiology,Chinese Academy of Sciences,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,nebnext,bulk,unknown,unknown,,China,2024-03-16,Larval,Larval,Trunk,Surface Structure
31491,SRR28362840,SRX23967967,SRS20767198,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.,,,,noxo1a ctrl#2,noxo1a ctrl#2,,strain:AB strain|dev stage:Larvae|collection date:2023 03 05|geo loc name:China: Wuhan|sex:not determined|tissue:Whole body|genotype:noxo1a mutant with indel|treatment:Collected at 96 hpf|replicate:replicate = biological replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,noxo1a ctrl#2,noxo1a ctrl#2,noxo1a ctrl#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.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP495638,,,noxo1a-ctrl-2_S33_L004_R1_001.fastq.gz noxo1a-ctrl-2_S33_L004_R2_001.fastq.gz,fastq fastq,6591167700.0,21970559.0,noxo1a ctrl 2 S33 L004 R1 001.fastq.gz,0:150 1:150,A:1750729608;C:1535828938;G:1566173485;T:1738090384;N:345285,150,150,,,1750729608,1535828938,1566173485,1738090384,345285,SRX23967967,SRS20767198,SRA1825819,Chinese Academy of Sciences|Institute of Hydrobiology,Chinese Academy of Sciences,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,nebnext,bulk,unknown,unknown,,China,2024-03-16,Larval,Larval,Trunk,Surface Structure
31492,SRR28362841,SRX23967966,SRS20767197,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.,,,,noxo1a ctrl#1,noxo1a ctrl#1,,strain:AB strain|dev stage:Larvae|collection date:2023 03 05|geo loc name:China: Wuhan|sex:not determined|tissue:Whole body|genotype:noxo1a mutant with indel|treatment:Collected at 96 hpf|replicate:replicate = biological replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,noxo1a ctrl#1,noxo1a ctrl#1,noxo1a ctrl#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.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP495638,,,noxo1a-ctrl-1_S32_L004_R1_001.fastq.gz noxo1a-ctrl-1_S32_L004_R2_001.fastq.gz,fastq fastq,7083186300.0,23610621.0,noxo1a ctrl 1 S32 L004 R1 001.fastq.gz,0:150 1:150,A:1869161754;C:1663101510;G:1702666018;T:1847889969;N:367049,150,150,,,1869161754,1663101510,1702666018,1847889969,367049,SRX23967966,SRS20767197,SRA1825819,Chinese Academy of Sciences|Institute of Hydrobiology,Chinese Academy of Sciences,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,nebnext,bulk,unknown,unknown,,China,2024-03-16,Larval,Larval,Trunk,Surface Structure
31493,SRR28362842,SRX23967965,SRS20767196,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.,,,,WT re#4,WT re#4,,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 °C for 12 h followed by recovery at 28 °C for 6 h|replicate:replicate = biological replicate 4|BioSampleModel:Model organism or animal,,,,,,,,,WT re#4,WT re#4,WT re#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.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP495638,,,wt-re-4_S24_L004_R1_001.fastq.gz wt-re-4_S24_L004_R2_001.fastq.gz,fastq fastq,6571058100.0,21903527.0,wt re 4 S24 L004 R1 001.fastq.gz,0:150 1:150,A:1733008779;C:1544891080;G:1572067431;T:1720784422;N:306388,150,150,,,1733008779,1544891080,1572067431,1720784422,306388,SRX23967965,SRS20767196,SRA1825819,Chinese Academy of Sciences|Institute of Hydrobiology,Chinese Academy of Sciences,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,nebnext,bulk,unknown,unknown,,China,2024-03-16,Larval,Larval,Trunk,Surface Structure
31494,SRR28362843,SRX23967964,SRS20767195,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.,,,,WT re#3,WT re#3,,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 °C for 12 h followed by recovery at 28 °C for 6 h|replicate:replicate = biological replicate 3|BioSampleModel:Model organism or animal,,,,,,,,,WT re#3,WT re#3,WT re#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.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP495638,,,wt-re-3_S43_L004_R1_001.fastq.gz wt-re-3_S43_L004_R2_001.fastq.gz,fastq fastq,7263273300.0,24210911.0,wt re 3 S43 L004 R1 001.fastq.gz,0:150 1:150,A:1933925580;C:1690509128;G:1721840325;T:1916618378;N:379889,150,150,,,1933925580,1690509128,1721840325,1916618378,379889,SRX23967964,SRS20767195,SRA1825819,Chinese Academy of Sciences|Institute of Hydrobiology,Chinese Academy of Sciences,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,nebnext,bulk,unknown,unknown,,China,2024-03-16,Larval,Larval,Trunk,Surface Structure
31495,SRR28362844,SRX23967963,SRS20767194,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.,,,,WT ctrl#2,WT ctrl#2,,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 2|BioSampleModel:Model organism or animal,,,,,,,,,WT ctrl#2,WT ctrl#2,WT ctrl#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.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP495638,,,wt-ctrl-2_S19_L004_R1_001.fastq.gz wt-ctrl-2_S19_L004_R2_001.fastq.gz,fastq fastq,6989097000.0,23296990.0,wt ctrl 2 S19 L004 R1 001.fastq.gz,0:150 1:150,A:1831914872;C:1651035418;G:1692865635;T:1812968538;N:312537,150,150,,,1831914872,1651035418,1692865635,1812968538,312537,SRX23967963,SRS20767194,SRA1825819,Chinese Academy of Sciences|Institute of Hydrobiology,Chinese Academy of Sciences,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,nebnext,bulk,unknown,unknown,,China,2024-03-16,Larval,Larval,Trunk,Surface Structure
31496,SRR28362845,SRX23967962,SRS20767193,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.,,,,WT ctrl#1,WT ctrl#1,,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 1|BioSampleModel:Model organism or animal,,,,,,,,,WT ctrl#1,WT ctrl#1,WT ctrl#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.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP495638,,,wt-ctrl-1_S30_L004_R1_001.fastq.gz wt-ctrl-1_S30_L004_R2_001.fastq.gz,fastq fastq,7158502800.0,23861676.0,wt ctrl 1 S30 L004 R1 001.fastq.gz,0:150 1:150,A:1880251200;C:1687764492;G:1727478938;T:1862632997;N:375173,150,150,,,1880251200,1687764492,1727478938,1862632997,375173,SRX23967962,SRS20767193,SRA1825819,Chinese Academy of Sciences|Institute of Hydrobiology,Chinese Academy of Sciences,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,nebnext,bulk,unknown,unknown,,China,2024-03-16,Larval,Larval,Trunk,Surface Structure
32018,SRR28960817,SRX24490444,SRS21239720,SRP506336,PRJNA1108487,First formal characterization of the fish specific molecule Immunoglobulin like domain containing protein Igldcp in zebrafish Danio rerio: clues about its implication in the immune response,PRJNA1108487,Other,Numerous evidences demonstrate that the fish exclusive gene immunoglobulin Ig like domain containing protein igldcp is involved in the protection against viruses. Because of this  we wanted to study its mode of action in the model species zebrafish Danio rerio. RNA Seq analyses of zebrafish larvae overexpressing or not igldcp and in the presence or absence of an infection with the nodavirus RGNNV were conducted.,,,,,Empty RGNNV 2,,strain:wild type|isolate:10|age:4 dpf|dev stage:larvae|collection date:2023|geo loc name:Spain: Vigo|sex:not applicable|tissue:whole larvae|BioSampleModel:Model organism or animal,,,,,,,,,Rna Seq of zebrafish larvae,Empty RGNNV 2,Empty RGNNV 2,RNA from the different pooled samples 3 larvae/sample was isolated using the Maxwell RSC simplyRNA Tissue Kit Promega with an automated Maxwell RSC 48 Instrument in accordance with the instructions provided by the manufacturer. The quantity of RNA was measured on a Qubit 4 fluorometer Thermo Fisher Scientific  and RNA integrity was analysed in an Agilent 2100 Bioanalyzer Agilent Technologies Inc.  Santa Clara  CA  USA according to the manufacturer's instructions.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP506336,,,C-V2_2.fastq.gz C-V2_1.fastq.gz,fastq fastq,4988932790.0,16519645.0,C V2 1.fastq.gz,0:151 1:151,A:1355149914;C:1135513565;G:1149109922;T:1349135360;N:24029,151,151,,,1355149914,1135513565,1149109922,1349135360,24029,SRX24490444,SRS21239720,SRA1861741,IIM-CSIC|Immunology and Genomics,IIM-CSIC,2,0.94379,0.94549,0.11621,0.11505,0.65423,0.65577,0.48135,0.48232,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Spain,2024-05-08,Larval,Larval,Whole Organism,All anatomical structures
32019,SRR28960818,SRX24490443,SRS21239719,SRP506336,PRJNA1108487,First formal characterization of the fish specific molecule Immunoglobulin like domain containing protein Igldcp in zebrafish Danio rerio: clues about its implication in the immune response,PRJNA1108487,Other,Numerous evidences demonstrate that the fish exclusive gene immunoglobulin Ig like domain containing protein igldcp is involved in the protection against viruses. Because of this  we wanted to study its mode of action in the model species zebrafish Danio rerio. RNA Seq analyses of zebrafish larvae overexpressing or not igldcp and in the presence or absence of an infection with the nodavirus RGNNV were conducted.,,,,,Empty RGNNV 1,,strain:wild type|isolate:9|age:4 dpf|dev stage:larvae|collection date:2023|geo loc name:Spain: Vigo|sex:not applicable|tissue:whole larvae|BioSampleModel:Model organism or animal,,,,,,,,,Rna Seq of zebrafish larvae,Empty RGNNV 1,Empty RGNNV 1,RNA from the different pooled samples 3 larvae/sample was isolated using the Maxwell RSC simplyRNA Tissue Kit Promega with an automated Maxwell RSC 48 Instrument in accordance with the instructions provided by the manufacturer. The quantity of RNA was measured on a Qubit 4 fluorometer Thermo Fisher Scientific  and RNA integrity was analysed in an Agilent 2100 Bioanalyzer Agilent Technologies Inc.  Santa Clara  CA  USA according to the manufacturer's instructions.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP506336,,,C-V1_2.fastq.gz C-V1_1.fastq.gz,fastq fastq,5032900970.0,16665235.0,C V1 1.fastq.gz,0:151 1:151,A:1378766254;C:1133849186;G:1146563693;T:1373698300;N:23537,151,151,,,1378766254,1133849186,1146563693,1373698300,23537,SRX24490443,SRS21239719,SRA1861741,IIM-CSIC|Immunology and Genomics,IIM-CSIC,2,0.9444,0.94533,0.11258,0.11038,0.65194,0.65259,0.48812,0.48428,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Spain,2024-05-08,Larval,Larval,Whole Organism,All anatomical structures
32020,SRR28960819,SRX24490442,SRS21239718,SRP506336,PRJNA1108487,First formal characterization of the fish specific molecule Immunoglobulin like domain containing protein Igldcp in zebrafish Danio rerio: clues about its implication in the immune response,PRJNA1108487,Other,Numerous evidences demonstrate that the fish exclusive gene immunoglobulin Ig like domain containing protein igldcp is involved in the protection against viruses. Because of this  we wanted to study its mode of action in the model species zebrafish Danio rerio. RNA Seq analyses of zebrafish larvae overexpressing or not igldcp and in the presence or absence of an infection with the nodavirus RGNNV were conducted.,,,,,igldcp C4,,strain:wild type|isolate:8|age:4 dpf|dev stage:larvae|collection date:2023|geo loc name:Spain: Vigo|sex:not applicable|tissue:whole larvae|BioSampleModel:Model organism or animal,,,,,,,,,Rna Seq of zebrafish larvae,igldcp C4,igldcp C4,RNA from the different pooled samples 3 larvae/sample was isolated using the Maxwell RSC simplyRNA Tissue Kit Promega with an automated Maxwell RSC 48 Instrument in accordance with the instructions provided by the manufacturer. The quantity of RNA was measured on a Qubit 4 fluorometer Thermo Fisher Scientific  and RNA integrity was analysed in an Agilent 2100 Bioanalyzer Agilent Technologies Inc.  Santa Clara  CA  USA according to the manufacturer's instructions.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP506336,,,G17-C4_2.fastq.gz G17-C4_1.fastq.gz,fastq fastq,5008644028.0,16584914.0,G17 C4 1.fastq.gz,0:151 1:151,A:1365541116;C:1135139643;G:1150040618;T:1357899842;N:22809,151,151,,,1365541116,1135139643,1150040618,1357899842,22809,SRX24490442,SRS21239718,SRA1861741,IIM-CSIC|Immunology and Genomics,IIM-CSIC,2,0.94527,0.94533,0.10689,0.10479,0.65535,0.65681,0.47637,0.48487,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Spain,2024-05-08,Larval,Larval,Whole Organism,All anatomical structures
32021,SRR28960820,SRX24490441,SRS21239717,SRP506336,PRJNA1108487,First formal characterization of the fish specific molecule Immunoglobulin like domain containing protein Igldcp in zebrafish Danio rerio: clues about its implication in the immune response,PRJNA1108487,Other,Numerous evidences demonstrate that the fish exclusive gene immunoglobulin Ig like domain containing protein igldcp is involved in the protection against viruses. Because of this  we wanted to study its mode of action in the model species zebrafish Danio rerio. RNA Seq analyses of zebrafish larvae overexpressing or not igldcp and in the presence or absence of an infection with the nodavirus RGNNV were conducted.,,,,,igldcp C3,,strain:wild type|isolate:7|age:4 dpf|dev stage:larvae|collection date:2023|geo loc name:Spain: Vigo|sex:not applicable|tissue:whole larvae|BioSampleModel:Model organism or animal,,,,,,,,,Rna Seq of zebrafish larvae,igldcp C3,igldcp C3,RNA from the different pooled samples 3 larvae/sample was isolated using the Maxwell RSC simplyRNA Tissue Kit Promega with an automated Maxwell RSC 48 Instrument in accordance with the instructions provided by the manufacturer. The quantity of RNA was measured on a Qubit 4 fluorometer Thermo Fisher Scientific  and RNA integrity was analysed in an Agilent 2100 Bioanalyzer Agilent Technologies Inc.  Santa Clara  CA  USA according to the manufacturer's instructions.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP506336,,,G17-C3_2.fastq.gz G17-C3_1.fastq.gz,fastq fastq,4980119222.0,16490461.0,G17 C3 1.fastq.gz,0:151 1:151,A:1360303556;C:1126738486;G:1145297479;T:1347756591;N:23110,151,151,,,1360303556,1126738486,1145297479,1347756591,23110,SRX24490441,SRS21239717,SRA1861741,IIM-CSIC|Immunology and Genomics,IIM-CSIC,2,0.9466,0.94717,0.11289,0.11094,0.66257,0.66464,0.47181,0.47916,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Spain,2024-05-08,Larval,Larval,Whole Organism,All anatomical structures
32022,SRR28960821,SRX24490440,SRS21239716,SRP506336,PRJNA1108487,First formal characterization of the fish specific molecule Immunoglobulin like domain containing protein Igldcp in zebrafish Danio rerio: clues about its implication in the immune response,PRJNA1108487,Other,Numerous evidences demonstrate that the fish exclusive gene immunoglobulin Ig like domain containing protein igldcp is involved in the protection against viruses. Because of this  we wanted to study its mode of action in the model species zebrafish Danio rerio. RNA Seq analyses of zebrafish larvae overexpressing or not igldcp and in the presence or absence of an infection with the nodavirus RGNNV were conducted.,,,,,igldcp C2,,strain:wild type|isolate:6|age:4 dpf|dev stage:larvae|collection date:2023|geo loc name:Spain: Vigo|sex:not applicable|tissue:whole larvae|BioSampleModel:Model organism or animal,,,,,,,,,Rna Seq of zebrafish larvae,igldcp C2,igldcp C2,RNA from the different pooled samples 3 larvae/sample was isolated using the Maxwell RSC simplyRNA Tissue Kit Promega with an automated Maxwell RSC 48 Instrument in accordance with the instructions provided by the manufacturer. The quantity of RNA was measured on a Qubit 4 fluorometer Thermo Fisher Scientific  and RNA integrity was analysed in an Agilent 2100 Bioanalyzer Agilent Technologies Inc.  Santa Clara  CA  USA according to the manufacturer's instructions.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP506336,,,G17-C2_2.fastq.gz G17-C2_1.fastq.gz,fastq fastq,5007933422.0,16582561.0,G17 C2 1.fastq.gz,0:151 1:151,A:1372213671;C:1129918132;G:1143655284;T:1362122899;N:23436,151,151,,,1372213671,1129918132,1143655284,1362122899,23436,SRX24490440,SRS21239716,SRA1861741,IIM-CSIC|Immunology and Genomics,IIM-CSIC,2,0.94572,0.94517,0.11003,0.10818,0.65658,0.65805,0.4773,0.48344,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Spain,2024-05-08,Larval,Larval,Whole Organism,All anatomical structures
32023,SRR28960822,SRX24490439,SRS21239715,SRP506336,PRJNA1108487,First formal characterization of the fish specific molecule Immunoglobulin like domain containing protein Igldcp in zebrafish Danio rerio: clues about its implication in the immune response,PRJNA1108487,Other,Numerous evidences demonstrate that the fish exclusive gene immunoglobulin Ig like domain containing protein igldcp is involved in the protection against viruses. Because of this  we wanted to study its mode of action in the model species zebrafish Danio rerio. RNA Seq analyses of zebrafish larvae overexpressing or not igldcp and in the presence or absence of an infection with the nodavirus RGNNV were conducted.,,,,,igldcp C1,,strain:wild type|isolate:5|age:4 dpf|dev stage:larvae|collection date:2023|geo loc name:Spain: Vigo|sex:not applicable|tissue:whole larvae|BioSampleModel:Model organism or animal,,,,,,,,,Rna Seq of zebrafish larvae,igldcp C1,igldcp C1,RNA from the different pooled samples 3 larvae/sample was isolated using the Maxwell RSC simplyRNA Tissue Kit Promega with an automated Maxwell RSC 48 Instrument in accordance with the instructions provided by the manufacturer. The quantity of RNA was measured on a Qubit 4 fluorometer Thermo Fisher Scientific  and RNA integrity was analysed in an Agilent 2100 Bioanalyzer Agilent Technologies Inc.  Santa Clara  CA  USA according to the manufacturer's instructions.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP506336,,,G17-C1_1.fastq.gz G17-C1_2.fastq.gz,fastq fastq,5024913070.0,16638785.0,G17 C1 1.fastq.gz,0:151 1:151,A:1380366672;C:1129585807;G:1150817244;T:1364119307;N:24040,151,151,,,1380366672,1129585807,1150817244,1364119307,24040,SRX24490439,SRS21239715,SRA1861741,IIM-CSIC|Immunology and Genomics,IIM-CSIC,2,0.94287,0.94431,0.11558,0.11383,0.65277,0.65382,0.4826,0.48102,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Spain,2024-05-08,Larval,Larval,Whole Organism,All anatomical structures
32024,SRR28960823,SRX24490438,SRS21239714,SRP506336,PRJNA1108487,First formal characterization of the fish specific molecule Immunoglobulin like domain containing protein Igldcp in zebrafish Danio rerio: clues about its implication in the immune response,PRJNA1108487,Other,Numerous evidences demonstrate that the fish exclusive gene immunoglobulin Ig like domain containing protein igldcp is involved in the protection against viruses. Because of this  we wanted to study its mode of action in the model species zebrafish Danio rerio. RNA Seq analyses of zebrafish larvae overexpressing or not igldcp and in the presence or absence of an infection with the nodavirus RGNNV were conducted.,,,,,Empty C4,,strain:wild type|isolate:4|age:4 dpf|dev stage:larvae|collection date:2023|geo loc name:Spain: Vigo|sex:not applicable|tissue:whole larvae|BioSampleModel:Model organism or animal,,,,,,,,,Rna Seq of zebrafish larvae,Empty C4,Empty C4,RNA from the different pooled samples 3 larvae/sample was isolated using the Maxwell RSC simplyRNA Tissue Kit Promega with an automated Maxwell RSC 48 Instrument in accordance with the instructions provided by the manufacturer. The quantity of RNA was measured on a Qubit 4 fluorometer Thermo Fisher Scientific  and RNA integrity was analysed in an Agilent 2100 Bioanalyzer Agilent Technologies Inc.  Santa Clara  CA  USA according to the manufacturer's instructions.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP506336,,,C-C4_2.fastq.gz C-C4_1.fastq.gz,fastq fastq,4979945874.0,16489887.0,C C4 1.fastq.gz,0:151 1:151,A:1355600042;C:1132041799;G:1147315384;T:1344965018;N:23631,151,151,,,1355600042,1132041799,1147315384,1344965018,23631,SRX24490438,SRS21239714,SRA1861741,IIM-CSIC|Immunology and Genomics,IIM-CSIC,2,0.94757,0.94857,0.10346,0.10203,0.65539,0.65673,0.4708,0.46117,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Spain,2024-05-08,Larval,Larval,Whole Organism,All anatomical structures
32025,SRR28960827,SRX24490437,SRS21239713,SRP506336,PRJNA1108487,First formal characterization of the fish specific molecule Immunoglobulin like domain containing protein Igldcp in zebrafish Danio rerio: clues about its implication in the immune response,PRJNA1108487,Other,Numerous evidences demonstrate that the fish exclusive gene immunoglobulin Ig like domain containing protein igldcp is involved in the protection against viruses. Because of this  we wanted to study its mode of action in the model species zebrafish Danio rerio. RNA Seq analyses of zebrafish larvae overexpressing or not igldcp and in the presence or absence of an infection with the nodavirus RGNNV were conducted.,,,,,Empty C3,,strain:wild type|isolate:3|age:4 dpf|dev stage:larvae|collection date:2023|geo loc name:Spain: Vigo|sex:not applicable|tissue:whole larvae|BioSampleModel:Model organism or animal,,,,,,,,,Rna Seq of zebrafish larvae,Empty C3,Empty C3,RNA from the different pooled samples 3 larvae/sample was isolated using the Maxwell RSC simplyRNA Tissue Kit Promega with an automated Maxwell RSC 48 Instrument in accordance with the instructions provided by the manufacturer. The quantity of RNA was measured on a Qubit 4 fluorometer Thermo Fisher Scientific  and RNA integrity was analysed in an Agilent 2100 Bioanalyzer Agilent Technologies Inc.  Santa Clara  CA  USA according to the manufacturer's instructions.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP506336,,,C-C3_2.fastq.gz C-C3_1.fastq.gz,fastq fastq,5029174894.0,16652897.0,C C3 1.fastq.gz,0:151 1:151,A:1374911488;C:1136783068;G:1150269816;T:1367186209;N:24313,151,151,,,1374911488,1136783068,1150269816,1367186209,24313,SRX24490437,SRS21239713,SRA1861741,IIM-CSIC|Immunology and Genomics,IIM-CSIC,2,0.94336,0.94484,0.11529,0.11371,0.65305,0.65488,0.47386,0.4875,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Spain,2024-05-08,Larval,Larval,Whole Organism,All anatomical structures
32026,SRR28960824,SRX24490436,SRS21239712,SRP506336,PRJNA1108487,First formal characterization of the fish specific molecule Immunoglobulin like domain containing protein Igldcp in zebrafish Danio rerio: clues about its implication in the immune response,PRJNA1108487,Other,Numerous evidences demonstrate that the fish exclusive gene immunoglobulin Ig like domain containing protein igldcp is involved in the protection against viruses. Because of this  we wanted to study its mode of action in the model species zebrafish Danio rerio. RNA Seq analyses of zebrafish larvae overexpressing or not igldcp and in the presence or absence of an infection with the nodavirus RGNNV were conducted.,,,,,igldcp RGNNV 4,,strain:wild type|isolate:15|age:4 dpf|dev stage:larvae|collection date:2023|geo loc name:Spain: Vigo|sex:not applicable|tissue:whole larvae|BioSampleModel:Model organism or animal,,,,,,,,,Rna Seq of zebrafish larvae,igldcp RGNNV 4,igldcp RGNNV 4,RNA from the different pooled samples 3 larvae/sample was isolated using the Maxwell RSC simplyRNA Tissue Kit Promega with an automated Maxwell RSC 48 Instrument in accordance with the instructions provided by the manufacturer. The quantity of RNA was measured on a Qubit 4 fluorometer Thermo Fisher Scientific  and RNA integrity was analysed in an Agilent 2100 Bioanalyzer Agilent Technologies Inc.  Santa Clara  CA  USA according to the manufacturer's instructions.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP506336,,,G17-V4_1.fastq.gz G17-V4_2.fastq.gz,fastq fastq,5038044634.0,16682267.0,G17 V4 1.fastq.gz,0:151 1:151,A:1373754614;C:1142848550;G:1159235100;T:1362182221;N:24149,151,151,,,1373754614,1142848550,1159235100,1362182221,24149,SRX24490436,SRS21239712,SRA1861741,IIM-CSIC|Immunology and Genomics,IIM-CSIC,2,0.94236,0.94358,0.10841,0.10623,0.65429,0.65512,0.47952,0.47896,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Spain,2024-05-08,Larval,Larval,Whole Organism,All anatomical structures
32027,SRR28960825,SRX24490435,SRS21239711,SRP506336,PRJNA1108487,First formal characterization of the fish specific molecule Immunoglobulin like domain containing protein Igldcp in zebrafish Danio rerio: clues about its implication in the immune response,PRJNA1108487,Other,Numerous evidences demonstrate that the fish exclusive gene immunoglobulin Ig like domain containing protein igldcp is involved in the protection against viruses. Because of this  we wanted to study its mode of action in the model species zebrafish Danio rerio. RNA Seq analyses of zebrafish larvae overexpressing or not igldcp and in the presence or absence of an infection with the nodavirus RGNNV were conducted.,,,,,igldcp RGNNV 2,,strain:wild type|isolate:14|age:4 dpf|dev stage:larvae|collection date:2023|geo loc name:Spain: Vigo|sex:not applicable|tissue:whole larvae|BioSampleModel:Model organism or animal,,,,,,,,,Rna Seq of zebrafish larvae,igldcp RGNNV 2,igldcp RGNNV 2,RNA from the different pooled samples 3 larvae/sample was isolated using the Maxwell RSC simplyRNA Tissue Kit Promega with an automated Maxwell RSC 48 Instrument in accordance with the instructions provided by the manufacturer. The quantity of RNA was measured on a Qubit 4 fluorometer Thermo Fisher Scientific  and RNA integrity was analysed in an Agilent 2100 Bioanalyzer Agilent Technologies Inc.  Santa Clara  CA  USA according to the manufacturer's instructions.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP506336,,,G17-V2_2.fastq.gz G17-V2_1.fastq.gz,fastq fastq,4992836442.0,16532571.0,G17 V2 1.fastq.gz,0:151 1:151,A:1370989397;C:1121917932;G:1135482493;T:1364423268;N:23352,151,151,,,1370989397,1121917932,1135482493,1364423268,23352,SRX24490435,SRS21239711,SRA1861741,IIM-CSIC|Immunology and Genomics,IIM-CSIC,2,0.94244,0.94361,0.11703,0.11517,0.65297,0.65305,0.47906,0.47762,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Spain,2024-05-08,Larval,Larval,Whole Organism,All anatomical structures
32028,SRR28960826,SRX24490434,SRS21239710,SRP506336,PRJNA1108487,First formal characterization of the fish specific molecule Immunoglobulin like domain containing protein Igldcp in zebrafish Danio rerio: clues about its implication in the immune response,PRJNA1108487,Other,Numerous evidences demonstrate that the fish exclusive gene immunoglobulin Ig like domain containing protein igldcp is involved in the protection against viruses. Because of this  we wanted to study its mode of action in the model species zebrafish Danio rerio. RNA Seq analyses of zebrafish larvae overexpressing or not igldcp and in the presence or absence of an infection with the nodavirus RGNNV were conducted.,,,,,igldcp RGNNV 1,,strain:wild type|isolate:13|age:4 dpf|dev stage:larvae|collection date:2023|geo loc name:Spain: Vigo|sex:not applicable|tissue:whole larvae|BioSampleModel:Model organism or animal,,,,,,,,,Rna Seq of zebrafish larvae,igldcp RGNNV 1,igldcp RGNNV 1,RNA from the different pooled samples 3 larvae/sample was isolated using the Maxwell RSC simplyRNA Tissue Kit Promega with an automated Maxwell RSC 48 Instrument in accordance with the instructions provided by the manufacturer. The quantity of RNA was measured on a Qubit 4 fluorometer Thermo Fisher Scientific  and RNA integrity was analysed in an Agilent 2100 Bioanalyzer Agilent Technologies Inc.  Santa Clara  CA  USA according to the manufacturer's instructions.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP506336,,,G17-V1_2.fastq.gz G17-V1_1.fastq.gz,fastq fastq,5022577402.0,16631051.0,G17 V1 1.fastq.gz,0:151 1:151,A:1373133624;C:1136711402;G:1147351250;T:1365356916;N:24210,151,151,,,1373133624,1136711402,1147351250,1365356916,24210,SRX24490434,SRS21239710,SRA1861741,IIM-CSIC|Immunology and Genomics,IIM-CSIC,2,0.94548,0.9457,0.11091,0.10876,0.6566,0.65794,0.47672,0.47334,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Spain,2024-05-08,Larval,Larval,Whole Organism,All anatomical structures
32029,SRR28960828,SRX24490433,SRS21239709,SRP506336,PRJNA1108487,First formal characterization of the fish specific molecule Immunoglobulin like domain containing protein Igldcp in zebrafish Danio rerio: clues about its implication in the immune response,PRJNA1108487,Other,Numerous evidences demonstrate that the fish exclusive gene immunoglobulin Ig like domain containing protein igldcp is involved in the protection against viruses. Because of this  we wanted to study its mode of action in the model species zebrafish Danio rerio. RNA Seq analyses of zebrafish larvae overexpressing or not igldcp and in the presence or absence of an infection with the nodavirus RGNNV were conducted.,,,,,Empty RGNNV 4,,strain:wild type|isolate:12|age:4 dpf|dev stage:larvae|collection date:2023|geo loc name:Spain: Vigo|sex:not applicable|tissue:whole larvae|BioSampleModel:Model organism or animal,,,,,,,,,Rna Seq of zebrafish larvae,Empty RGNNV 4,Empty RGNNV 4,RNA from the different pooled samples 3 larvae/sample was isolated using the Maxwell RSC simplyRNA Tissue Kit Promega with an automated Maxwell RSC 48 Instrument in accordance with the instructions provided by the manufacturer. The quantity of RNA was measured on a Qubit 4 fluorometer Thermo Fisher Scientific  and RNA integrity was analysed in an Agilent 2100 Bioanalyzer Agilent Technologies Inc.  Santa Clara  CA  USA according to the manufacturer's instructions.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP506336,,,C-V4_1.fastq.gz C-V4_2.fastq.gz,fastq fastq,4996580940.0,16544970.0,C V4 1.fastq.gz,0:151 1:151,A:1365771383;C:1129645420;G:1139771568;T:1361369690;N:22879,151,151,,,1365771383,1129645420,1139771568,1361369690,22879,SRX24490433,SRS21239709,SRA1861741,IIM-CSIC|Immunology and Genomics,IIM-CSIC,2,0.94201,0.94399,0.10865,0.10729,0.65295,0.65397,0.47378,0.48264,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Spain,2024-05-08,Larval,Larval,Whole Organism,All anatomical structures
32030,SRR28960829,SRX24490432,SRS21239708,SRP506336,PRJNA1108487,First formal characterization of the fish specific molecule Immunoglobulin like domain containing protein Igldcp in zebrafish Danio rerio: clues about its implication in the immune response,PRJNA1108487,Other,Numerous evidences demonstrate that the fish exclusive gene immunoglobulin Ig like domain containing protein igldcp is involved in the protection against viruses. Because of this  we wanted to study its mode of action in the model species zebrafish Danio rerio. RNA Seq analyses of zebrafish larvae overexpressing or not igldcp and in the presence or absence of an infection with the nodavirus RGNNV were conducted.,,,,,Empty RGNNV 3,,strain:wild type|isolate:11|age:4 dpf|dev stage:larvae|collection date:2023|geo loc name:Spain: Vigo|sex:not applicable|tissue:whole larvae|BioSampleModel:Model organism or animal,,,,,,,,,Rna Seq of zebrafish larvae,Empty RGNNV 3,Empty RGNNV 3,RNA from the different pooled samples 3 larvae/sample was isolated using the Maxwell RSC simplyRNA Tissue Kit Promega with an automated Maxwell RSC 48 Instrument in accordance with the instructions provided by the manufacturer. The quantity of RNA was measured on a Qubit 4 fluorometer Thermo Fisher Scientific  and RNA integrity was analysed in an Agilent 2100 Bioanalyzer Agilent Technologies Inc.  Santa Clara  CA  USA according to the manufacturer's instructions.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP506336,,,C-V3_1.fastq.gz C-V3_2.fastq.gz,fastq fastq,4990782540.0,16525770.0,C V3 1.fastq.gz,0:151 1:151,A:1370883963;C:1121960304;G:1139361266;T:1358553278;N:23729,151,151,,,1370883963,1121960304,1139361266,1358553278,23729,SRX24490432,SRS21239708,SRA1861741,IIM-CSIC|Immunology and Genomics,IIM-CSIC,2,0.94311,0.94426,0.10644,0.10476,0.65535,0.65756,0.46134,0.44955,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Spain,2024-05-08,Larval,Larval,Whole Organism,All anatomical structures
32031,SRR28960830,SRX24490431,SRS21239707,SRP506336,PRJNA1108487,First formal characterization of the fish specific molecule Immunoglobulin like domain containing protein Igldcp in zebrafish Danio rerio: clues about its implication in the immune response,PRJNA1108487,Other,Numerous evidences demonstrate that the fish exclusive gene immunoglobulin Ig like domain containing protein igldcp is involved in the protection against viruses. Because of this  we wanted to study its mode of action in the model species zebrafish Danio rerio. RNA Seq analyses of zebrafish larvae overexpressing or not igldcp and in the presence or absence of an infection with the nodavirus RGNNV were conducted.,,,,,Empty C2,,strain:wild type|isolate:2|age:4 dpf|dev stage:larvae|collection date:2023|geo loc name:Spain: Vigo|sex:not applicable|tissue:whole larvae|BioSampleModel:Model organism or animal,,,,,,,,,Rna Seq of zebrafish larvae,Empty C2,Empty C2,RNA from the different pooled samples 3 larvae/sample was isolated using the Maxwell RSC simplyRNA Tissue Kit Promega with an automated Maxwell RSC 48 Instrument in accordance with the instructions provided by the manufacturer. The quantity of RNA was measured on a Qubit 4 fluorometer Thermo Fisher Scientific  and RNA integrity was analysed in an Agilent 2100 Bioanalyzer Agilent Technologies Inc.  Santa Clara  CA  USA according to the manufacturer's instructions.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP506336,,,C-C2_2.fastq.gz C-C2_1.fastq.gz,fastq fastq,4991313154.0,16527527.0,C C2 1.fastq.gz,0:151 1:151,A:1366713096;C:1125818845;G:1141236594;T:1357520576;N:24043,151,151,,,1366713096,1125818845,1141236594,1357520576,24043,SRX24490431,SRS21239707,SRA1861741,IIM-CSIC|Immunology and Genomics,IIM-CSIC,2,0.94263,0.94476,0.10847,0.10745,0.65928,0.65904,0.47366,0.47959,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Spain,2024-05-08,Larval,Larval,Whole Organism,All anatomical structures
32032,SRR28960831,SRX24490430,SRS21239702,SRP506336,PRJNA1108487,First formal characterization of the fish specific molecule Immunoglobulin like domain containing protein Igldcp in zebrafish Danio rerio: clues about its implication in the immune response,PRJNA1108487,Other,Numerous evidences demonstrate that the fish exclusive gene immunoglobulin Ig like domain containing protein igldcp is involved in the protection against viruses. Because of this  we wanted to study its mode of action in the model species zebrafish Danio rerio. RNA Seq analyses of zebrafish larvae overexpressing or not igldcp and in the presence or absence of an infection with the nodavirus RGNNV were conducted.,,,,,Empty C1,,strain:wild type|isolate:1|age:4 dpf|dev stage:larvae|collection date:2023|geo loc name:Spain: Vigo|sex:not applicable|tissue:whole larvae|BioSampleModel:Model organism or animal,,,,,,,,,Rna Seq of zebrafish larvae,Empty C1,Empty C1,RNA from the different pooled samples 3 larvae/sample was isolated using the Maxwell RSC simplyRNA Tissue Kit Promega with an automated Maxwell RSC 48 Instrument in accordance with the instructions provided by the manufacturer. The quantity of RNA was measured on a Qubit 4 fluorometer Thermo Fisher Scientific  and RNA integrity was analysed in an Agilent 2100 Bioanalyzer Agilent Technologies Inc.  Santa Clara  CA  USA according to the manufacturer's instructions.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP506336,,,C-C1_1.fastq.gz C-C1_2.fastq.gz,fastq fastq,5031068434.0,16659167.0,C C1 1.fastq.gz,0:151 1:151,A:1369231804;C:1143688515;G:1163238884;T:1354885267;N:23964,151,151,,,1369231804,1143688515,1163238884,1354885267,23964,SRX24490430,SRS21239702,SRA1861741,IIM-CSIC|Immunology and Genomics,IIM-CSIC,2,0.94547,0.94589,0.10958,0.10835,0.6564,0.6565,0.48608,0.48591,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Spain,2024-05-08,Larval,Larval,Whole Organism,All anatomical structures
39756,SRR2125736,SRX1117105,SRS1010315,SRP061528,PRJNA290839,Danio rerio Transcriptome or Gene expression,PRJNA290839,Transcriptome Analysis,RNA Seq of Danio rerio transcriptome,,,,,Polr1c2,,breed:not applicable|strain:not applicable|age:5 dpf provider:not applicable|sex:not collected|tissue:whole fish Polr1c2|treatment:KO|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Polr1c2,RNA Seq of Polr1c2,1,Total RNA was extracted from the cells using the mirVanaTM isolation kit Applied Biosystems and treated with DNase Ambion to remove contaminating genomic DNA. Agilent 2100 Bioanalyzer system was used to assess RNA quality of samples and the samples with a RNA Integrity Number RIN greater than 9 were used for transcriptome library construction. cDNA library wasconstructed using TruSeq Stranded Total RNA LT Sample Prep Kit Illumina  each prepared from 300ng of total RNA. The cDNA libraries were constructed according to manufacturer’s instruction and index codes were ligated as identification to individual samples as previous described. Briefly  mRNA was purified from the total RNA using poly T oligo  attached magnetic beads Illumina  San Diego  USA to remove the ribosomal RNA. Then the Mrna was fragmented by using divalent cations in Illumina proprietary fragmentation buffer at 94 ?C for 1 min. First strand cDNAs were synthesized using random oligonucleotides and SuperScript II  then and second cDNAs were synthesized using DNA polymerase I and RNase H. Overhangs were blunted by using exonuclease/polymerase  followed by 3’ end adenylation. post adenylation of 3’ ends of DNA fragments  Illumina PE adapter oligonucleotides were ligated to DNA fragments. DNA fragments that ligated with adaptor molecules on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycles PCR reaction. Libraries were purified using AMPure XP system and quantified using the KAPA Library Quantification Kits. Before submitted to sequencing  the libraries were normalized and pooled together in a single lane on an Illumina MiSeq platform and 150 bp paired end reads were generated.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina MiSeq,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>302</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>152</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP061528,,,Polr1c2_S2_L001_R1_001.fastq.gz Polr1c2_S2_L001_R2_001.fastq.gz,bam fastq,1024040592.0,3467167.0,RNA Seq of Polr1c2,0:147.69 1:147.67,A:280222262;C:231619577;G:229733851;T:282415559;N:49343,147,147,,,280222262,231619577,229733851,282415559,49343,SRX1117105,SRS1010315,SRA279862,The Chinese University of Hong Kong,The Chinese University of Hong Kong,2,0.94843,0.95151,0.09589,0.09554,0.68747,0.68694,0.48798,0.48429,150,151,B,B,biological fallback assumption,illumina,miseq,unknown,random_priming,trueseq,bulk,bulk,bulk,,China,2016-07-24,Larval,Larval,Whole Organism,All anatomical structures
39757,SRR2125735,SRX1117104,SRS1010314,SRP061528,PRJNA290839,Danio rerio Transcriptome or Gene expression,PRJNA290839,Transcriptome Analysis,RNA Seq of Danio rerio transcriptome,,,,,polr1cKO,,breed:not applicable|strain:not applicable|age:5 dpf provider:not applicable|sex:not collected|tissue:whole fish of polr1cKO|treatment:KO|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of polr1cKO,RNA Seq of polr1cKO,1,Total RNA was extracted from the cells using the mirVanaTM isolation kit Applied Biosystems and treated with DNase Ambion to remove contaminating genomic DNA. Agilent 2100 Bioanalyzer system was used to assess RNA quality of samples and the samples with a RNA Integrity Number RIN greater than 9 were used for transcriptome library construction. cDNA library wasconstructed using TruSeq Stranded Total RNA LT Sample Prep Kit Illumina  each prepared from 300ng of total RNA. The cDNA libraries were constructed according to manufacturer’s instruction and index codes were ligated as identification to individual samples as previous described. Briefly  mRNA was purified from the total RNA using poly T oligo  attached magnetic beads Illumina  San Diego  USA to remove the ribosomal RNA. Then the Mrna was fragmented by using divalent cations in Illumina proprietary fragmentation buffer at 94 ?C for 1 min. First strand cDNAs were synthesized using random oligonucleotides and SuperScript II  then and second cDNAs were synthesized using DNA polymerase I and RNase H. Overhangs were blunted by using exonuclease/polymerase  followed by 3’ end adenylation. post adenylation of 3’ ends of DNA fragments  Illumina PE adapter oligonucleotides were ligated to DNA fragments. DNA fragments that ligated with adaptor molecules on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycles PCR reaction. Libraries were purified using AMPure XP system and quantified using the KAPA Library Quantification Kits. Before submitted to sequencing  the libraries were normalized and pooled together in a single lane on an Illumina MiSeq platform and 150 bp paired end reads were generated.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina MiSeq,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>302</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>152</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP061528,,,polr1cKO_S2_L001_R2_001.fastq.gz polr1cKO_S2_L001_R1_001.fastq.gz,fastq fastq,2153644339.0,7160972.0,RNA Seq of polr1cKO,0:150.40 1:150.34,A:558724957;C:517375772;G:514543839;T:562990605;N:9166,150,150,,,558724957,517375772,514543839,562990605,9166,SRX1117104,SRS1010314,SRA279862,The Chinese University of Hong Kong,The Chinese University of Hong Kong,2,0.95998,0.9611,0.07455,0.0729,0.65354,0.65496,0.45853,0.46158,151,151,B,B,biological fallback assumption,illumina,miseq,unknown,random_priming,trueseq,bulk,bulk,bulk,,China,2015-07-24,Larval,Larval,Whole Organism,All anatomical structures
39758,SRR2125734,SRX1117103,SRS1010313,SRP061528,PRJNA290839,Danio rerio Transcriptome or Gene expression,PRJNA290839,Transcriptome Analysis,RNA Seq of Danio rerio transcriptome,,,,,AB2,,breed:not applicable|strain:not applicable|age:5 dpf provider:not applicable|sex:not collected|tissue:whole fish of AB2|treatment:WT|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of AB2,RNA Seq of AB2,1,Total RNA was extracted from the cells using the mirVanaTM isolation kit Applied Biosystems and treated with DNase Ambion to remove contaminating genomic DNA. Agilent 2100 Bioanalyzer system was used to assess RNA quality of samples and the samples with a RNA Integrity Number RIN greater than 9 were used for transcriptome library construction. cDNA library wasconstructed using TruSeq Stranded Total RNA LT Sample Prep Kit Illumina  each prepared from 300ng of total RNA. The cDNA libraries were constructed according to manufacturer’s instruction and index codes were ligated as identification to individual samples as previous described. Briefly  mRNA was purified from the total RNA using poly T oligo  attached magnetic beads Illumina  San Diego  USA to remove the ribosomal RNA. Then the Mrna was fragmented by using divalent cations in Illumina proprietary fragmentation buffer at 94 ?C for 1 min. First strand cDNAs were synthesized using random oligonucleotides and SuperScript II  then and second cDNAs were synthesized using DNA polymerase I and RNase H. Overhangs were blunted by using exonuclease/polymerase  followed by 3’ end adenylation. post adenylation of 3’ ends of DNA fragments  Illumina PE adapter oligonucleotides were ligated to DNA fragments. DNA fragments that ligated with adaptor molecules on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycles PCR reaction. Libraries were purified using AMPure XP system and quantified using the KAPA Library Quantification Kits. Before submitted to sequencing  the libraries were normalized and pooled together in a single lane on an Illumina MiSeq platform and 150 bp paired end reads were generated.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina MiSeq,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>302</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>152</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP061528,,,AB2_S1_L001_R2_001.fastq.gz AB2_S1_L001_R1_001.fastq.gz,fastq fastq,829696252.0,2784590.0,RNA Seq of AB2,0:149.00 1:148.96,A:218353676;C:195998962;G:195017076;T:220297820;N:28718,149,148,,,218353676,195998962,195017076,220297820,28718,SRX1117103,SRS1010313,SRA279862,The Chinese University of Hong Kong,The Chinese University of Hong Kong,2,0.96274,0.96494,0.05571,0.05462,0.73588,0.73657,0.48938,0.48219,149,151,B,B,biological fallback assumption,illumina,miseq,unknown,random_priming,trueseq,bulk,bulk,bulk,,China,2015-07-24,Larval,Larval,Whole Organism,All anatomical structures
39759,SRR2125733,SRX1117102,SRS1010312,SRP061528,PRJNA290839,Danio rerio Transcriptome or Gene expression,PRJNA290839,Transcriptome Analysis,RNA Seq of Danio rerio transcriptome,,,,,WT,,breed:not applicable|strain:not applicable|age:5 dpf provider:not applicable|sex:not collected|tissue:whole fish of WT|treatment:WT|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of WT,RNA Seq of WT,1,Total RNA was extracted from the cells using the mirVanaTM isolation kit Applied Biosystems and treated with DNase Ambion to remove contaminating genomic DNA. Agilent 2100 Bioanalyzer system was used to assess RNA quality of samples and the samples with a RNA Integrity Number RIN greater than 9 were used for transcriptome library construction. cDNA library wasconstructed using TruSeq Stranded Total RNA LT Sample Prep Kit Illumina  each prepared from 300ng of total RNA. The cDNA libraries were constructed according to manufacturer’s instruction and index codes were ligated as identification to individual samples as previous described. Briefly  mRNA was purified from the total RNA using poly T oligo  attached magnetic beads Illumina  San Diego  USA to remove the ribosomal RNA. Then the Mrna was fragmented by using divalent cations in Illumina proprietary fragmentation buffer at 94 ?C for 1 min. First strand cDNAs were synthesized using random oligonucleotides and SuperScript II  then and second cDNAs were synthesized using DNA polymerase I and RNase H. Overhangs were blunted by using exonuclease/polymerase  followed by 3’ end adenylation. post adenylation of 3’ ends of DNA fragments  Illumina PE adapter oligonucleotides were ligated to DNA fragments. DNA fragments that ligated with adaptor molecules on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycles PCR reaction. Libraries were purified using AMPure XP system and quantified using the KAPA Library Quantification Kits. Before submitted to sequencing  the libraries were normalized and pooled together in a single lane on an Illumina MiSeq platform and 150 bp paired end reads were generated.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina MiSeq,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>302</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>152</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP061528,,,wt_S1_L001_R1_001.fastq.gz wt_S1_L001_R2_001.fastq.gz,fastq fastq,1937209279.0,6445507.0,RNA Seq of WT,0:150.30 1:150.25,A:496555264;C:470694471;G:467911055;T:502040892;N:7597,150,150,,,496555264,470694471,467911055,502040892,7597,SRX1117102,SRS1010312,SRA279862,The Chinese University of Hong Kong,The Chinese University of Hong Kong,2,0.95931,0.96087,0.06913,0.06787,0.66101,0.66431,0.45529,0.4629,151,151,B,B,biological fallback assumption,illumina,miseq,unknown,random_priming,trueseq,bulk,bulk,bulk,,China,2016-07-24,Larval,Larval,Whole Organism,All anatomical structures
39835,SRR2382596,SRX1321825,SRS1109647,SRP062493,PRJNA293106,Danio rerio Raw sequence reads,PRJNA293106,Metagenomics,Zebrafish Hypoxia RNAseq,,,RNAseq at 72hpf following normoxia,,72hpf normoxia,,strain:TU|age:72hpf|sex:not determined|tissue:brain|treatment:normoxia|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample       72hpf normoxia,72hpf.normoxia.3.10329X30,72hpf.normoxia.3.10329X30,We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition.  For hypoxia  we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected.  We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages.  At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation.  RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer.  The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides  single end  stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer  providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP062493,,,10329X30_130822_SN141_0719_AD2CK5ACXX_8.txt.gz,fastq,1202543000.0,24050860.0,72hpf.normoxia.3.10329X30,0:50,A:317814132;C:265339479;G:263354488;T:356015292;N:19609,50,,,,317814132,265339479,263354488,356015292,19609,SRX1321825,SRS1109647,SRA289450,University of Utah|Bonkowsky,University of Utah,1,0.94396,,0.39792,,0.68592,,0.51696,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United States,2015-10-10,Larval,Larval,Brain,Nervous System
39836,SRR2346975,SRX1321824,SRS1109649,SRP062493,PRJNA293106,Danio rerio Raw sequence reads,PRJNA293106,Metagenomics,Zebrafish Hypoxia RNAseq,,,RNAseq at 72hpf following hypoxia,,72hpf hypoxia,,strain:TU|age:72hpf|sex:not determined|tissue:brain|treatment:hypoxia|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample       72hpf hypoxia,72hpf.hypoxia.3.10329X29,72hpf.hypoxia.3.10329X29,We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition.  For hypoxia  we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected.  We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages.  At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation.  RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer.  The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides  single end  stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer  providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP062493,,,10329X29_130822_SN141_0719_AD2CK5ACXX_8.txt.gz,fastq,977694000.0,19553880.0,72hpf.hypoxia.3.10329X29,0:50,A:252845467;C:218082615;G:213237499;T:293512810;N:15609,50,,,,252845467,218082615,213237499,293512810,15609,SRX1321824,SRS1109649,SRA289450,University of Utah|Bonkowsky,University of Utah,1,0.94858,,0.35206,,0.68889,,0.53177,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United States,2015-09-10,Larval,Larval,Brain,Nervous System
39842,SRR2243358,SRX1321818,SRS1109647,SRP062493,PRJNA293106,Danio rerio Raw sequence reads,PRJNA293106,Metagenomics,Zebrafish Hypoxia RNAseq,,,RNAseq at 72hpf following normoxia,,72hpf normoxia,,strain:TU|age:72hpf|sex:not determined|tissue:brain|treatment:normoxia|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample       72hpf normoxia,72hpf.normoxia.2.10329X20,72hpf.normoxia.2.10329X20,We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition.  For hypoxia  we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected.  We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages.  At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation.  RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer.  The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides  single end  stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer  providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP062493,,,10329X20_130822_SN141_0719_AD2CK5ACXX_7.txt.gz,fastq,1530276050.0,30605521.0,72hpf.normoxia.2.10329X20,0:50,A:387360143;C:340062704;G:324515181;T:458965961;N:19372061,50,,,,387360143,340062704,324515181,458965961,19372061,SRX1321818,SRS1109647,SRA289450,University of Utah|Bonkowsky,University of Utah,1,0.8774,,0.25469,,0.68799,,0.52777,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United States,2015-10-10,Larval,Larval,Brain,Nervous System
39843,SRR2243161,SRX1321817,SRS1109649,SRP062493,PRJNA293106,Danio rerio Raw sequence reads,PRJNA293106,Metagenomics,Zebrafish Hypoxia RNAseq,,,RNAseq at 72hpf following hypoxia,,72hpf hypoxia,,strain:TU|age:72hpf|sex:not determined|tissue:brain|treatment:hypoxia|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample       72hpf hypoxia,72hpf.hypoxia.2.10329X19,72hpf.hypoxia.2.10329X19,We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition.  For hypoxia  we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected.  We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages.  At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation.  RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer.  The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides  single end  stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer  providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP062493,,,10329X19_130822_SN141_0719_AD2CK5ACXX_7.txt.gz,fastq,1866619850.0,37332397.0,72hpf.hypoxia.2.10329X19,0:50,A:465524152;C:423400277;G:418937882;T:535202326;N:23555213,50,,,,465524152,423400277,418937882,535202326,23555213,SRX1321817,SRS1109649,SRA289450,University of Utah|Bonkowsky,University of Utah,1,0.85514,,0.26828,,0.7041,,0.54006,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United States,2015-10-10,Larval,Larval,Brain,Nervous System
39850,SRR2227378,SRX1321810,SRS1109647,SRP062493,PRJNA293106,Danio rerio Raw sequence reads,PRJNA293106,Metagenomics,Zebrafish Hypoxia RNAseq,,,RNAseq at 72hpf following normoxia,,72hpf normoxia,,strain:TU|age:72hpf|sex:not determined|tissue:brain|treatment:normoxia|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample       72hpf normoxia,72hpf.normoxia.1.10329X10,72hpf.normoxia.1.10329X10,We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition.  For hypoxia  we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected.  We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages.  At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation.  RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer.  The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides  single end  stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer  providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP062493,,,10329X10_130822_SN141_0719_AD2CK5ACXX_5.txt.gz,fastq,1268552500.0,25371050.0,72hpf.normoxia.1.10329X10,0:50,A:334230065;C:286785060;G:271795849;T:375668734;N:72792,50,,,,334230065,286785060,271795849,375668734,72792,SRX1321810,SRS1109647,SRA289450,University of Utah|Bonkowsky,University of Utah,1,0.94017,,0.34471,,0.67109,,0.5244,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United States,2015-09-18,Larval,Larval,Brain,Nervous System
39851,SRR2226742,SRX1321809,SRS1109649,SRP062493,PRJNA293106,Danio rerio Raw sequence reads,PRJNA293106,Metagenomics,Zebrafish Hypoxia RNAseq,,,RNAseq at 72hpf following hypoxia,,72hpf hypoxia,,strain:TU|age:72hpf|sex:not determined|tissue:brain|treatment:hypoxia|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample       72hpf hypoxia,72hpf.hypoxia.1.10329X9,72hpf.hypoxia.1.10329X9,We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition.  For hypoxia  we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected.  We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages.  At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation.  RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer.  The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides  single end  stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer  providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP062493,,,10329X9_130822_SN141_0719_AD2CK5ACXX_5.txt.gz,fastq,1625518100.0,32510362.0,72hpf.hypoxia.1.10329X9,0:50,A:428393257;C:366720934;G:349089971;T:481221434;N:92504,50,,,,428393257,366720934,349089971,481221434,92504,SRX1321809,SRS1109649,SRA289450,University of Utah|Bonkowsky,University of Utah,1,0.9444,,0.36232,,0.67503,,0.53278,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United States,2015-10-10,Larval,Larval,Brain,Nervous System
39911,SRR2255651,SRX1187765,SRS1056695,SRP063370,PRJNA294819,Danio rerio PFOS FL transcriptome project,PRJNA294819,Other,,,,,,TRAPPC11 Mutant2,,breed:not applicable|strain:not applicable|age:6 dpf provider:not applicable|sex:not collected|tissue:embryro|treatment:TRAPPC11 Mutant2|BioSampleModel:Model organism or animal,,,,,,,,,TRAPPC11 Mutant2,TRAPPC11 Mutant2,TRAPPC11 Mutant2,cDNA library from 300 ng of total RNA were constructed from two biological replicates using the TruSeq Stranded RNA LT Sample Prep Kit Illumina. The cDNA library was prepared according to the manufacturer’s instruction as previously described Gu et al.  2015. Briefly  Index barcodes were first ligated for identification of individual samples. mRNA was purified from the total RNA using poly T oligo attached magnetic beads Illumina  San Diego  USA  follows by random fragmentation using divalent cations at 94?C for 1 min. First and second strand cDNAs were synthesized using random oligonucleotides and SuperScript II  followed by DNA polymerase I and RNase H. Exonuclease/polymerase was used to produce blunted overhangs. Illumina PE adapter oligonucleotides were ligated to the cDNA post 3’ end adenylation. DNA fragments were enriched by 15 cycles of PCR reaction. The libraries were purified using the AMPure XP and were quantified using KAPA Library Quantification Kits.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina MiSeq,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</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>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP063370,,,fattyliver2_S6_L001_R1_001.fastq.gz fattyliver2_S6_L001_R2_001.fastq.gz,fastq fastq,836752562.0,5540752.0,TRAPPC11 Mutant2,0:75.54 1:75.48,A:219401421;C:198252489;G:195663968;T:223211242;N:223442,75,75,,,219401421,198252489,195663968,223211242,223442,SRX1187765,SRS1056695,SRA295687,The Chinese University of Hong Kong,The Chinese University of Hong Kong,2,0.96204,0.96259,0.05777,0.05527,0.74142,0.74089,0.47566,0.47333,75,52,B,B,biological fallback assumption,illumina,miseq,unknown,random_priming,trueseq,bulk,unknown,unknown,,China,2016-09-05,Larval,Larval,Embryo Imprecise,All anatomical structures
39912,SRR2255629,SRX1187764,SRS1056694,SRP063370,PRJNA294819,Danio rerio PFOS FL transcriptome project,PRJNA294819,Other,,,,,,TRAPPC11 Mutant1,,breed:not applicable|strain:not applicable|age:6 dpf provider:not applicable|sex:not collected|tissue:embryro|treatment:TRAPPC11 Mutant1|BioSampleModel:Model organism or animal,,,,,,,,,TRAPPC11 Mutant1,TRAPPC11 Mutant1,TRAPPC11 Mutant1,cDNA library from 300 ng of total RNA were constructed from two biological replicates using the TruSeq Stranded RNA LT Sample Prep Kit Illumina. The cDNA library was prepared according to the manufacturer’s instruction as previously described Gu et al.  2015. Briefly  Index barcodes were first ligated for identification of individual samples. mRNA was purified from the total RNA using poly T oligo attached magnetic beads Illumina  San Diego  USA  follows by random fragmentation using divalent cations at 94?C for 1 min. First and second strand cDNAs were synthesized using random oligonucleotides and SuperScript II  followed by DNA polymerase I and RNase H. Exonuclease/polymerase was used to produce blunted overhangs. Illumina PE adapter oligonucleotides were ligated to the cDNA post 3’ end adenylation. DNA fragments were enriched by 15 cycles of PCR reaction. The libraries were purified using the AMPure XP and were quantified using KAPA Library Quantification Kits.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina MiSeq,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</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>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP063370,,,fattyliver1_S5_L001_R1_001.fastq.gz fattyliver1_S5_L001_R2_001.fastq.gz,fastq fastq,752730180.0,4984563.0,TRAPPC11 Mutant1,0:75.53 1:75.48,A:201453785;C:174638707;G:171041330;T:205386632;N:209726,75,75,,,201453785,174638707,171041330,205386632,209726,SRX1187764,SRS1056694,SRA295687,The Chinese University of Hong Kong,The Chinese University of Hong Kong,2,0.95653,0.95631,0.07274,0.06976,0.70573,0.70664,0.49403,0.49925,74,76,B,B,biological fallback assumption,illumina,miseq,unknown,random_priming,trueseq,bulk,unknown,unknown,,China,2015-09-05,Larval,Larval,Embryo Imprecise,All anatomical structures
39913,SRR2255628,SRX1187763,SRS1056693,SRP063370,PRJNA294819,Danio rerio PFOS FL transcriptome project,PRJNA294819,Other,,,,,,PFOS2,,breed:not applicable|strain:not applicable|age:6 dpf provider:not applicable|sex:not collected|tissue:embryro|treatment:PFOS2|BioSampleModel:Model organism or animal,,,,,,,,,PFOS2,PFOS2,PFOS2,cDNA library from 300 ng of total RNA were constructed from two biological replicates using the TruSeq Stranded RNA LT Sample Prep Kit Illumina. The cDNA library was prepared according to the manufacturer’s instruction as previously described Gu et al.  2015. Briefly  Index barcodes were first ligated for identification of individual samples. mRNA was purified from the total RNA using poly T oligo attached magnetic beads Illumina  San Diego  USA  follows by random fragmentation using divalent cations at 94?C for 1 min. First and second strand cDNAs were synthesized using random oligonucleotides and SuperScript II  followed by DNA polymerase I and RNase H. Exonuclease/polymerase was used to produce blunted overhangs. Illumina PE adapter oligonucleotides were ligated to the cDNA post 3’ end adenylation. DNA fragments were enriched by 15 cycles of PCR reaction. The libraries were purified using the AMPure XP and were quantified using KAPA Library Quantification Kits.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina MiSeq,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</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>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP063370,,,PFOS2_S4_L001_R1_001.fastq.gz PFOS2_S4_L001_R2_001.fastq.gz,fastq fastq,660339622.0,4372724.0,PFOS2,0:75.53 1:75.48,A:174477377;C:155458423;G:152138367;T:178072878;N:192577,75,75,,,174477377,155458423,152138367,178072878,192577,SRX1187763,SRS1056693,SRA295687,The Chinese University of Hong Kong,The Chinese University of Hong Kong,2,0.95841,0.95943,0.06213,0.06061,0.71664,0.71717,0.49605,0.5046,76,52,B,B,biological fallback assumption,illumina,miseq,unknown,random_priming,trueseq,bulk,unknown,unknown,,China,2016-09-05,Larval,Larval,Embryo Imprecise,All anatomical structures
39914,SRR2255627,SRX1187762,SRS1056692,SRP063370,PRJNA294819,Danio rerio PFOS FL transcriptome project,PRJNA294819,Other,,,,,,PFOS1,,breed:not applicable|strain:not applicable|age:6 dpf provider:not applicable|sex:not collected|tissue:embryro|treatment:PFOS1|BioSampleModel:Model organism or animal,,,,,,,,,PFOS1,PFOS1,PFOS1,cDNA library from 300 ng of total RNA were constructed from two biological replicates using the TruSeq Stranded RNA LT Sample Prep Kit Illumina. The cDNA library was prepared according to the manufacturer’s instruction as previously described Gu et al.  2015. Briefly  Index barcodes were first ligated for identification of individual samples. mRNA was purified from the total RNA using poly T oligo attached magnetic beads Illumina  San Diego  USA  follows by random fragmentation using divalent cations at 94?C for 1 min. First and second strand cDNAs were synthesized using random oligonucleotides and SuperScript II  followed by DNA polymerase I and RNase H. Exonuclease/polymerase was used to produce blunted overhangs. Illumina PE adapter oligonucleotides were ligated to the cDNA post 3’ end adenylation. DNA fragments were enriched by 15 cycles of PCR reaction. The libraries were purified using the AMPure XP and were quantified using KAPA Library Quantification Kits.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina MiSeq,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</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>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP063370,,,PFOS1_S3_L001_R1_001.fastq.gz PFOS1_S3_L001_R2_001.fastq.gz,fastq fastq,791950817.0,5244084.0,PFOS1,0:75.53 1:75.48,A:207476025;C:187690975;G:185784999;T:210781701;N:217117,75,75,,,207476025,187690975,185784999,210781701,217117,SRX1187762,SRS1056692,SRA295687,The Chinese University of Hong Kong,The Chinese University of Hong Kong,2,0.96195,0.96213,0.051,0.04857,0.7386,0.73927,0.49669,0.49151,76,53,B,B,biological fallback assumption,illumina,miseq,unknown,random_priming,trueseq,bulk,unknown,unknown,,China,2016-09-05,Larval,Larval,Embryo Imprecise,All anatomical structures
39915,SRR2255626,SRX1187761,SRS1056691,SRP063370,PRJNA294819,Danio rerio PFOS FL transcriptome project,PRJNA294819,Other,,,,,,DMSO2,,breed:not applicable|strain:not applicable|age:6 dpf provider:not applicable|sex:not collected|tissue:embryro|treatment:DMSO2|BioSampleModel:Model organism or animal,,,,,,,,,DMSO2,DMSO2,DMSO2,cDNA library from 300 ng of total RNA were constructed from two biological replicates using the TruSeq Stranded RNA LT Sample Prep Kit Illumina. The cDNA library was prepared according to the manufacturer’s instruction as previously described Gu et al.  2015. Briefly  Index barcodes were first ligated for identification of individual samples. mRNA was purified from the total RNA using poly T oligo attached magnetic beads Illumina  San Diego  USA  follows by random fragmentation using divalent cations at 94?C for 1 min. First and second strand cDNAs were synthesized using random oligonucleotides and SuperScript II  followed by DNA polymerase I and RNase H. Exonuclease/polymerase was used to produce blunted overhangs. Illumina PE adapter oligonucleotides were ligated to the cDNA post 3’ end adenylation. DNA fragments were enriched by 15 cycles of PCR reaction. The libraries were purified using the AMPure XP and were quantified using KAPA Library Quantification Kits.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina MiSeq,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</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>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP063370,,,DMSO2_S2_L001_R1_001.fastq.gz DMSO2_S2_L001_R2_001.fastq.gz,fastq fastq,847975709.0,5615263.0,DMSO2,0:75.53 1:75.48,A:222828293;C:200598370;G:196827420;T:227477582;N:244044,75,75,,,222828293,200598370,196827420,227477582,244044,SRX1187761,SRS1056691,SRA295687,The Chinese University of Hong Kong,The Chinese University of Hong Kong,2,0.95825,0.95852,0.06376,0.06156,0.71224,0.71313,0.49629,0.49076,76,76,B,B,biological fallback assumption,illumina,miseq,unknown,random_priming,trueseq,bulk,unknown,unknown,,China,2016-09-05,Larval,Larval,Embryo Imprecise,All anatomical structures
39916,SRR2255625,SRX1187760,SRS1056690,SRP063370,PRJNA294819,Danio rerio PFOS FL transcriptome project,PRJNA294819,Other,,,,,,DMSO1,,breed:not applicable|strain:not applicable|age:6 dpf provider:not applicable|sex:not collected|tissue:embryro|treatment:DMSO1|BioSampleModel:Model organism or animal,,,,,,,,,DMSO1,DMSO1,DMSO1,cDNA library from 300 ng of total RNA were constructed from two biological replicates using the TruSeq Stranded RNA LT Sample Prep Kit Illumina. The cDNA library was prepared according to the manufacturer’s instruction as previously described Gu et al.  2015. Briefly  Index barcodes were first ligated for identification of individual samples. mRNA was purified from the total RNA using poly T oligo attached magnetic beads Illumina  San Diego  USA  follows by random fragmentation using divalent cations at 94?C for 1 min. First and second strand cDNAs were synthesized using random oligonucleotides and SuperScript II  followed by DNA polymerase I and RNase H. Exonuclease/polymerase was used to produce blunted overhangs. Illumina PE adapter oligonucleotides were ligated to the cDNA post 3’ end adenylation. DNA fragments were enriched by 15 cycles of PCR reaction. The libraries were purified using the AMPure XP and were quantified using KAPA Library Quantification Kits.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina MiSeq,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</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>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP063370,,,DMSO1_S1_L001_R1_001.fastq.gz DMSO1_S1_L001_R2_001.fastq.gz,fastq fastq,825003413.0,5463030.0,DMSO1,0:75.53 1:75.48,A:217714985;C:193454273;G:192078021;T:221527657;N:228477,75,75,,,217714985,193454273,192078021,221527657,228477,SRX1187760,SRS1056690,SRA295687,The Chinese University of Hong Kong,The Chinese University of Hong Kong,2,0.96443,0.9657,0.05205,0.04878,0.76581,0.76465,0.49046,0.47298,76,54,B,B,biological fallback assumption,illumina,miseq,unknown,random_priming,trueseq,bulk,unknown,unknown,,China,2016-09-05,Larval,Larval,Embryo Imprecise,All anatomical structures
41032,SRR3581739,SRX1797279,SRS1465200,SRP075626,PRJNA322629,Mycobacterial infection of adult zebrafish,PRJNA322629,Other,RNA seq based profiling of Mycobacterium marinum granulomas from adult zebrafish and matched macrophage samples.,,,,Larval non fluorescent cells post macrophage sorting3,C NF3,,breed:*AB|age:4dpf|dev stage:Larval|sex:not determined|tissue:Whole animal following macrophage depletion via FACS|BioSampleModel:Model organism or animal,,,,,,,,,C NF3,C NF3,C NF3,1,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP075626,,,C_NF3.fastq.gz,fastq,1745512893.0,34225743.0,C NF3.fastq.gz,0:51,A:470456301;C:396221813;G:401458508;T:477287506;N:88765,51,,,,470456301,396221813,401458508,477287506,88765,SRX1797279,SRS1465200,SRA429046,Duke University|Molecular Genetics &amp; Microbiology,Duke University,1,0.92839,,0.06821,,0.73099,,0.44395,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,United States,2016-05-25,Larval,Larval,Blood,Hematopoietic System
41033,SRR3581729,SRX1797278,SRS1465199,SRP075626,PRJNA322629,Mycobacterial infection of adult zebrafish,PRJNA322629,Other,RNA seq based profiling of Mycobacterium marinum granulomas from adult zebrafish and matched macrophage samples.,,,,Larval non fluorescent cells post macrophage sorting2,C NF2,,breed:*AB|age:4dpf|dev stage:Larval|sex:not determined|tissue:Whole animal following macrophage depletion via FACS|BioSampleModel:Model organism or animal,,,,,,,,,C NF2,C NF2,C NF2,1,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP075626,,,C_NF2.fastq.gz,fastq,2116510506.0,41500206.0,C NF2.fastq.gz,0:51,A:580244434;C:475940957;G:474848964;T:585459729;N:16422,51,,,,580244434,475940957,474848964,585459729,16422,SRX1797278,SRS1465199,SRA429045,Duke University|Molecular Genetics &amp; Microbiology,Duke University,1,0.90388,,0.06926,,0.78963,,0.49501,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,United States,2017-06-24,Larval,Larval,Blood,Hematopoietic System
41034,SRR3581718,SRX1797274,SRS1465196,SRP075626,PRJNA322629,Mycobacterial infection of adult zebrafish,PRJNA322629,Other,RNA seq based profiling of Mycobacterium marinum granulomas from adult zebrafish and matched macrophage samples.,,,,Larval non fluorescent cells post macrophage sorting1,C NF1,,breed:*AB|age:4dpf|dev stage:Larval|sex:not determined|tissue:Whole animal following macrophage depletion via FACS|BioSampleModel:Model organism or animal,,,,,,,,,C NF1,C NF1,C NF1,1,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP075626,,,C_NF1.fastq.gz,fastq,1492422690.0,29263190.0,C NF1.fastq.gz,0:51,A:421145406;C:327412398;G:328273236;T:415327504;N:264146,51,,,,421145406,327412398,328273236,415327504,264146,SRX1797274,SRS1465196,SRA429041,Duke University|Molecular Genetics &amp; Microbiology,Duke University,1,0.82347,,0.08561,,0.75207,,0.45637,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,United States,2017-06-24,Larval,Larval,Blood,Hematopoietic System
41782,SRR5162099,SRX2480053,SRS1910957,SRP096313,PRJNA360680,S6K1 project raw sequence reads,PRJNA360680,Other,,,,,,PLC5shCtrl1,,breed:not applicable|strain:not applicable|age:6 dpf provider:not applicable|sex:not collected|tissue:embryro|treatment:PLC5shCtrl1|BioSampleModel:Model organism or animal,,,,,,,,,PLC5shCtrl1,PLC5shCtrl1,PLC5shCtrl1,Total RNA was isolated from the stable transfected cells shCtrl and shS6K1 from Hep3B and PLC5 cells using the mirVanaTM RNA isolation kit Applied Biosystems. The quality of RNA was assessed using the Agilent 2100 Bioanalyzer system and samples with a RNA Integrity Number RIN greater than 8 were used for RNA library construction. The RNA library was sequenced by the Beijing Genomics Institute Wuhan  China. Single end reads  50 bp read length  were sequenced on the BGISEQ 500RS sequencer. Qualified raw data were provided by the Beijing Genomics Institute in FASTQ format.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,COMPLETE_GENOMICS,Complete Genomics,,SRP096313,,,,,1201388650.0,24027773.0,CL100006841 L02 24 1.fq.gz,0:50,A:297299471;C:292335863;G:332701724;T:278571616;N:479976,50,,,,297299471,292335863,332701724,278571616,479976,SRX2480053,SRS1910957,SRA525651,The Chinese University of Hong Kong|School of Life Sciences,The Chinese University of Hong Kong|School of Life Sciences,1,0.00295,,0.00039,,0.99754,,0.63223,,50,,T,,under 1.2% mapping rate,legacy,early,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2017-01-10,Larval,Larval,Embryo Imprecise,All anatomical structures
41783,SRR5162098,SRX2480052,SRS1910956,SRP096313,PRJNA360680,S6K1 project raw sequence reads,PRJNA360680,Other,,,,,,Hep3BshS6K1,,breed:not applicable|strain:not applicable|age:6 dpf provider:not applicable|sex:not collected|tissue:embryro|treatment:Hep3BshS6K1|BioSampleModel:Model organism or animal,,,,,,,,,Hep3BshS6K1,Hep3BshS6K1,Hep3BshS6K1,Total RNA was isolated from the stable transfected cells shCtrl and shS6K1 from Hep3B and PLC5 cells using the mirVanaTM RNA isolation kit Applied Biosystems. The quality of RNA was assessed using the Agilent 2100 Bioanalyzer system and samples with a RNA Integrity Number RIN greater than 8 were used for RNA library construction. The RNA library was sequenced by the Beijing Genomics Institute Wuhan  China. Single end reads  50 bp read length  were sequenced on the BGISEQ 500RS sequencer. Qualified raw data were provided by the Beijing Genomics Institute in FASTQ format.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,COMPLETE_GENOMICS,Complete Genomics,,SRP096313,,,,,1205347750.0,24106955.0,CL100006841 L02 21 1.fq.gz,0:50,A:312935885;C:282462046;G:322914710;T:286516924;N:518185,50,,,,312935885,282462046,322914710,286516924,518185,SRX2480052,SRS1910956,SRA525651,The Chinese University of Hong Kong|School of Life Sciences,The Chinese University of Hong Kong|School of Life Sciences,1,0.00262,,0.00033,,0.99764,,0.69195,,50,,T,,under 1.2% mapping rate,legacy,early,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2017-01-10,Larval,Larval,Embryo Imprecise,All anatomical structures
41784,SRR5162097,SRX2480051,SRS1910955,SRP096313,PRJNA360680,S6K1 project raw sequence reads,PRJNA360680,Other,,,,,,PLC5shS6K1,,breed:not applicable|strain:not applicable|age:6 dpf provider:not applicable|sex:not collected|tissue:embryro|treatment:PLC5shS6K1|BioSampleModel:Model organism or animal,,,,,,,,,PLC5shS6K1,PLC5shS6K1,PLC5shS6K1,1,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,COMPLETE_GENOMICS,Complete Genomics,,SRP096313,,,,,1205157400.0,24103148.0,CL100006841 L02 25 1.fq.gz,0:50,A:305738728;C:286350102;G:329378158;T:283136091;N:554321,50,,,,305738728,286350102,329378158,283136091,554321,SRX2480051,SRS1910955,SRA525651,The Chinese University of Hong Kong|School of Life Sciences,The Chinese University of Hong Kong|School of Life Sciences,1,0.00275,,0.00036,,0.99801,,0.66666,,50,,T,,under 1.2% mapping rate,legacy,early,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2017-01-10,Larval,Larval,Embryo Imprecise,All anatomical structures
41785,SRR5162096,SRX2480050,SRS1910954,SRP096313,PRJNA360680,S6K1 project raw sequence reads,PRJNA360680,Other,,,,,,HepG2shS6K1,,breed:not applicable|strain:not applicable|age:6 dpf provider:not applicable|sex:not collected|tissue:embryro|treatment:HepG2shS6K1|BioSampleModel:Model organism or animal,,,,,,,,,HepG2shS6K1,HepG2shS6K1,HepG2shS6K1,Total RNA was isolated from the stable transfected cells shCtrl and shS6K1 from Hep3B and PLC5 cells using the mirVanaTM RNA isolation kit Applied Biosystems. The quality of RNA was assessed using the Agilent 2100 Bioanalyzer system and samples with a RNA Integrity Number RIN greater than 8 were used for RNA library construction. The RNA library was sequenced by the Beijing Genomics Institute Wuhan  China. Single end reads  50 bp read length  were sequenced on the BGISEQ 500RS sequencer. Qualified raw data were provided by the Beijing Genomics Institute in FASTQ format.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,COMPLETE_GENOMICS,Complete Genomics,,SRP096313,,,,,1203548150.0,24070963.0,CL100006841 L02 23 1.fq.gz,0:50,A:307598832;C:285812241;G:331356323;T:278082314;N:698440,50,,,,307598832,285812241,331356323,278082314,698440,SRX2480050,SRS1910954,SRA525651,The Chinese University of Hong Kong|School of Life Sciences,The Chinese University of Hong Kong|School of Life Sciences,1,0.00192,,0.00012,,0.99784,,0.60818,,50,,T,,under 1.2% mapping rate,legacy,early,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2017-01-10,Larval,Larval,Embryo Imprecise,All anatomical structures
41786,SRR5162095,SRX2480049,SRS1910953,SRP096313,PRJNA360680,S6K1 project raw sequence reads,PRJNA360680,Other,,,,,,Hep3BshCtrl1,,breed:not applicable|strain:not applicable|age:6 dpf provider:not applicable|sex:not collected|tissue:embryro|treatment:Hep3BshCtrl1|BioSampleModel:Model organism or animal,,,,,,,,,Hep3BshCtrl1,Hep3BshCtrl1,Hep3BshCtrl1,Total RNA was isolated from the stable transfected cells shCtrl and shS6K1 from Hep3B and PLC5 cells using the mirVanaTM RNA isolation kit Applied Biosystems. The quality of RNA was assessed using the Agilent 2100 Bioanalyzer system and samples with a RNA Integrity Number RIN greater than 8 were used for RNA library construction. The RNA library was sequenced by the Beijing Genomics Institute Wuhan  China. Single end reads  50 bp read length  were sequenced on the BGISEQ 500RS sequencer. Qualified raw data were provided by the Beijing Genomics Institute in FASTQ format.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,COMPLETE_GENOMICS,Complete Genomics,,SRP096313,,,,,1201618100.0,24032362.0,CL100006841 L02 20 1.fq.gz,0:50,A:301938424;C:291014141;G:326734280;T:281455564;N:475691,50,,,,301938424,291014141,326734280,281455564,475691,SRX2480049,SRS1910953,SRA525651,The Chinese University of Hong Kong|School of Life Sciences,The Chinese University of Hong Kong|School of Life Sciences,1,0.00522,,0.00084,,0.99722,,0.61317,,50,,T,,under 1.2% mapping rate,legacy,early,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2017-01-10,Larval,Larval,Embryo Imprecise,All anatomical structures
41787,SRR5162094,SRX2480048,SRS1910952,SRP096313,PRJNA360680,S6K1 project raw sequence reads,PRJNA360680,Other,,,,,,HepG2shCtrl1,,breed:not applicable|strain:not applicable|age:6 dpf provider:not applicable|sex:not collected|tissue:embryro|treatment:HepG2shCtrl1|BioSampleModel:Model organism or animal,,,,,,,,,HepG2shCtrl1,HepG2shCtrl1,HepG2shCtrl1,Total RNA was isolated from the stable transfected cells shCtrl and shS6K1 from Hep3B and PLC5 cells using the mirVanaTM RNA isolation kit Applied Biosystems. The quality of RNA was assessed using the Agilent 2100 Bioanalyzer system and samples with a RNA Integrity Number RIN greater than 8 were used for RNA library construction. The RNA library was sequenced by the Beijing Genomics Institute Wuhan  China. Single end reads  50 bp read length  were sequenced on the BGISEQ 500RS sequencer. Qualified raw data were provided by the Beijing Genomics Institute in FASTQ format.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,COMPLETE_GENOMICS,Complete Genomics,,SRP096313,,,,,1205042850.0,24100857.0,CL100006841 L02 22 1.fq.gz,0:50,A:310292006;C:282567913;G:329631833;T:282050651;N:500447,50,,,,310292006,282567913,329631833,282050651,500447,SRX2480048,SRS1910952,SRA525651,The Chinese University of Hong Kong|School of Life Sciences,The Chinese University of Hong Kong|School of Life Sciences,1,0.00164,,0.00012,,0.99784,,0.62847,,50,,T,,under 1.2% mapping rate,legacy,early,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2017-01-10,Larval,Larval,Embryo Imprecise,All anatomical structures
43749,SRR6047139,SRX3194198,SRS2520599,SRP117794,PRJNA407650,Danio rerio Transcriptome or Gene expression,PRJNA407650,Transcriptome Analysis,We performed RNA sequencing on four groups of zebrafish larvae: control  TgMyc  TgKras  TgMyc&amp;TgKras to analyze the expression of genes involved in the lipid associated pathways.The results revealed high dynamic alterations in almost all aspects of lipid metabolism  among which  the expressions of genes involved in TG/DG/GP transformation and FA desaturation/elongation displayed intensive changes  in consistent with our observations in lipodomics profiling,,,,,Control,,strain:AB|breed:breed with AB|cultivar:not applicable|ecotype:not applicable|age:6dpf|dev stage:larval|sex:not determined|tissue:whole larvae|treatment:E3 with Doxcyclin40ug/ml|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish larvaeAB at 6dpf,Control,Control,In our project  we sequence 4 samples use Illumina Hiseq platform  and on average we generated about 6.56Gb bases from each sample. We also map clean reads to reference genome  on average 71.49% reads are mapped,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP117794,,,FCHCKWTBBXX-WHZEBleaEAACRAAPEI-20_L1_1.fq.gz FCHCKWTBBXX-WHZEBleaEAACRAAPEI-20_L1_2.fq.gz,fastq fastq,6648275100.0,22160917.0,FCHCKWTBBXX WHZEBleaEAACRAAPEI 20 L1 2.fq.gz,0:150 1:150,A:1742296604;C:1590637599;G:1588423459;T:1726207133;N:710305,150,150,,,1742296604,1590637599,1588423459,1726207133,710305,SRX3194198,SRS2520599,SRA608833,"Fudan University|Department of Biochemistry and Molecular Biology,",Fudan University,2,0.91275,0.9117,0.06243,0.06238,0.6743,0.68002,0.48294,0.4832,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2017-09-17,Larval,Larval,Whole Organism,All anatomical structures
43750,SRR6047140,SRX3194197,SRS2520598,SRP117794,PRJNA407650,Danio rerio Transcriptome or Gene expression,PRJNA407650,Transcriptome Analysis,We performed RNA sequencing on four groups of zebrafish larvae: control  TgMyc  TgKras  TgMyc&amp;TgKras to analyze the expression of genes involved in the lipid associated pathways.The results revealed high dynamic alterations in almost all aspects of lipid metabolism  among which  the expressions of genes involved in TG/DG/GP transformation and FA desaturation/elongation displayed intensive changes  in consistent with our observations in lipodomics profiling,,,,,Myc,,strain:Tgfabp10a:TetON; TRE:Myc|breed:breed with AB|cultivar:not applicable|ecotype:not applicable|age:6dpf|dev stage:larval|sex:not determined|tissue:whole larvae|treatment:E3 with Doxcyclin41ug/ml|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish larvaeMyc at 6dpf,Myc,Myc,In our project  we sequence 4 samples use Illumina Hiseq platform  and on average we generated about 6.56Gb bases from each sample. We also map clean reads to reference genome  on average 71.49% reads are mapped,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP117794,,,FCHCKWTBBXX-WHZEBleaEAABRAAPEI-19_L1_1.fq.gz FCHCKWTBBXX-WHZEBleaEAABRAAPEI-19_L1_2.fq.gz,fastq fastq,6562440900.0,21874803.0,FCHCKWTBBXX WHZEBleaEAABRAAPEI 19 L1 2.fq.gz,0:150 1:150,A:1690373636;C:1597720217;G:1597100889;T:1676557094;N:689064,150,150,,,1690373636,1597720217,1597100889,1676557094,689064,SRX3194197,SRS2520598,SRA608833,"Fudan University|Department of Biochemistry and Molecular Biology,",Fudan University,2,0.9112,0.9098,0.05364,0.05314,0.68199,0.68826,0.47506,0.48785,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2017-09-17,Larval,Larval,Whole Organism,All anatomical structures
43751,SRR6047141,SRX3194196,SRS2520597,SRP117794,PRJNA407650,Danio rerio Transcriptome or Gene expression,PRJNA407650,Transcriptome Analysis,We performed RNA sequencing on four groups of zebrafish larvae: control  TgMyc  TgKras  TgMyc&amp;TgKras to analyze the expression of genes involved in the lipid associated pathways.The results revealed high dynamic alterations in almost all aspects of lipid metabolism  among which  the expressions of genes involved in TG/DG/GP transformation and FA desaturation/elongation displayed intensive changes  in consistent with our observations in lipodomics profiling,,,,,Kras,,strain:Tgfabp10a:TetON; TRE:eGFP krasv12|breed:breed with AB|cultivar:not applicable|ecotype:not applicable|age:6dpf|dev stage:larval|sex:not determined|tissue:whole larvae|treatment:E3 with Doxcyclin42ug/ml|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish larvaeKras at 6dpf,Kras,Kras,In our project  we sequence 4 samples use Illumina Hiseq platform  and on average we generated about 6.56Gb bases from each sample. We also map clean reads to reference genome  on average 71.49% reads are mapped,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP117794,,,FCHCKWTBBXX-WHZEBleaEAADRAAPEI-21_L1_1.fq.gz FCHCKWTBBXX-WHZEBleaEAADRAAPEI-21_L1_2.fq.gz,fastq fastq,6567871200.0,21892904.0,FCHCKWTBBXX WHZEBleaEAADRAAPEI 21 L1 2.fq.gz,0:150 1:150,A:1728249052;C:1564137653;G:1559231198;T:1715565790;N:687507,150,150,,,1728249052,1564137653,1559231198,1715565790,687507,SRX3194196,SRS2520597,SRA608833,"Fudan University|Department of Biochemistry and Molecular Biology,",Fudan University,2,0.93087,0.92811,0.06342,0.06328,0.66941,0.67493,0.47581,0.47601,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2017-09-17,Larval,Larval,Whole Organism,All anatomical structures
43752,SRR6047142,SRX3194195,SRS2520596,SRP117794,PRJNA407650,Danio rerio Transcriptome or Gene expression,PRJNA407650,Transcriptome Analysis,We performed RNA sequencing on four groups of zebrafish larvae: control  TgMyc  TgKras  TgMyc&amp;TgKras to analyze the expression of genes involved in the lipid associated pathways.The results revealed high dynamic alterations in almost all aspects of lipid metabolism  among which  the expressions of genes involved in TG/DG/GP transformation and FA desaturation/elongation displayed intensive changes  in consistent with our observations in lipodomics profiling,,,,,Kras&amp;Myc,,strain:Tgfabp10a:TetON; TRE:Myc&Tgfabp10a:TetON; TRE:eGFP krasv12|breed:breed with AB|cultivar:not applicable|ecotype:not applicable|age:6dpf|dev stage:larval|sex:not determined|tissue:whole larvae|treatment:E3 with Doxcyclin43ug/ml|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish larvaeKras&Myc at 6dpf,Kras&amp;Myc,Kras&Myc,In our project  we sequence 4 samples use Illumina Hiseq platform  and on average we generated about 6.56Gb bases from each sample. We also map clean reads to reference genome  on average 71.49% reads are mapped,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP117794,,,FCHCKWTBBXX-WHZEBleaEAAARAAPEI-18_L1_1.fq.gz FCHCKWTBBXX-WHZEBleaEAAARAAPEI-18_L1_2.fq.gz,fastq fastq,6464892900.0,21549643.0,FCHCKWTBBXX WHZEBleaEAAARAAPEI 18 L1 2.fq.gz,0:150 1:150,A:1676039250;C:1565410813;G:1564742343;T:1658019117;N:681377,150,150,,,1676039250,1565410813,1564742343,1658019117,681377,SRX3194195,SRS2520596,SRA608833,"Fudan University|Department of Biochemistry and Molecular Biology,",Fudan University,2,0.8919,0.88916,0.05486,0.05403,0.67882,0.68505,0.49625,0.49784,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2017-09-17,Larval,Larval,Whole Organism,All anatomical structures
49393,SRR7896793,SRX4734232,SRS3816349,SRP162489,PRJNA492836,Danio rerio Transcriptome or Gene expression,PRJNA492836,Transcriptome Analysis,to study the feasibility of gene therapy of TNNT2 mutant related cardiomyopathy,,,,,homozygous mutant,,strain:tnnt2a / |cultivar:not applicable|ecotype:not applicable|age:3 dpf stage:larval|sex:pooled male and female|tissue:whole larvae|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of tnnt2a homozygous mutant zebrafish post Dox induction,homozygous mutant,homozygous mutant,In our project  we sequence 4 samples use Illumina Hiseq platform  and on average we generated about 6.56Gb bases from each sample. We also map clean reads to reference genome  on average 71.49% reads are mapped,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP162489,,,mutant_L1_1.fq.gz mutant_L1_2.fq.gz,fastq fastq,6615980100.0,22053267.0,mutant L1 2.fq.gz,0:150 1:150,A:1714364351;C:1596934293;G:1606676062;T:1697294755;N:710639,150,150,,,1714364351,1596934293,1606676062,1697294755,710639,SRX4734232,SRS3816349,,,Children's hospital of Fudan University,2,0.88229,0.88599,0.05373,0.05345,0.67042,0.67259,0.45764,0.46314,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2018-09-24,Larval,Larval,Whole Organism,All anatomical structures
49394,SRR7896794,SRX4734231,SRS3816348,SRP162489,PRJNA492836,Danio rerio Transcriptome or Gene expression,PRJNA492836,Transcriptome Analysis,to study the feasibility of gene therapy of TNNT2 mutant related cardiomyopathy,,,,,non homozygous mutant,,strain:tnnt2a+/ |cultivar:not applicable|ecotype:not applicable|age:3 dpf stage:larval|sex:pooled male and female|tissue:whole larvae|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of non tnnt2a homozygous mutant zebrafish post Dox induction,non homozygous mutant,non homozygous mutant,In our project  we sequence 4 samples use Illumina Hiseq platform  and on average we generated about 6.56Gb bases from each sample. We also map clean reads to reference genome  on average 71.49% reads are mapped,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP162489,,,non mutant_L1_1.fq.gz non mutant_L1_2.fq.gz,fastq fastq,6561723600.0,21872412.0,non mutant L1 2.fq.gz,0:150 1:150,A:1689788269;C:1592764528;G:1601424044;T:1677002898;N:743861,150,150,,,1689788269,1592764528,1601424044,1677002898,743861,SRX4734231,SRS3816348,,,Children's hospital of Fudan University,2,0.8991,0.90343,0.05565,0.05598,0.66752,0.66929,0.4567,0.46188,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2018-09-24,Larval,Larval,Whole Organism,All anatomical structures