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
38,DRR408248,DRX393854,DRS407179,DRP012042,PRJDB14275,Zebrafish EN/ENCDC RNA seq,DRP012042,Transcriptome Analysis,A project to find differential expressed genes between enteric neurons ENs and enteric neural crest derived cells ENCDCs in larval zebrafish gut. We dissected guts of transgenic line TgSAGFFLF217B; uas:gfp for ENs and Tgsox10:cre; EF1alpha:loxP gfp loxP dsred for ENCDCs and isolated GFP+ ENs and dsRed+ ENCDCs. Three duplicates for each of ENs and ENCDCs are prepared. Libraries for NGS are prepared using SMART Seq V4 Ultra Low Input RNA Kit.,,,zebrafish 5 day DsRed positive enteric neural crest derived cells replicate 3,zebrafish ENCDC replicate 3,SAMD00529468,,sample name:zebrafish ENCDC replicate 3|biological replicate:enteric neural crest derived cells 3|strain:Tgsox10:cre; EF3alpha:loxP gfp loxP dsred,,,,,,,,,NextSeq 550 paired end sequencing of SAMD00529468,DRX393854,190326ENvsNC N706 5day;NeuralCrestDerivedCell;rep3,1,1,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,NextSeq 550,1600Application ReadForward11Application ReadReverse81,DRP012042,NextSeq 550 paired end sequencing of SAMD00529468,,,,3803721121.0,24526633.0,DRR408248,0:77.54 1:77.54,A:999106107;C:897663781;G:921501114;T:979486853;N:5963266,77,77,,,999106107,897663781,921501114,979486853,5963266,DRX393854,DRS407179,DRA014886,"NIBB|NIBB core research facilities, National Institute for Basic Biology",University of Hyogo,,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,bulk,unknown,unknown,,Japan,2024-09-22,Undetermined,Larval,Brain,Nervous System
39,DRR408247,DRX393853,DRS407178,DRP012042,PRJDB14275,Zebrafish EN/ENCDC RNA seq,DRP012042,Transcriptome Analysis,A project to find differential expressed genes between enteric neurons ENs and enteric neural crest derived cells ENCDCs in larval zebrafish gut. We dissected guts of transgenic line TgSAGFFLF217B; uas:gfp for ENs and Tgsox10:cre; EF1alpha:loxP gfp loxP dsred for ENCDCs and isolated GFP+ ENs and dsRed+ ENCDCs. Three duplicates for each of ENs and ENCDCs are prepared. Libraries for NGS are prepared using SMART Seq V4 Ultra Low Input RNA Kit.,,,zebrafish 5 day DsRed positive enteric neural crest derived cells replicate 2,zebrafish ENCDC replicate 2,SAMD00529467,,sample name:zebrafish ENCDC replicate 2|biological replicate:enteric neural crest derived cells 2|strain:Tgsox10:cre; EF2alpha:loxP gfp loxP dsred,,,,,,,,,NextSeq 550 paired end sequencing of SAMD00529467,DRX393853,190326ENvsNC N705 5day;NeuralCrestDerivedCell;rep2,1,1,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,NextSeq 550,1600Application ReadForward11Application ReadReverse81,DRP012042,NextSeq 550 paired end sequencing of SAMD00529467,,,,3436798274.0,22156202.0,DRR408247,0:77.56 1:77.56,A:900848174;C:812031426;G:832960423;T:885671203;N:5287048,77,77,,,900848174,812031426,832960423,885671203,5287048,DRX393853,DRS407178,DRA014886,"NIBB|NIBB core research facilities, National Institute for Basic Biology",University of Hyogo,,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,bulk,unknown,unknown,,Japan,2024-09-22,Undetermined,Larval,Brain,Nervous System
40,DRR408246,DRX393852,DRS407177,DRP012042,PRJDB14275,Zebrafish EN/ENCDC RNA seq,DRP012042,Transcriptome Analysis,A project to find differential expressed genes between enteric neurons ENs and enteric neural crest derived cells ENCDCs in larval zebrafish gut. We dissected guts of transgenic line TgSAGFFLF217B; uas:gfp for ENs and Tgsox10:cre; EF1alpha:loxP gfp loxP dsred for ENCDCs and isolated GFP+ ENs and dsRed+ ENCDCs. Three duplicates for each of ENs and ENCDCs are prepared. Libraries for NGS are prepared using SMART Seq V4 Ultra Low Input RNA Kit.,,,zebrafish 5 day DsRed positive enteric neural crest derived cells replicate 1,zebrafish ENCDC replicate 1,SAMD00529466,,sample name:zebrafish ENCDC replicate 1|biological replicate:enteric neural crest derived cells 1|strain:Tgsox10:cre; EF1alpha:loxP gfp loxP dsred,,,,,,,,,NextSeq 550 paired end sequencing of SAMD00529466,DRX393852,190326ENvsNC N704 5day;NeuralCrestDerivedCell;rep1,1,1,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,NextSeq 550,1600Application ReadForward11Application ReadReverse81,DRP012042,NextSeq 550 paired end sequencing of SAMD00529466,,,,3582073512.0,23135170.0,DRR408246,0:77.41 1:77.42,A:943152815;C:841972211;G:863627245;T:927361159;N:5960082,77,77,,,943152815,841972211,863627245,927361159,5960082,DRX393852,DRS407177,DRA014886,"NIBB|NIBB core research facilities, National Institute for Basic Biology",University of Hyogo,,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,bulk,unknown,unknown,,Japan,2024-09-22,Undetermined,Larval,Brain,Nervous System
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 2500,2000FApplication ReadForward11RApplication ReadReverse101,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 2500,2000FApplication ReadForward11RApplication ReadReverse101,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 2500,2000FApplication ReadForward11RApplication ReadReverse101,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 2500,2000FApplication ReadForward11RApplication ReadReverse101,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 2500,2000FApplication ReadForward11RApplication ReadReverse101,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 2500,2000FApplication ReadForward11RApplication ReadReverse101,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
10391,ERR8516975,ERX8083451,ERS10521298,ERP135383,PRJEB50776,Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,E-MTAB-11431,Other,Zebrafish primary neurons either sfpq sibling/control +/+ +/ or null / were cultured in transwell inserts. At DIV2 for each genotype cellular and neurite tissues were separately isolated RNA extracted and total RNAseq performed.,ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19,,Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion,Sibling neurite,SAMEA12922152,"Centre for Developmental Neurobiology, King's College London",ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922152|INSDC center alias:Centre for Developmental Neurobiology King's College London|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Sibling neurite|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq sibling +/+ and +/ |growth condition:transwell culture|organism part:neurite|sample name:E MTAB 11431:Sibling neurite,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,E MTAB 11431:Sibling neurite p,Sibling neurite p,Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion,Experimental Factor: genotype:sfpq sibling +/+ and +/ |Experimental Factor: organism part:neurite,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP135383,Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py,15812X4_190227_A00421_38_AH7523DRXX_S56_R1_001.fastq.gz 15812X4_190227_A00421_38_AH7523DRXX_S56_R2_001.fastq.gz,fastq fastq,,,E MTAB 11431:15812X4 190227 A00421 38 AH7523DRXX S56 R,0:51 1:51,A:1077092958;C:949537387;G:955020348;T:1099432979;N:20556852,51,51,,,1077092958,949537387,955020348,1099432979,20556852,ERX8083451,ERS10521298,ERA8932807,"Centre for Developmental Neurobiology, King","Centre for Developmental Neurobiology, King",2,0.9053,0.9259,0.21658,0.22155,0.69369,0.69179,0.50726,0.50871,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,ribozero,bulk,bulk,bulk,,United Kingdom,2022-02-19,Undetermined,Undetermined,Brain,Nervous System
10392,ERR8516976,ERX8083451,ERS10521298,ERP135383,PRJEB50776,Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,E-MTAB-11431,Other,Zebrafish primary neurons either sfpq sibling/control +/+ +/ or null / were cultured in transwell inserts. At DIV2 for each genotype cellular and neurite tissues were separately isolated RNA extracted and total RNAseq performed.,ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19,,Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion,Sibling neurite,SAMEA12922152,"Centre for Developmental Neurobiology, King's College London",ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922152|INSDC center alias:Centre for Developmental Neurobiology King's College London|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Sibling neurite|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq sibling +/+ and +/ |growth condition:transwell culture|organism part:neurite|sample name:E MTAB 11431:Sibling neurite,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,E MTAB 11431:Sibling neurite p,Sibling neurite p,Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion,Experimental Factor: genotype:sfpq sibling +/+ and +/ |Experimental Factor: organism part:neurite,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP135383,Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py,15812X5_190227_A00421_38_AH7523DRXX_S55_R1_001.fastq.gz 15812X5_190227_A00421_38_AH7523DRXX_S55_R2_001.fastq.gz,fastq fastq,,,E MTAB 11431:15812X5 190227 A00421 38 AH7523DRXX S55 R,0:51 1:51,A:972081222;C:890179393;G:888655698;T:998443264;N:18934747,51,51,,,972081222,890179393,888655698,998443264,18934747,ERX8083451,ERS10521298,ERA8932807,"Centre for Developmental Neurobiology, King","Centre for Developmental Neurobiology, King",2,0.86107,0.87807,0.22063,0.23029,0.70859,0.70561,0.51656,0.51946,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,ribozero,bulk,bulk,bulk,,United Kingdom,2022-02-19,Undetermined,Undetermined,Brain,Nervous System
10393,ERR8516977,ERX8083451,ERS10521298,ERP135383,PRJEB50776,Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,E-MTAB-11431,Other,Zebrafish primary neurons either sfpq sibling/control +/+ +/ or null / were cultured in transwell inserts. At DIV2 for each genotype cellular and neurite tissues were separately isolated RNA extracted and total RNAseq performed.,ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19,,Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion,Sibling neurite,SAMEA12922152,"Centre for Developmental Neurobiology, King's College London",ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922152|INSDC center alias:Centre for Developmental Neurobiology King's College London|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Sibling neurite|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq sibling +/+ and +/ |growth condition:transwell culture|organism part:neurite|sample name:E MTAB 11431:Sibling neurite,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,E MTAB 11431:Sibling neurite p,Sibling neurite p,Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion,Experimental Factor: genotype:sfpq sibling +/+ and +/ |Experimental Factor: organism part:neurite,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP135383,Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py,15812X6_190227_A00421_38_AH7523DRXX_S54_R1_001.fastq.gz 15812X6_190227_A00421_38_AH7523DRXX_S54_R2_001.fastq.gz,fastq fastq,,,E MTAB 11431:15812X6 190227 A00421 38 AH7523DRXX S54 R,0:51 1:51,A:728798881;C:962223604;G:958876331;T:735449513;N:17094231,51,51,,,728798881,962223604,958876331,735449513,17094231,ERX8083451,ERS10521298,ERA8932807,"Centre for Developmental Neurobiology, King","Centre for Developmental Neurobiology, King",2,0.54616,0.55881,0.13313,0.14036,0.84295,0.84185,0.64193,0.59762,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,ribozero,bulk,bulk,bulk,,United Kingdom,2022-02-19,Undetermined,Undetermined,Brain,Nervous System
10394,ERR8516972,ERX8083450,ERS10521297,ERP135383,PRJEB50776,Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,E-MTAB-11431,Other,Zebrafish primary neurons either sfpq sibling/control +/+ +/ or null / were cultured in transwell inserts. At DIV2 for each genotype cellular and neurite tissues were separately isolated RNA extracted and total RNAseq performed.,ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19,,Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion,Sibling cellular,SAMEA12922151,"Centre for Developmental Neurobiology, King's College London",ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922151|INSDC center alias:Centre for Developmental Neurobiology King's College London|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Sibling cellular|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq sibling +/+ and +/ |growth condition:transwell culture|organism part:neuron|sample name:E MTAB 11431:Sibling cellular,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,E MTAB 11431:Sibling cellular p,Sibling cellular p,Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion,Experimental Factor: genotype:sfpq sibling +/+ and +/ |Experimental Factor: organism part:neuron,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP135383,Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py,15812X1_190227_A00421_38_AH7523DRXX_S59_R1_001.fastq.gz 15812X1_190227_A00421_38_AH7523DRXX_S59_R2_001.fastq.gz,fastq fastq,,,E MTAB 11431:15812X1 190227 A00421 38 AH7523DRXX S59 R,0:51 1:51,A:837274632;C:1062368015;G:1049892288;T:853310517;N:19213786,51,51,,,837274632,1062368015,1049892288,853310517,19213786,ERX8083450,ERS10521297,ERA8932807,"Centre for Developmental Neurobiology, King","Centre for Developmental Neurobiology, King",2,0.5726,0.57788,0.13781,0.14082,0.80616,0.80452,0.61581,0.60389,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,ribozero,bulk,bulk,bulk,,United Kingdom,2022-02-19,Undetermined,Undetermined,Brain,Nervous System
10395,ERR8516973,ERX8083450,ERS10521297,ERP135383,PRJEB50776,Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,E-MTAB-11431,Other,Zebrafish primary neurons either sfpq sibling/control +/+ +/ or null / were cultured in transwell inserts. At DIV2 for each genotype cellular and neurite tissues were separately isolated RNA extracted and total RNAseq performed.,ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19,,Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion,Sibling cellular,SAMEA12922151,"Centre for Developmental Neurobiology, King's College London",ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922151|INSDC center alias:Centre for Developmental Neurobiology King's College London|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Sibling cellular|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq sibling +/+ and +/ |growth condition:transwell culture|organism part:neuron|sample name:E MTAB 11431:Sibling cellular,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,E MTAB 11431:Sibling cellular p,Sibling cellular p,Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion,Experimental Factor: genotype:sfpq sibling +/+ and +/ |Experimental Factor: organism part:neuron,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP135383,Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py,15812X2_190227_A00421_38_AH7523DRXX_S58_R1_001.fastq.gz 15812X2_190227_A00421_38_AH7523DRXX_S58_R2_001.fastq.gz,fastq fastq,,,E MTAB 11431:15812X2 190227 A00421 38 AH7523DRXX S58 R,0:51 1:51,A:897813231;C:796012893;G:794839496;T:923696030;N:17221274,51,51,,,897813231,796012893,794839496,923696030,17221274,ERX8083450,ERS10521297,ERA8932807,"Centre for Developmental Neurobiology, King","Centre for Developmental Neurobiology, King",2,0.92095,0.94156,0.18892,0.20024,0.6901,0.68905,0.49377,0.50086,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,ribozero,bulk,bulk,bulk,,United Kingdom,2022-02-19,Undetermined,Undetermined,Brain,Nervous System
10396,ERR8516974,ERX8083450,ERS10521297,ERP135383,PRJEB50776,Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,E-MTAB-11431,Other,Zebrafish primary neurons either sfpq sibling/control +/+ +/ or null / were cultured in transwell inserts. At DIV2 for each genotype cellular and neurite tissues were separately isolated RNA extracted and total RNAseq performed.,ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19,,Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion,Sibling cellular,SAMEA12922151,"Centre for Developmental Neurobiology, King's College London",ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922151|INSDC center alias:Centre for Developmental Neurobiology King's College London|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Sibling cellular|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq sibling +/+ and +/ |growth condition:transwell culture|organism part:neuron|sample name:E MTAB 11431:Sibling cellular,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,E MTAB 11431:Sibling cellular p,Sibling cellular p,Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion,Experimental Factor: genotype:sfpq sibling +/+ and +/ |Experimental Factor: organism part:neuron,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP135383,Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py,15812X3_190227_A00421_38_AH7523DRXX_S57_R1_001.fastq.gz 15812X3_190227_A00421_38_AH7523DRXX_S57_R2_001.fastq.gz,fastq fastq,,,E MTAB 11431:15812X3 190227 A00421 38 AH7523DRXX S57 R,0:51 1:51,A:951912827;C:1107150666;G:1086060798;T:973791571;N:20785248,51,51,,,951912827,1107150666,1086060798,973791571,20785248,ERX8083450,ERS10521297,ERA8932807,"Centre for Developmental Neurobiology, King","Centre for Developmental Neurobiology, King",2,0.63792,0.62667,0.18547,0.18671,0.78756,0.78549,0.59274,0.55478,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,ribozero,bulk,bulk,bulk,,United Kingdom,2022-02-19,Undetermined,Undetermined,Brain,Nervous System
10397,ERR8516969,ERX8083449,ERS10521296,ERP135383,PRJEB50776,Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,E-MTAB-11431,Other,Zebrafish primary neurons either sfpq sibling/control +/+ +/ or null / were cultured in transwell inserts. At DIV2 for each genotype cellular and neurite tissues were separately isolated RNA extracted and total RNAseq performed.,ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19,,Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion,Null neurite,SAMEA12922150,"Centre for Developmental Neurobiology, King's College London",ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922150|INSDC center alias:Centre for Developmental Neurobiology King's College London|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Null neurite|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq null / |growth condition:transwell culture|organism part:neurite|sample name:E MTAB 11431:Null neurite,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,E MTAB 11431:Null neurite p,Null neurite p,Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion,Experimental Factor: genotype:sfpq null / |Experimental Factor: organism part:neurite,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP135383,Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py,15812X10_190227_A00421_38_AH7523DRXX_S48_R1_001.fastq.gz 15812X10_190227_A00421_38_AH7523DRXX_S48_R2_001.fastq.gz,fastq fastq,,,E MTAB 11431:15812X10 190227 A00421 38 AH7523DRXX S48 R,0:51 1:51,A:925784769;C:934445856;G:959155668;T:924080408;N:18878983,51,51,,,925784769,934445856,959155668,924080408,18878983,ERX8083449,ERS10521296,ERA8932807,"Centre for Developmental Neurobiology, King","Centre for Developmental Neurobiology, King",2,0.59503,0.61112,0.1947,0.20225,0.76512,0.76337,0.54584,0.54345,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,ribozero,bulk,bulk,bulk,,United Kingdom,2022-02-19,Undetermined,Undetermined,Brain,Nervous System
10398,ERR8516970,ERX8083449,ERS10521296,ERP135383,PRJEB50776,Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,E-MTAB-11431,Other,Zebrafish primary neurons either sfpq sibling/control +/+ +/ or null / were cultured in transwell inserts. At DIV2 for each genotype cellular and neurite tissues were separately isolated RNA extracted and total RNAseq performed.,ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19,,Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion,Null neurite,SAMEA12922150,"Centre for Developmental Neurobiology, King's College London",ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922150|INSDC center alias:Centre for Developmental Neurobiology King's College London|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Null neurite|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq null / |growth condition:transwell culture|organism part:neurite|sample name:E MTAB 11431:Null neurite,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,E MTAB 11431:Null neurite p,Null neurite p,Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion,Experimental Factor: genotype:sfpq null / |Experimental Factor: organism part:neurite,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP135383,Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py,15812X11_190227_A00421_38_AH7523DRXX_S52_R1_001.fastq.gz 15812X11_190227_A00421_38_AH7523DRXX_S52_R2_001.fastq.gz,fastq fastq,,,E MTAB 11431:15812X11 190227 A00421 38 AH7523DRXX S52 R,0:51 1:51,A:991755033;C:864808531;G:892202564;T:992188806;N:18881958,51,51,,,991755033,864808531,892202564,992188806,18881958,ERX8083449,ERS10521296,ERA8932807,"Centre for Developmental Neurobiology, King","Centre for Developmental Neurobiology, King",2,0.86612,0.88689,0.26181,0.2728,0.7094,0.7091,0.53639,0.53906,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,ribozero,bulk,bulk,bulk,,United Kingdom,2022-02-19,Undetermined,Undetermined,Brain,Nervous System
10399,ERR8516971,ERX8083449,ERS10521296,ERP135383,PRJEB50776,Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,E-MTAB-11431,Other,Zebrafish primary neurons either sfpq sibling/control +/+ +/ or null / were cultured in transwell inserts. At DIV2 for each genotype cellular and neurite tissues were separately isolated RNA extracted and total RNAseq performed.,ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19,,Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion,Null neurite,SAMEA12922150,"Centre for Developmental Neurobiology, King's College London",ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922150|INSDC center alias:Centre for Developmental Neurobiology King's College London|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Null neurite|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq null / |growth condition:transwell culture|organism part:neurite|sample name:E MTAB 11431:Null neurite,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,E MTAB 11431:Null neurite p,Null neurite p,Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion,Experimental Factor: genotype:sfpq null / |Experimental Factor: organism part:neurite,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP135383,Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py,15812X12_190227_A00421_38_AH7523DRXX_S50_R1_001.fastq.gz 15812X12_190227_A00421_38_AH7523DRXX_S50_R2_001.fastq.gz,fastq fastq,,,E MTAB 11431:15812X12 190227 A00421 38 AH7523DRXX S50 R,0:51 1:51,A:766707527;C:798667604;G:818782599;T:773280942;N:15938306,51,51,,,766707527,798667604,818782599,773280942,15938306,ERX8083449,ERS10521296,ERA8932807,"Centre for Developmental Neurobiology, King","Centre for Developmental Neurobiology, King",2,0.88811,0.92834,0.21869,0.22669,0.72878,0.72604,0.55598,0.57831,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,ribozero,bulk,bulk,bulk,,United Kingdom,2022-02-19,Undetermined,Undetermined,Brain,Nervous System
10400,ERR8516966,ERX8083448,ERS10521295,ERP135383,PRJEB50776,Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,E-MTAB-11431,Other,Zebrafish primary neurons either sfpq sibling/control +/+ +/ or null / were cultured in transwell inserts. At DIV2 for each genotype cellular and neurite tissues were separately isolated RNA extracted and total RNAseq performed.,ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19,,Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion,Null cellular,SAMEA12922149,"Centre for Developmental Neurobiology, King's College London",ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922149|INSDC center alias:Centre for Developmental Neurobiology King's College London|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Null cellular|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq null / |growth condition:transwell culture|organism part:neuron|sample name:E MTAB 11431:Null cellular,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,E MTAB 11431:Null cellular p,Null cellular p,Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion,Experimental Factor: genotype:sfpq null / |Experimental Factor: organism part:neuron,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP135383,Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py,15812X7_190227_A00421_38_AH7523DRXX_S53_R1_001.fastq.gz 15812X7_190227_A00421_38_AH7523DRXX_S53_R2_001.fastq.gz,fastq fastq,,,E MTAB 11431:15812X7 190227 A00421 38 AH7523DRXX S53 R,0:51 1:51,A:774360373;C:720215184;G:719479745;T:796239200;N:15182374,51,51,,,774360373,720215184,719479745,796239200,15182374,ERX8083448,ERS10521295,ERA8932807,"Centre for Developmental Neurobiology, King","Centre for Developmental Neurobiology, King",2,0.79643,0.81194,0.25554,0.2603,0.72236,0.72021,0.51775,0.51678,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,ribozero,bulk,bulk,bulk,,United Kingdom,2022-02-19,Undetermined,Undetermined,Brain,Nervous System
10401,ERR8516967,ERX8083448,ERS10521295,ERP135383,PRJEB50776,Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,E-MTAB-11431,Other,Zebrafish primary neurons either sfpq sibling/control +/+ +/ or null / were cultured in transwell inserts. At DIV2 for each genotype cellular and neurite tissues were separately isolated RNA extracted and total RNAseq performed.,ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19,,Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion,Null cellular,SAMEA12922149,"Centre for Developmental Neurobiology, King's College London",ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922149|INSDC center alias:Centre for Developmental Neurobiology King's College London|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Null cellular|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq null / |growth condition:transwell culture|organism part:neuron|sample name:E MTAB 11431:Null cellular,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,E MTAB 11431:Null cellular p,Null cellular p,Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion,Experimental Factor: genotype:sfpq null / |Experimental Factor: organism part:neuron,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP135383,Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py,15812X8_190227_A00421_38_AH7523DRXX_S51_R1_001.fastq.gz 15812X8_190227_A00421_38_AH7523DRXX_S51_R2_001.fastq.gz,fastq fastq,,,E MTAB 11431:15812X8 190227 A00421 38 AH7523DRXX S51 R,0:51 1:51,A:739921027;C:667375549;G:663864111;T:764302396;N:14288091,51,51,,,739921027,667375549,663864111,764302396,14288091,ERX8083448,ERS10521295,ERA8932807,"Centre for Developmental Neurobiology, King","Centre for Developmental Neurobiology, King",2,0.90817,0.92909,0.23387,0.24814,0.70088,0.69842,0.51238,0.51267,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,ribozero,bulk,bulk,bulk,,United Kingdom,2022-02-19,Undetermined,Undetermined,Brain,Nervous System
10402,ERR8516968,ERX8083448,ERS10521295,ERP135383,PRJEB50776,Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,E-MTAB-11431,Other,Zebrafish primary neurons either sfpq sibling/control +/+ +/ or null / were cultured in transwell inserts. At DIV2 for each genotype cellular and neurite tissues were separately isolated RNA extracted and total RNAseq performed.,ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19,,Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion,Null cellular,SAMEA12922149,"Centre for Developmental Neurobiology, King's College London",ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922149|INSDC center alias:Centre for Developmental Neurobiology King's College London|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Null cellular|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq null / |growth condition:transwell culture|organism part:neuron|sample name:E MTAB 11431:Null cellular,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,E MTAB 11431:Null cellular p,Null cellular p,Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion,Experimental Factor: genotype:sfpq null / |Experimental Factor: organism part:neuron,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP135383,Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue,ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py,15812X9_190227_A00421_38_AH7523DRXX_S49_R1_001.fastq.gz 15812X9_190227_A00421_38_AH7523DRXX_S49_R2_001.fastq.gz,fastq fastq,,,E MTAB 11431:15812X9 190227 A00421 38 AH7523DRXX S49 R,0:51 1:51,A:882831441;C:935213418;G:957033335;T:879085993;N:18444957,51,51,,,882831441,935213418,957033335,879085993,18444957,ERX8083448,ERS10521295,ERA8932807,"Centre for Developmental Neurobiology, King","Centre for Developmental Neurobiology, King",2,0.76218,0.7682,0.18357,0.18521,0.74444,0.74272,0.46714,0.55518,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,ribozero,bulk,bulk,bulk,,United Kingdom,2022-02-19,Undetermined,Undetermined,Brain,Nervous System
34262,SRR31595085,SRX26959911,SRS23429841,SRP549196,PRJNA1193812,Single cell transcriptome sequencing of zebrafish olfactory epithelium,PRJNA1193812,Other,We performed single cell sequencing in the olfactory epithelium of wild type zebrafish and zebrafish treated with alarm substances and compared them.,,,Alarm substances treatment Group,,CAS,,strain:AB strain|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:1 year old|dev stage:adult CAS group|collection date:2020 10 10|geo loc name:China: Wuhan|sex:male|tissue:Olfactory epithelium CAS group|BioSampleModel:Model organism or animal,,,,,,,,,Single cell transcriptome of the AB zebrafish olfactory epithelium post treatment with alarm substances,CAS OE,CAS OE,sequencing libraries were loaded on an Illumina NextSeq 550AR with paired end kits. Read 1 was used to distinguish different transcripts of different cells. Read 2 was used to determine the genetic information.,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,RANDOM,PAIRED,ILLUMINA,NextSeq 550,,SRP549196,,,CAS_S1_L001_R1_001.fastq.gz CAS_S1_L001_R2_001.fastq.gz,fastq fastq,54518124857.0,458135503.0,CAS S1 L001 R1 001.fastq.gz,0:28 1:91,A:15384916510;C:12274547586;G:14008767028;T:12837270924;N:12622809,28,91,,,15384916510,12274547586,14008767028,12837270924,12622809,SRX26959911,SRS23429841,SRA2027027,"Institute of Hydrobiology, Chinese Academy of Sciences|Chinese Academy of Sciences","Institute of Hydrobiology, Chinese Academy of Sciences",,,,,,,,,,,,T,B,sc-like readlen,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_generic,generic-scrnaseq-only,,China,2024-12-04,Adult,Adult,Brain,Nervous System
34263,SRR31595086,SRX26959910,SRS23429840,SRP549196,PRJNA1193812,Single cell transcriptome sequencing of zebrafish olfactory epithelium,PRJNA1193812,Other,We performed single cell sequencing in the olfactory epithelium of wild type zebrafish and zebrafish treated with alarm substances and compared them.,,,Blank control group,,CTR,,strain:AB strain|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:1 year old|dev stage:adult CTR group|collection date:2020 10 10|geo loc name:China: Wuhan|sex:male|tissue:Olfactory epithelium CTR group|BioSampleModel:Model organism or animal,,,,,,,,,Single cell transcriptome of the AB strain zebrafish olfactory epithelium,CTR OE,CTR OE,sequencing libraries were loaded on an Illumina NextSeq 550AR with paired end kits. Read 1 was used to distinguish different transcripts of different cells. Read 2 was used to determine the genetic information.,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,RANDOM,PAIRED,ILLUMINA,NextSeq 550,,SRP549196,,,CTR_S1_L001_R1_001.fastq.gz CTR_S1_L001_R2_001.fastq.gz,fastq fastq,50773421790.0,426667410.0,CTR S1 L001 R1 001.fastq.gz,0:28 1:91,A:14105926130;C:11510784907;G:13135577448;T:12011516484;N:9616821,28,91,,,14105926130,11510784907,13135577448,12011516484,9616821,SRX26959910,SRS23429840,SRA2027027,"Institute of Hydrobiology, Chinese Academy of Sciences|Chinese Academy of Sciences","Institute of Hydrobiology, Chinese Academy of Sciences",,,,,,,,,,,,T,B,sc-like readlen,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_generic,generic-scrnaseq-only,,China,2024-12-04,Adult,Adult,Brain,Nervous System
37104,SRR891511,SRX298191,SRS673881,SRP024369,PRJNA207719,Tissue specific transcriptome profiling of zebrafish,PRJNA207719,Other,Tissue specific transcriptome profiling of zebrafish.,,,,,Danio rerio brain,,sex:missing|strain:wild type|tissue:brain|health state:normal|collection date:2013|geo loc name:India|biomaterial provider:CSIR Institute of Genomics and Integrative Biology|age:adult|BioSampleModel:Model organism or animal,,,,,,,,,Tissue specific transcriptome of zebrafish,Transcriptome of zebrafish Danio rerio brain,zebrafish brain,1,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina Genome Analyzer IIx,1020Application ReadForward11Application ReadReverse52,SRP024369,,,lane5_NoIndex_L005_R2_cat.fastq lane5_NoIndex_L005_R1_cat.fastq,fastq fastq,1597586730.0,15662615.0,Transcriptome of zebrafish Danio rerio brain,0:51 1:51,A:408194270;C:393362321;G:391996499;T:403728707;N:304933,51,51,,,408194270,393362321,391996499,403728707,304933,SRX298191,SRS673881,SRA089174,CSIR-IGIB,CSIR-Institute of Genomics and Integrative Biology CSIR-Institute of Genomics and Integrative Biology,2,0.8957,0.89547,0.13204,0.13077,0.70514,0.70504,0.48733,0.48703,51,51,B,B,biological fallback assumption,illumina,early_illumina,unknown,random_priming,unknown,bulk,unknown,unknown,,India,2013-10-10,Adult,Adult,Brain,Nervous System
39827,SRR2441454,SRX1321833,SRS1109642,SRP062493,PRJNA293106,Danio rerio Raw sequence reads,PRJNA293106,Metagenomics,Zebrafish Hypoxia RNAseq,,,RNAseq at 24hpf following hypoxia,,24hpf hypoxia,,strain:TU|age:24hpf|sex:not determined|tissue:brain|treatment:hypoxia|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample 24hpf hypoxia,24hpf.hypoxia.3.10329X21,24hpf.hypoxia.3.10329X21,We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition. For hypoxia we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected. We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages. At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation. RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer. The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides single end stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2000,500Application ReadForward1,SRP062493,,,10329X21_130822_SN141_0719_AD2CK5ACXX_7.txt.gz,fastq,1205447950.0,24108959.0,24hpf.hypoxia.3.10329X21,0:50,A:299680333;C:267717935;G:264833481;T:357936794;N:15279407,50,,,,299680333,267717935,264833481,357936794,15279407,SRX1321833,SRS1109642,SRA289450,University of Utah|Bonkowsky,University of Utah,1,0.87455,,0.24266,,0.74121,,0.57777,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United States,2015-10-10,Pharyngula,Embryo,Brain,Nervous System
39828,SRR2437828,SRX1321832,SRS1109643,SRP062493,PRJNA293106,Danio rerio Raw sequence reads,PRJNA293106,Metagenomics,Zebrafish Hypoxia RNAseq,,,RNAseq at 48hpf following normoxia,,48hpf normoxia,,strain:TU|age:48hpf|sex:not determined|tissue:brain|treatment:normoxia|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample 48hpf normoxia,48hpf.normoxia.3.10329X16,48hpf.normoxia.3.10329X16,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 2000,500Application ReadForward1,SRP062493,,,10329X16_130822_SN141_0719_AD2CK5ACXX_6.txt.gz,fastq,985942500.0,19718850.0,48hpf.normoxia.3.10329X16,0:50,A:251856100;C:223081125;G:216430606;T:294554748;N:19921,50,,,,251856100,223081125,216430606,294554748,19921,SRX1321832,SRS1109643,SRA289450,University of Utah|Bonkowsky,University of Utah,1,0.94791,,0.26704,,0.68708,,0.54445,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United States,2015-10-10,Hatching,Embryo,Brain,Nervous System
39829,SRR2434699,SRX1321831,SRS1109642,SRP062493,PRJNA293106,Danio rerio Raw sequence reads,PRJNA293106,Metagenomics,Zebrafish Hypoxia RNAseq,,,RNAseq at 24hpf following hypoxia,,24hpf hypoxia,,strain:TU|age:24hpf|sex:not determined|tissue:brain|treatment:hypoxia|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample 24hpf hypoxia,24hpf.hypoxia.2.10329X11,24hpf.hypoxia.2.10329X11,We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition. For hypoxia we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected. We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages. At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation. RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer. The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides single end stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2000,500Application ReadForward1,SRP062493,,,10329X11_130822_SN141_0719_AD2CK5ACXX_5.txt.gz,fastq,1227682750.0,24553655.0,24hpf.hypoxia.2.10329X11,0:50,A:299759613;C:292757497;G:281904026;T:353193075;N:68539,50,,,,299759613,292757497,281904026,353193075,68539,SRX1321831,SRS1109642,SRA289450,University of Utah|Bonkowsky,University of Utah,1,0.94855,,0.27579,,0.73298,,0.58307,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United States,2015-10-07,Pharyngula,Embryo,Brain,Nervous System
39830,SRR2433795,SRX1321830,SRS1109644,SRP062493,PRJNA293106,Danio rerio Raw sequence reads,PRJNA293106,Metagenomics,Zebrafish Hypoxia RNAseq,,,RNAseq at 60hpf following normoxia,,60hpf Normoxia,,strain:TU|age:60hpf|sex:not determined|tissue:brain|treatment:normoxia|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample 60hpf Normoxia,60hpf.normoxia.3.,60hpf.normoxia.3.,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 2000,500Application ReadForward1,SRP062493,,,10329X8_130822_SN141_0719_AD2CK5ACXX_5.txt.gz,fastq,1112799950.0,22255999.0,60hpf.normoxia.3.,0:50,A:294304558;C:248234752;G:238088577;T:332109252;N:62811,50,,,,294304558,248234752,238088577,332109252,62811,SRX1321830,SRS1109644,SRA289450,University of Utah|Bonkowsky,University of Utah,1,0.94922,,0.34314,,0.67838,,0.51455,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United States,2015-10-10,Hatching,Embryo,Brain,Nervous System
39831,SRR2426760,SRX1321829,SRS1109645,SRP062493,PRJNA293106,Danio rerio Raw sequence reads,PRJNA293106,Metagenomics,Zebrafish Hypoxia RNAseq,,,RNAseq at 36hpf following hypoxia,,36hpf hypoxia,,strain:TU|age:36hpf|sex:not determined|tissue:brain|treatment:hypoxia|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample 36hpf hypoxia,36hpf.hypoxia.1.10329X4,36hpf.hypoxia.1.10329X4,We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition. For hypoxia we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected. We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages. At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation. RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer. The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides single end stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2000,500Application ReadForward1,SRP062493,,,10329X4_130822_SN141_0719_AD2CK5ACXX_4.txt.gz,fastq,1604107450.0,32082149.0,36hpf.hypoxia.1.10329X4,0:50,A:395786409;C:358263833;G:358391489;T:491601452;N:64267,50,,,,395786409,358263833,358391489,491601452,64267,SRX1321829,SRS1109645,SRA289450,University of Utah|Bonkowsky,University of Utah,1,0.95408,,0.28965,,0.69593,,0.54826,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United States,2015-10-10,Pharyngula,Embryo,Brain,Nervous System
39832,SRR2417497,SRX1321828,SRS1109646,SRP062493,PRJNA293106,Danio rerio Raw sequence reads,PRJNA293106,Metagenomics,Zebrafish Hypoxia RNAseq,,,RNAseq at 48hpf following hypoxia,,48hpf hypoxia,,strain:TU|age:48hpf|sex:not determined|tissue:brain|treatment:hypoxia|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample 48hpf hypoxia,48hpf.hypoxia.3.10329X25,48hpf.hypoxia.3.10329X25,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 2000,500Application ReadForward1,SRP062493,,,10329X25_130822_SN141_0719_AD2CK5ACXX_8.txt.gz,fastq,1234710500.0,24694210.0,48hpf.hypoxia.3.10329X25,0:50,A:309392529;C:284311489;G:275471070;T:365515358;N:20054,50,,,,309392529,284311489,275471070,365515358,20054,SRX1321828,SRS1109646,SRA289450,University of Utah|Bonkowsky,University of Utah,1,0.94675,,0.25877,,0.71453,,0.5239,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United States,2015-09-16,Hatching,Embryo,Brain,Nervous System
39833,SRR2417496,SRX1321827,SRS1109644,SRP062493,PRJNA293106,Danio rerio Raw sequence reads,PRJNA293106,Metagenomics,Zebrafish Hypoxia RNAseq,,,RNAseq at 60hpf following normoxia,,60hpf Normoxia,,strain:TU|age:60hpf|sex:not determined|tissue:brain|treatment:normoxia|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample 60hpf Normoxia,60hpf.normoxia.2.10329X28,60hpf.normoxia.2.10329X28,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 2000,500Application ReadForward1,SRP062493,,,10329X28_130822_SN141_0719_AD2CK5ACXX_8.txt.gz,fastq,1015786750.0,20315735.0,60hpf.normoxia.2.10329X28,0:50,A:259102784;C:230364456;G:226008843;T:300294199;N:16468,50,,,,259102784,230364456,226008843,300294199,16468,SRX1321827,SRS1109644,SRA289450,University of Utah|Bonkowsky,University of Utah,1,0.95197,,0.30503,,0.68333,,0.52243,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United States,2015-09-16,Hatching,Embryo,Brain,Nervous System
39834,SRR2400601,SRX1321826,SRS1109642,SRP062493,PRJNA293106,Danio rerio Raw sequence reads,PRJNA293106,Metagenomics,Zebrafish Hypoxia RNAseq,,,RNAseq at 24hpf following hypoxia,,24hpf hypoxia,,strain:TU|age:24hpf|sex:not determined|tissue:brain|treatment:hypoxia|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample 24hpf hypoxia,24hpf.hypoxia.1.10329X2,24hpf.hypoxia.1.10329X2,We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition. For hypoxia we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected. We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages. At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation. RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer. The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides single end stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2000,500Application ReadForward1,SRP062493,,,10329X2_130822_SN141_0719_AD2CK5ACXX_4.txt.gz,fastq,1249046350.0,24980927.0,24hpf.hypoxia.1.10329X2,0:50,A:309098695;C:281875016;G:278706888;T:379315616;N:50135,50,,,,309098695,281875016,278706888,379315616,50135,SRX1321826,SRS1109642,SRA289450,University of Utah|Bonkowsky,University of Utah,1,0.95443,,0.27405,,0.69747,,0.40987,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United States,2015-10-10,Pharyngula,Embryo,Brain,Nervous System
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 2000,500Application ReadForward1,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 2000,500Application ReadForward1,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
39837,SRR2342161,SRX1321823,SRS1109648,SRP062493,PRJNA293106,Danio rerio Raw sequence reads,PRJNA293106,Metagenomics,Zebrafish Hypoxia RNAseq,,,RNAseq at 60hpf following hypoxia,,60hpf hypoxia,,strain:TU|age:60hpf|sex:not determined|tissue:brain|treatment:hypoxia|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample 60hpf hypoxia,60hpf.hypoxia.3.10329X27,60hpf.hypoxia.3.10329X27,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 2000,500Application ReadForward1,SRP062493,,,10329X27_130822_SN141_0719_AD2CK5ACXX_8.txt.gz,fastq,1073269500.0,21465390.0,60hpf.hypoxia.3.10329X27,0:50,A:280500644;C:237758835;G:234061287;T:320931292;N:17442,50,,,,280500644,237758835,234061287,320931292,17442,SRX1321823,SRS1109648,SRA289450,University of Utah|Bonkowsky,University of Utah,1,0.94774,,0.36354,,0.70065,,0.51075,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United States,2015-10-10,Hatching,Embryo,Brain,Nervous System
39838,SRR2341509,SRX1321822,SRS1109643,SRP062493,PRJNA293106,Danio rerio Raw sequence reads,PRJNA293106,Metagenomics,Zebrafish Hypoxia RNAseq,,,RNAseq at 48hpf following normoxia,,48hpf normoxia,,strain:TU|age:48hpf|sex:not determined|tissue:brain|treatment:normoxia|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample 48hpf normoxia,48hpf.normoxia.210329X26,48hpf.normoxia.210329X26,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 2000,500Application ReadForward1,SRP062493,,,10329X26_130822_SN141_0719_AD2CK5ACXX_8.txt.gz,fastq,1075868850.0,21517377.0,48hpf.normoxia.210329X26,0:50,A:271795722;C:246789566;G:240496674;T:316769688;N:17200,50,,,,271795722,246789566,240496674,316769688,17200,SRX1321822,SRS1109643,SRA289450,University of Utah|Bonkowsky,University of Utah,1,0.94644,,0.26805,,0.68745,,0.53833,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United States,2015-10-10,Hatching,Embryo,Brain,Nervous System
39839,SRR2340149,SRX1321821,SRS1109650,SRP062493,PRJNA293106,Danio rerio Raw sequence reads,PRJNA293106,Metagenomics,Zebrafish Hypoxia RNAseq,,,RNAseq at 36hpf following normoxia,,36hpf normoxia,,strain:TU|age:36hpf|sex:not determined|tissue:brain|treatment:normoxia|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample 36hpf normoxia,36hpf.normoxia.3.10329X24,36hpf.normoxia.3.10329X24,We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition. For hypoxia we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected. We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages. At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation. RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer. The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides single end stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2000,500Application ReadForward1,SRP062493,,,10329X24_130822_SN141_0719_AD2CK5ACXX_7.txt.gz,fastq,1588630750.0,31772615.0,36hpf.normoxia.3.10329X24,0:50,A:404319446;C:349459823;G:346545846;T:468209953;N:20095682,50,,,,404319446,349459823,346545846,468209953,20095682,SRX1321821,SRS1109650,SRA289450,University of Utah|Bonkowsky,University of Utah,1,0.8739,,0.32489,,0.71701,,0.51646,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United States,2015-10-10,Pharyngula,Embryo,Brain,Nervous System
39840,SRR2245887,SRX1321820,SRS1109645,SRP062493,PRJNA293106,Danio rerio Raw sequence reads,PRJNA293106,Metagenomics,Zebrafish Hypoxia RNAseq,,,RNAseq at 36hpf following hypoxia,,36hpf hypoxia,,strain:TU|age:36hpf|sex:not determined|tissue:brain|treatment:hypoxia|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample 36hpf hypoxia,36hpf.hypoxia.3.10329X23,36hpf.hypoxia.3.10329X23,We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition. For hypoxia we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected. We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages. At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation. RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer. The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides single end stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2000,500Application ReadForward1,SRP062493,,,10329X23_130822_SN141_0719_AD2CK5ACXX_7.txt.gz,fastq,1207331350.0,24146627.0,36hpf.hypoxia.3.10329X23,0:50,A:305628501;C:266059461;G:259888045;T:360487730;N:15267613,50,,,,305628501,266059461,259888045,360487730,15267613,SRX1321820,SRS1109645,SRA289450,University of Utah|Bonkowsky,University of Utah,1,0.87814,,0.27249,,0.72853,,0.53527,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United States,2015-10-10,Pharyngula,Embryo,Brain,Nervous System
39841,SRR2245257,SRX1321819,SRS1109651,SRP062493,PRJNA293106,Danio rerio Raw sequence reads,PRJNA293106,Metagenomics,Zebrafish Hypoxia RNAseq,,,RNAseq at 24hpf following normoxia,,24hpf normoxia,,strain:TU|age:24hpf|sex:not determined|tissue:brain|treatment:normoxia|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample 24hpf normoxia,24hpf.normoxia.3.10329X22,24hpf.normoxia.3.10329X22,We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition. For hypoxia we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected. We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages. At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation. RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer. The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides single end stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2000,500Application ReadForward1,SRP062493,,,10329X22_130822_SN141_0719_AD2CK5ACXX_7.txt.gz,fastq,1257159050.0,25143181.0,24hpf.normoxia.3.10329X22,0:50,A:320558638;C:275312235;G:271710647;T:373637690;N:15939840,50,,,,320558638,275312235,271710647,373637690,15939840,SRX1321819,SRS1109651,SRA289450,University of Utah|Bonkowsky,University of Utah,1,0.87634,,0.30298,,0.71356,,0.54673,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United States,2015-10-10,Pharyngula,Embryo,Brain,Nervous System
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 2000,500Application ReadForward1,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 2000,500Application ReadForward1,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
39844,SRR2241311,SRX1321816,SRS1109644,SRP062493,PRJNA293106,Danio rerio Raw sequence reads,PRJNA293106,Metagenomics,Zebrafish Hypoxia RNAseq,,,RNAseq at 60hpf following normoxia,,60hpf Normoxia,,strain:TU|age:60hpf|sex:not determined|tissue:brain|treatment:normoxia|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample 60hpf Normoxia,60hpf.normoxia.1.10329X18,60hpf.normoxia.1.10329X18,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 2000,500Application ReadForward1,SRP062493,,,10329X18_130822_SN141_0719_AD2CK5ACXX_6.txt.gz,fastq,1118115050.0,22362301.0,60hpf.normoxia.1.10329X18,0:50,A:287072563;C:255244675;G:248573701;T:327203388;N:20723,50,,,,287072563,255244675,248573701,327203388,20723,SRX1321816,SRS1109644,SRA289450,University of Utah|Bonkowsky,University of Utah,1,0.93238,,0.30064,,0.68574,,0.51934,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United States,2015-10-10,Hatching,Embryo,Brain,Nervous System
39845,SRR2240748,SRX1321815,SRS1109648,SRP062493,PRJNA293106,Danio rerio Raw sequence reads,PRJNA293106,Metagenomics,Zebrafish Hypoxia RNAseq,,,RNAseq at 60hpf following hypoxia,,60hpf hypoxia,,strain:TU|age:60hpf|sex:not determined|tissue:brain|treatment:hypoxia|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample 60hpf hypoxia,60hpf.hypoxia.2.10329X17,60hpf.hypoxia.2.10329X17,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 2000,500Application ReadForward1,SRP062493,,,10329X17_130822_SN141_0719_AD2CK5ACXX_6.txt.gz,fastq,1074686900.0,21493738.0,60hpf.hypoxia.2.10329X17,0:50,A:276432361;C:244039609;G:234638386;T:319556004;N:20540,50,,,,276432361,244039609,234638386,319556004,20540,SRX1321815,SRS1109648,SRA289450,University of Utah|Bonkowsky,University of Utah,1,0.9502,,0.3077,,0.6899,,0.50645,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United States,2015-09-03,Hatching,Embryo,Brain,Nervous System
39846,SRR2239869,SRX1321814,SRS1109646,SRP062493,PRJNA293106,Danio rerio Raw sequence reads,PRJNA293106,Metagenomics,Zebrafish Hypoxia RNAseq,,,RNAseq at 48hpf following hypoxia,,48hpf hypoxia,,strain:TU|age:48hpf|sex:not determined|tissue:brain|treatment:hypoxia|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample 48hpf hypoxia,48hpf.hypoxia.2.10329X15,48hpf.hypoxia.2.10329X15,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 2000,500Application ReadForward1,SRP062493,,,10329X15_130822_SN141_0719_AD2CK5ACXX_6.txt.gz,fastq,1111913550.0,22238271.0,48hpf.hypoxia.2.10329X15,0:50,A:288023952;C:248947169;G:243195362;T:331723738;N:23329,50,,,,288023952,248947169,243195362,331723738,23329,SRX1321814,SRS1109646,SRA289450,University of Utah|Bonkowsky,University of Utah,1,0.93753,,0.34521,,0.70246,,0.51535,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United States,2015-10-10,Hatching,Embryo,Brain,Nervous System
39847,SRR2239772,SRX1321813,SRS1109650,SRP062493,PRJNA293106,Danio rerio Raw sequence reads,PRJNA293106,Metagenomics,Zebrafish Hypoxia RNAseq,,,RNAseq at 36hpf following normoxia,,36hpf normoxia,,strain:TU|age:36hpf|sex:not determined|tissue:brain|treatment:normoxia|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample 36hpf normoxia,36hpf.normoxia.2.10329X14,36hpf.normoxia.2.10329X14,We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition. For hypoxia we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected. We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages. At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation. RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer. The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides single end stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2000,500Application ReadForward1,SRP062493,,,10329X14_130822_SN141_0719_AD2CK5ACXX_6.txt.gz,fastq,1533885200.0,30677704.0,36hpf.normoxia.2.10329X14,0:50,A:392813056;C:354469675;G:348871622;T:437692730;N:38117,50,,,,392813056,354469675,348871622,437692730,38117,SRX1321813,SRS1109650,SRA289450,University of Utah|Bonkowsky,University of Utah,1,0.91439,,0.31812,,0.70863,,0.51667,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United States,2015-10-10,Pharyngula,Embryo,Brain,Nervous System
39848,SRR2232685,SRX1321812,SRS1109645,SRP062493,PRJNA293106,Danio rerio Raw sequence reads,PRJNA293106,Metagenomics,Zebrafish Hypoxia RNAseq,,,RNAseq at 36hpf following hypoxia,,36hpf hypoxia,,strain:TU|age:36hpf|sex:not determined|tissue:brain|treatment:hypoxia|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample 36hpf hypoxia,36hpf.hypoxia.2.10329X13,36hpf.hypoxia.2.10329X13,We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition. For hypoxia we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected. We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages. At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation. RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer. The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides single end stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2000,500Application ReadForward1,SRP062493,,,10329X13_130822_SN141_0719_AD2CK5ACXX_6.txt.gz,fastq,1112846200.0,22256924.0,36hpf.hypoxia.2.10329X13,0:50,A:279147206;C:259582122;G:249642505;T:324452965;N:21402,50,,,,279147206,259582122,249642505,324452965,21402,SRX1321812,SRS1109645,SRA289450,University of Utah|Bonkowsky,University of Utah,1,0.94469,,0.25952,,0.72243,,0.52701,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United States,2015-10-10,Pharyngula,Embryo,Brain,Nervous System
39849,SRR2227658,SRX1321811,SRS1109651,SRP062493,PRJNA293106,Danio rerio Raw sequence reads,PRJNA293106,Metagenomics,Zebrafish Hypoxia RNAseq,,,RNAseq at 24hpf following normoxia,,24hpf normoxia,,strain:TU|age:24hpf|sex:not determined|tissue:brain|treatment:normoxia|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample 24hpf normoxia,24hpf.normoxia.2.10329X12,24hpf.normoxia.2.10329X12,We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition. For hypoxia we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected. We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages. At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation. RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer. The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides single end stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2000,500Application ReadForward1,SRP062493,,,10329X12_130822_SN141_0719_AD2CK5ACXX_5.txt.gz,fastq,1243623750.0,24872475.0,24hpf.normoxia.2.10329X12,0:50,A:317179221;C:285081899;G:274648790;T:366643275;N:70565,50,,,,317179221,285081899,274648790,366643275,70565,SRX1321811,SRS1109651,SRA289450,University of Utah|Bonkowsky,University of Utah,1,0.95045,,0.27525,,0.69688,,0.53555,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United States,2015-09-01,Pharyngula,Embryo,Brain,Nervous System
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 2000,500Application ReadForward1,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 2000,500Application ReadForward1,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
39852,SRR2225888,SRX1321808,SRS1109648,SRP062493,PRJNA293106,Danio rerio Raw sequence reads,PRJNA293106,Metagenomics,Zebrafish Hypoxia RNAseq,,,RNAseq at 60hpf following hypoxia,,60hpf hypoxia,,strain:TU|age:60hpf|sex:not determined|tissue:brain|treatment:hypoxia|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample 60hpf hypoxia,60hpf.hypoxia.1.10329X7,60hpf.hypoxia.1.10329X7,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 2000,500Application ReadForward1,SRP062493,,,10329X7_130822_SN141_0719_AD2CK5ACXX_5.txt.gz,fastq,1102232350.0,22044647.0,60hpf.hypoxia.1.10329X7,0:50,A:288570352;C:247978180;G:238128703;T:327492563;N:62552,50,,,,288570352,247978180,238128703,327492563,62552,SRX1321808,SRS1109648,SRA289450,University of Utah|Bonkowsky,University of Utah,1,0.94824,,0.31808,,0.69244,,0.51505,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United States,2015-10-10,Hatching,Embryo,Brain,Nervous System
39853,SRR2225789,SRX1321807,SRS1109646,SRP062493,PRJNA293106,Danio rerio Raw sequence reads,PRJNA293106,Metagenomics,Zebrafish Hypoxia RNAseq,,,RNAseq at 48hpf following hypoxia,,48hpf hypoxia,,strain:TU|age:48hpf|sex:not determined|tissue:brain|treatment:hypoxia|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample 48hpf hypoxia,48hpf.hypoxia.1.10329X6,48hpf.hypoxia.1.10329X6,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 2000,500Application ReadForward1,SRP062493,,,10329X6_130822_SN141_0719_AD2CK5ACXX_4.txt.gz,fastq,1250042950.0,25000859.0,48hpf.hypoxia.1.10329X6,0:50,A:312511165;C:283310381;G:277279378;T:376891744;N:50282,50,,,,312511165,283310381,277279378,376891744,50282,SRX1321807,SRS1109646,SRA289450,University of Utah|Bonkowsky,University of Utah,1,0.94959,,0.28331,,0.68757,,0.53976,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United States,2015-09-01,Hatching,Embryo,Brain,Nervous System
39854,SRR2225675,SRX1321806,SRS1109650,SRP062493,PRJNA293106,Danio rerio Raw sequence reads,PRJNA293106,Metagenomics,Zebrafish Hypoxia RNAseq,,,RNAseq at 36hpf following normoxia,,36hpf normoxia,,strain:TU|age:36hpf|sex:not determined|tissue:brain|treatment:normoxia|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample 36hpf normoxia,36hpf.normoxia.1.10329X5,36hpf.normoxia.1.10329X5,We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition. For hypoxia we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected. We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages. At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation. RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer. The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides single end stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2000,500Application ReadForward1,SRP062493,,,10329X5_130822_SN141_0719_AD2CK5ACXX_4.txt.gz,fastq,1244744700.0,24894894.0,36hpf.normoxia.1.10329X5,0:50,A:301597123;C:287750990;G:281194881;T:374152417;N:49289,50,,,,301597123,287750990,281194881,374152417,49289,SRX1321806,SRS1109650,SRA289450,University of Utah|Bonkowsky,University of Utah,1,0.95571,,0.22791,,0.71177,,0.53801,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United States,2015-10-10,Pharyngula,Embryo,Brain,Nervous System
39855,SRR2225572,SRX1321805,SRS1109651,SRP062493,PRJNA293106,Danio rerio Raw sequence reads,PRJNA293106,Metagenomics,Zebrafish Hypoxia RNAseq,,,RNAseq at 24hpf following normoxia,,24hpf normoxia,,strain:TU|age:24hpf|sex:not determined|tissue:brain|treatment:normoxia|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample 24hpf normoxia,24hpf.normoxia.1.10329X3,24hpf.normoxia.1.10329X3,We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition. For hypoxia we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected. We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages. At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation. RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer. The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides single end stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2000,500Application ReadForward1,SRP062493,,,10329X3_130822_SN141_0719_AD2CK5ACXX_4.txt.gz,fastq,1293605500.0,25872110.0,24hpf.normoxia.1.10329X3,0:50,A:310265067;C:296406990;G:295054246;T:391826687;N:52510,50,,,,310265067,296406990,295054246,391826687,52510,SRX1321805,SRS1109651,SRA289450,University of Utah|Bonkowsky,University of Utah,1,0.95596,,0.21907,,0.71512,,0.39029,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United States,2015-09-01,Pharyngula,Embryo,Brain,Nervous System
39856,SRR2222835,SRX1321804,SRS1109643,SRP062493,PRJNA293106,Danio rerio Raw sequence reads,PRJNA293106,Metagenomics,Zebrafish Hypoxia RNAseq,,,RNAseq at 48hpf following normoxia,,48hpf normoxia,,strain:TU|age:48hpf|sex:not determined|tissue:brain|treatment:normoxia|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample 48hpf normoxia,48hpf.1.10329X1,48hpf.1.10329X1,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 2000,500Application ReadForward1,SRP062493,,,10329X1_130822_SN141_0719_AD2CK5ACXX_4.txt.gz,fastq,1215136450.0,24302729.0,48hpf.1.10329X1,0:50,A:291802893;C:276442849;G:277217342;T:369624915;N:48451,50,,,,291802893,276442849,277217342,369624915,48451,SRX1321804,SRS1109643,SRA289450,University of Utah|Bonkowsky,University of Utah,1,0.95575,,0.23021,,0.72679,,0.60296,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United States,2015-09-01,Hatching,Embryo,Brain,Nervous System
48984,SRR7549092,SRX4415273,SRS3568563,SRP154651,PRJNA482207,zebrafish olfactory mucosae transcriptome,PRJNA482207,Other,To understand the gene expression changes of olfactory mucosae of zebrfish we sequenced their transcriptome.,,,,,OE,,strain:AB|age:missing|dev stage:adult|sex:missing|tissue:olfactory mucosa|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish olfactory mucosa,OE t2,OE t2,zebrafish olfactory mucosa test replicate 2,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP154651,,,,,6403694100.0,21345647.0,Tfb4 HF3GJALXX L6 2.clean.fq.gz,0:150 1:150,A:1864096877;C:1332910253;G:1350440813;T:1855944479;N:301678,150,150,,,1864096877,1332910253,1350440813,1855944479,301678,SRX4415273,SRS3568563,SRA743421,Institute of Hydrobiology|Chinese Academy of Sciences,Institute of Hydrobiology,2,0.88971,0.89734,0.2254,0.23012,0.71709,0.73464,0.50024,0.50191,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2018-07-21,Adult,Adult,Brain,Nervous System
48985,SRR7549093,SRX4415272,SRS3568563,SRP154651,PRJNA482207,zebrafish olfactory mucosae transcriptome,PRJNA482207,Other,To understand the gene expression changes of olfactory mucosae of zebrfish we sequenced their transcriptome.,,,,,OE,,strain:AB|age:missing|dev stage:adult|sex:missing|tissue:olfactory mucosa|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish olfactory mucosa,OE t3,OE t3,zebrafish olfactory mucosa test replicate 3,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP154651,,,,,7982518800.0,26608396.0,Tmb4 HCLTNALXX L8 1.clean.fq.gz,0:150 1:150,A:2306070257;C:1683318150;G:1707520071;T:2285318155;N:292167,150,150,,,2306070257,1683318150,1707520071,2285318155,292167,SRX4415272,SRS3568563,SRA743421,Institute of Hydrobiology|Chinese Academy of Sciences,Institute of Hydrobiology,2,0.88282,0.88437,0.19224,0.19336,0.71622,0.72324,0.50499,0.50441,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2018-07-21,Adult,Adult,Brain,Nervous System
48986,SRR7549094,SRX4415271,SRS3568563,SRP154651,PRJNA482207,zebrafish olfactory mucosae transcriptome,PRJNA482207,Other,To understand the gene expression changes of olfactory mucosae of zebrfish we sequenced their transcriptome.,,,,,OE,,strain:AB|age:missing|dev stage:adult|sex:missing|tissue:olfactory mucosa|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish olfactory mucosa,OE c1,OE c1,zebrafish olfactory mucosa control replicate 1,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP154651,,,,,7829009400.0,26096698.0,Cfb4 HF3GJALXX L7 1.clean.fq.gz,0:150 1:150,A:2257272118;C:1650607420;G:1672869808;T:2248202788;N:57266,150,150,,,2257272118,1650607420,1672869808,2248202788,57266,SRX4415271,SRS3568563,SRA743421,Institute of Hydrobiology|Chinese Academy of Sciences,Institute of Hydrobiology,2,0.89461,0.90234,0.18822,0.19048,0.7208,0.73497,0.50345,0.5065,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2018-07-21,Adult,Adult,Brain,Nervous System
48987,SRR7549095,SRX4415270,SRS3568563,SRP154651,PRJNA482207,zebrafish olfactory mucosae transcriptome,PRJNA482207,Other,To understand the gene expression changes of olfactory mucosae of zebrfish we sequenced their transcriptome.,,,,,OE,,strain:AB|age:missing|dev stage:adult|sex:missing|tissue:olfactory mucosa|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish olfactory mucosa,OE c2,OE c2,zebrafish olfactory mucosa control replicate 2,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP154651,,,,,6849670500.0,22832235.0,Cmb1 HF3GJALXX L6 2.clean.fq.gz,0:150 1:150,A:1951707162;C:1465417480;G:1485842771;T:1946379196;N:323891,150,150,,,1951707162,1465417480,1485842771,1946379196,323891,SRX4415270,SRS3568563,SRA743421,Institute of Hydrobiology|Chinese Academy of Sciences,Institute of Hydrobiology,2,0.89732,0.90448,0.17421,0.17754,0.72123,0.73994,0.50187,0.49523,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2018-07-21,Adult,Adult,Brain,Nervous System
48988,SRR7549096,SRX4415269,SRS3568563,SRP154651,PRJNA482207,zebrafish olfactory mucosae transcriptome,PRJNA482207,Other,To understand the gene expression changes of olfactory mucosae of zebrfish we sequenced their transcriptome.,,,,,OE,,strain:AB|age:missing|dev stage:adult|sex:missing|tissue:olfactory mucosa|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish olfactory mucosa,OE c3,OE c3,zebrafish olfactory mucosa control replicate 3,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP154651,,,,,6741047400.0,22470158.0,Cmb5 HF3GJALXX L7 2.clean.fq.gz,0:150 1:150,A:1913013275;C:1449571119;G:1471659050;T:1906755376;N:48580,150,150,,,1913013275,1449571119,1471659050,1906755376,48580,SRX4415269,SRS3568563,SRA743421,Institute of Hydrobiology|Chinese Academy of Sciences,Institute of Hydrobiology,2,0.89644,0.90431,0.1722,0.17575,0.71764,0.73393,0.49134,0.49904,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2018-07-21,Adult,Adult,Brain,Nervous System
48989,SRR7549097,SRX4415268,SRS3568563,SRP154651,PRJNA482207,zebrafish olfactory mucosae transcriptome,PRJNA482207,Other,To understand the gene expression changes of olfactory mucosae of zebrfish we sequenced their transcriptome.,,,,,OE,,strain:AB|age:missing|dev stage:adult|sex:missing|tissue:olfactory mucosa|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish olfactory mucosa,OE t1,OE t1,zebrafish olfactory mucosa test replicate 1,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP154651,,,,,7545597900.0,25151993.0,Tfb2 H7MTJALXX L2 2.clean.fq.gz,0:150 1:150,A:2239378192;C:1532314979;G:1546665402;T:2226389553;N:849774,150,150,,,2239378192,1532314979,1546665402,2226389553,849774,SRX4415268,SRS3568563,SRA743421,Institute of Hydrobiology|Chinese Academy of Sciences,Institute of Hydrobiology,2,0.88279,0.89146,0.24112,0.24221,0.72829,0.73462,0.50037,0.4932,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2018-07-21,Adult,Adult,Brain,Nervous System
55231,SRR10199495,SRX6919649,SRS5450535,SRP223604,PRJNA574807,comparative transcriptome between wildtype and chr23 KO zebrafish.,PRJNA574807,Other,the comparative transcriptome between wildtype and chr23 KO zebrafish were analyzed to uncover the cause of the failure of the oocyte maturation and ovulation in chr23 KO.,,,,,Chr23HY replicate 2,,strain:AB line|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:4 month|dev stage:sex mature|sex:female|tissue:hypothalamus|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: adult female hypothalamus,chr23 HY2,chr23 HY2,the libraries were constructed and sequenced on Illumina HiSeq using paired end protocol by GENEWIZ Biotechnology Co. LTD,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,HiSeq X Ten,,SRP223604,,,Chr23-HY12_combined_R1.fastq.gz Chr23-HY12_combined_R2.fastq.gz,fastq fastq,6340531500.0,21135105.0,Chr23 HY12 combined R1.fastq.gz,0:150 1:150,A:1861476220;C:1303154677;G:1318126457;T:1857629079;N:145067,150,150,,,1861476220,1303154677,1318126457,1857629079,145067,SRX6919649,SRS5450535,SRA969652,Huazhong Agricultural University|College of Fisheries,Huazhong Agricultural University,2,0.90269,0.90738,0.18668,0.18837,0.71196,0.7245,0.50641,0.51586,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2019-09-29,Adult,Adult,Brain,Nervous System
55232,SRR10199496,SRX6919648,SRS5450534,SRP223604,PRJNA574807,comparative transcriptome between wildtype and chr23 KO zebrafish.,PRJNA574807,Other,the comparative transcriptome between wildtype and chr23 KO zebrafish were analyzed to uncover the cause of the failure of the oocyte maturation and ovulation in chr23 KO.,,,,,Chr23HY replicate 1,,strain:AB line|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:3 month|dev stage:sex mature|sex:female|tissue:hypothalamus|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: adult female hypothalamus,chr23 HY1,chr23 HY1,the libraries were constructed and sequenced on Illumina HiSeq using paired end protocol by GENEWIZ Biotechnology Co. LTD,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,HiSeq X Ten,,SRP223604,,,Chr23-HY11_combined_R1.fastq.gz Chr23-HY11_combined_R2.fastq.gz,fastq fastq,6823757400.0,22745858.0,Chr23 HY11 combined R1.fastq.gz,0:150 1:150,A:1994443549;C:1416618133;G:1429169272;T:1983436064;N:90382,150,150,,,1994443549,1416618133,1429169272,1983436064,90382,SRX6919648,SRS5450534,SRA969652,Huazhong Agricultural University|College of Fisheries,Huazhong Agricultural University,2,0.90665,0.90931,0.18141,0.18274,0.71597,0.72425,0.51037,0.5177,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2019-09-29,Adult,Adult,Brain,Nervous System
55237,SRR10199501,SRX6919643,SRS5450529,SRP223604,PRJNA574807,comparative transcriptome between wildtype and chr23 KO zebrafish.,PRJNA574807,Other,the comparative transcriptome between wildtype and chr23 KO zebrafish were analyzed to uncover the cause of the failure of the oocyte maturation and ovulation in chr23 KO.,,,,,WTHY replicate 3,,strain:AB line|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:8 month|dev stage:sex mature|sex:female|tissue:hypothalamus|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: adult female hypothalamus,WT HY3,WT HY3,the libraries were constructed and sequenced on Illumina HiSeq using paired end protocol by GENEWIZ Biotechnology Co. LTD,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,HiSeq X Ten,,SRP223604,,,WT-HY3_combined_R1.fastq.gz WT-HY3_combined_R2.fastq.gz,fastq fastq,6724743000.0,22415810.0,WT HY3 combined R1.fastq.gz,0:150 1:150,A:1910360055;C:1448457188;G:1462924647;T:1902865881;N:135229,150,150,,,1910360055,1448457188,1462924647,1902865881,135229,SRX6919643,SRS5450529,SRA969652,Huazhong Agricultural University|College of Fisheries,Huazhong Agricultural University,2,0.91048,0.91287,0.17267,0.17338,0.70999,0.72165,0.49341,0.50968,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2019-09-29,Adult,Adult,Brain,Nervous System
55238,SRR10199502,SRX6919642,SRS5450528,SRP223604,PRJNA574807,comparative transcriptome between wildtype and chr23 KO zebrafish.,PRJNA574807,Other,the comparative transcriptome between wildtype and chr23 KO zebrafish were analyzed to uncover the cause of the failure of the oocyte maturation and ovulation in chr23 KO.,,,,,WTHY replicate 2,,strain:AB line|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:7 month|dev stage:sex mature|sex:female|tissue:hypothalamus|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: adult female hypothalamus,WT HY2,WT HY2,the libraries were constructed and sequenced on Illumina HiSeq using paired end protocol by GENEWIZ Biotechnology Co. LTD,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,HiSeq X Ten,,SRP223604,,,WT-HY2_combined_R1.fastq.gz WT-HY2_combined_R2.fastq.gz,fastq fastq,7302482700.0,24341609.0,WT HY2 combined R1.fastq.gz,0:150 1:150,A:2142054234;C:1508440530;G:1515506742;T:2136237150;N:244044,150,150,,,2142054234,1508440530,1515506742,2136237150,244044,SRX6919642,SRS5450528,SRA969652,Huazhong Agricultural University|College of Fisheries,Huazhong Agricultural University,2,0.90359,0.90475,0.18984,0.18986,0.71143,0.71762,0.50683,0.51228,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2019-09-29,Adult,Adult,Brain,Nervous System
55239,SRR10199503,SRX6919641,SRS5450527,SRP223604,PRJNA574807,comparative transcriptome between wildtype and chr23 KO zebrafish.,PRJNA574807,Other,the comparative transcriptome between wildtype and chr23 KO zebrafish were analyzed to uncover the cause of the failure of the oocyte maturation and ovulation in chr23 KO.,,,,,WTHY replicate 1,,strain:AB line|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:6 month|dev stage:sex mature|sex:female|tissue:hypothalamus|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: adult female hypothalamus,WT HY1,WT HY1,the libraries were constructed and sequenced on Illumina HiSeq using paired end protocol by GENEWIZ Biotechnology Co. LTD,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,HiSeq X Ten,,SRP223604,,,WT-HY1_combined_R1.fastq.gz WT-HY1_combined_R2.fastq.gz,fastq fastq,7402460700.0,24674869.0,WT HY1 combined R1.fastq.gz,0:150 1:150,A:2136220642;C:1566418401;G:1571064393;T:2128508722;N:248542,150,150,,,2136220642,1566418401,1571064393,2128508722,248542,SRX6919641,SRS5450527,SRA969652,Huazhong Agricultural University|College of Fisheries,Huazhong Agricultural University,2,0.90247,0.91066,0.18073,0.18277,0.71082,0.71593,0.51185,0.51186,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2019-09-29,Adult,Adult,Brain,Nervous System
55240,SRR10199504,SRX6919640,SRS5450526,SRP223604,PRJNA574807,comparative transcriptome between wildtype and chr23 KO zebrafish.,PRJNA574807,Other,the comparative transcriptome between wildtype and chr23 KO zebrafish were analyzed to uncover the cause of the failure of the oocyte maturation and ovulation in chr23 KO.,,,,,Chr23HY replicate 3,,strain:AB line|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:5 month|dev stage:sex mature|sex:female|tissue:hypothalamus|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: adult female hypothalamus,chr23 HY3,chr23 HY3,the libraries were constructed and sequenced on Illumina HiSeq using paired end protocol by GENEWIZ Biotechnology Co. LTD,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,HiSeq X Ten,,SRP223604,,,Chr23-HY13_combined_R1.fastq.gz Chr23-HY13_combined_R2.fastq.gz,fastq fastq,6659077800.0,22196926.0,Chr23 HY13 combined R1.fastq.gz,0:150 1:150,A:1961785093;C:1364974716;G:1376225996;T:1955977699;N:114296,150,150,,,1961785093,1364974716,1376225996,1955977699,114296,SRX6919640,SRS5450526,SRA969652,Huazhong Agricultural University|College of Fisheries,Huazhong Agricultural University,2,0.90283,0.90618,0.18606,0.18765,0.71289,0.72275,0.50983,0.51765,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2019-09-29,Adult,Adult,Brain,Nervous System
57203,SRR11267498,SRX7874156,SRS6282460,SRP252014,PRJNA611476,RNAseq between mutant and wild type zebrafish at different developmental stages,PRJNA611476,Other,,,,,,MB wt 3,,strain:Abtu|ecotype:wild type|dev stage:adult|sex:male|tissue:brain|replicate:biological replicate 3|BioSampleModel:Model organism or animal,,,,,,,,,wild type male brain replicate 3,MB wt 3,MB wt 3,common method,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP252014,,,s-24-W3MB_RRA121666-V_1.fq.gz s-24-W3MB_RRA121666-V_2.fq.gz,fastq fastq,8030257500.0,26767525.0,s 24 W3MB RRA121666 V 1.fq.gz,0:150 1:150,A:2266594626;C:1772821652;G:1761850965;T:2228697001;N:293256,150,150,,,2266594626,1772821652,1761850965,2228697001,293256,SRX7874156,SRS6282460,SRA1052323,Sun Yat-sen University|College of Life Sciences,Sun Yat-sen University,2,0.92219,0.91924,0.14148,0.14086,0.69674,0.69871,0.50563,0.49209,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-03-09,Adult,Adult,Brain,Nervous System
57204,SRR11267499,SRX7874155,SRS6282461,SRP252014,PRJNA611476,RNAseq between mutant and wild type zebrafish at different developmental stages,PRJNA611476,Other,,,,,,MB wt 2,,strain:Abtu|ecotype:wild type|dev stage:adult|sex:male|tissue:brain|replicate:biological replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,wild type male brain replicate 2,MB wt 2,MB wt 2,common method,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP252014,,,s-20-W2MB_RRA121662-V_1.fq.gz s-20-W2MB_RRA121662-V_2.fq.gz,fastq fastq,8242585500.0,27475285.0,s 20 W2MB RRA121662 V 1.fq.gz,0:150 1:150,A:2358981868;C:1788500903;G:1778818177;T:2315982567;N:301985,150,150,,,2358981868,1788500903,1778818177,2315982567,301985,SRX7874155,SRS6282461,SRA1052323,Sun Yat-sen University|College of Life Sciences,Sun Yat-sen University,2,0.91835,0.91723,0.14571,0.14463,0.68935,0.69065,0.51893,0.51759,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-03-09,Adult,Adult,Brain,Nervous System
57206,SRR11267501,SRX7874153,SRS6282458,SRP252014,PRJNA611476,RNAseq between mutant and wild type zebrafish at different developmental stages,PRJNA611476,Other,,,,,,MB wt 1,,strain:Abtu|ecotype:wild type|dev stage:adult|sex:male|tissue:brain|replicate:biological replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,wild type male brain replicate 1,MB wt 1,MB wt 1,common method,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP252014,,,s-16-W1MB_RRA121658-V_2.fq.gz s-16-W1MB_RRA121658-V_1.fq.gz,fastq fastq,7580269200.0,25267564.0,s 16 W1MB RRA121658 V 1.fq.gz,0:150 1:150,A:2153861028;C:1661179769;G:1648651518;T:2116299729;N:277156,150,150,,,2153861028,1661179769,1648651518,2116299729,277156,SRX7874153,SRS6282458,SRA1052323,Sun Yat-sen University|College of Life Sciences,Sun Yat-sen University,2,0.92151,0.92088,0.15096,0.15071,0.68152,0.6817,0.50831,0.51003,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-03-09,Adult,Adult,Brain,Nervous System
57207,SRR11267502,SRX7874152,SRS6282456,SRP252014,PRJNA611476,RNAseq between mutant and wild type zebrafish at different developmental stages,PRJNA611476,Other,,,,,,MB mut 3,,strain:Abtu|ecotype:mutant|dev stage:adult|sex:male|tissue:brain|replicate:biological replicate 3|BioSampleModel:Model organism or animal,,,,,,,,,mutant male brain replicate 3,MB mut 3,MB mut 3,common method,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP252014,,,s-12-MU3MB_RRA121654-V_1.fq.gz s-12-MU3MB_RRA121654-V_2.fq.gz,fastq fastq,6831513600.0,22771712.0,s 12 MU3MB RRA121654 V 1.fq.gz,0:150 1:150,A:1950541814;C:1484057251;G:1476404572;T:1920259952;N:250011,150,150,,,1950541814,1484057251,1476404572,1920259952,250011,SRX7874152,SRS6282456,SRA1052323,Sun Yat-sen University|College of Life Sciences,Sun Yat-sen University,2,0.9186,0.91654,0.15961,0.15836,0.68753,0.68716,0.48404,0.48187,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-03-09,Adult,Adult,Brain,Nervous System
57208,SRR11267503,SRX7874151,SRS6282455,SRP252014,PRJNA611476,RNAseq between mutant and wild type zebrafish at different developmental stages,PRJNA611476,Other,,,,,,MB mut 2,,strain:Abtu|ecotype:mutant|dev stage:adult|sex:male|tissue:brain|replicate:biological replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,mutant male brain replicate 2,MB mut 2,MB mut 2,common method,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP252014,,,s-8-MU2MB_RRA121650-V_1.fq.gz s-8-MU2MB_RRA121650-V_2.fq.gz,fastq fastq,6729120900.0,22430403.0,s 8 MU2MB RRA121650 V 1.fq.gz,0:150 1:150,A:1917626758;C:1465822780;G:1460845362;T:1884580956;N:245044,150,150,,,1917626758,1465822780,1460845362,1884580956,245044,SRX7874151,SRS6282455,SRA1052323,Sun Yat-sen University|College of Life Sciences,Sun Yat-sen University,2,0.91896,0.91602,0.15805,0.15664,0.69085,0.69357,0.50577,0.49914,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-03-09,Adult,Adult,Brain,Nervous System
57209,SRR11267504,SRX7874150,SRS6282457,SRP252014,PRJNA611476,RNAseq between mutant and wild type zebrafish at different developmental stages,PRJNA611476,Other,,,,,,MB mut 1,,strain:Abtu|ecotype:mutant|dev stage:adult|sex:male|tissue:brain|replicate:biological replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,mutant male brain replicate 1,MB mut 1,MB mut 1,common method,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP252014,,,s-4-MU1MB_RRA121646-V_2.fq.gz s-4-MU1MB_RRA121646-V_1.fq.gz,fastq fastq,6420599700.0,21401999.0,s 4 MU1MB RRA121646 V 1.fq.gz,0:150 1:150,A:1835409871;C:1392853166;G:1386013932;T:1806090455;N:232276,150,150,,,1835409871,1392853166,1386013932,1806090455,232276,SRX7874150,SRS6282457,SRA1052323,Sun Yat-sen University|College of Life Sciences,Sun Yat-sen University,2,0.9169,0.91391,0.16067,0.15873,0.69305,0.69528,0.50661,0.50845,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-03-09,Adult,Adult,Brain,Nervous System
57217,SRR11267512,SRX7874142,SRS6282447,SRP252014,PRJNA611476,RNAseq between mutant and wild type zebrafish at different developmental stages,PRJNA611476,Other,,,,,,FB wt 3,,strain:Abtu|ecotype:wild type|dev stage:adult|sex:female|tissue:brain|replicate:biological replicate 3|BioSampleModel:Model organism or animal,,,,,,,,,wild type female brain replicate 3,FB wt 3,FB wt 3,common method,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP252014,,,s-22-W3FB_RRA121664-V_1.fq.gz s-22-W3FB_RRA121664-V_2.fq.gz,fastq fastq,6798837300.0,22662791.0,s 22 W3FB RRA121664 V 1.fq.gz,0:150 1:150,A:1863597606;C:1554400278;G:1547917708;T:1832672957;N:248751,150,150,,,1863597606,1554400278,1547917708,1832672957,248751,SRX7874142,SRS6282447,SRA1052323,Sun Yat-sen University|College of Life Sciences,Sun Yat-sen University,2,0.84427,0.84184,0.10897,0.10821,0.69629,0.69662,0.50168,0.50451,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-03-09,Adult,Adult,Brain,Nervous System
57218,SRR11267513,SRX7874141,SRS6282445,SRP252014,PRJNA611476,RNAseq between mutant and wild type zebrafish at different developmental stages,PRJNA611476,Other,,,,,,FB wt 2,,strain:Abtu|ecotype:wild type|dev stage:adult|sex:female|tissue:brain|replicate:biological replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,wild type female brain replicate 2,FB wt 2,FB wt 2,common method,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP252014,,,s-18-W2FB_RRA121660-V_1.fq.gz s-18-W2FB_RRA121660-V_2.fq.gz,fastq fastq,6824973600.0,22749912.0,s 18 W2FB RRA121660 V 1.fq.gz,0:150 1:150,A:1938577376;C:1495865823;G:1486662757;T:1903618825;N:248819,150,150,,,1938577376,1495865823,1486662757,1903618825,248819,SRX7874141,SRS6282445,SRA1052323,Sun Yat-sen University|College of Life Sciences,Sun Yat-sen University,2,0.9193,0.91525,0.15035,0.14799,0.69315,0.69658,0.49841,0.47916,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-03-09,Adult,Adult,Brain,Nervous System
57219,SRR11267514,SRX7874140,SRS6282444,SRP252014,PRJNA611476,RNAseq between mutant and wild type zebrafish at different developmental stages,PRJNA611476,Other,,,,,,FB wt 1,,strain:Abtu|ecotype:wild type|dev stage:adult|sex:female|tissue:brain|replicate:biological replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,wild type female brain replicate 1,FB wt 1,FB wt 1,common method,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP252014,,,s-14-W1FB_RRA121656-V_1.fq.gz s-14-W1FB_RRA121656-V_2.fq.gz,fastq fastq,7169436000.0,23898120.0,s 14 W1FB RRA121656 V 1.fq.gz,0:150 1:150,A:2039478474;C:1568883502;G:1559807836;T:2001003232;N:262956,150,150,,,2039478474,1568883502,1559807836,2001003232,262956,SRX7874140,SRS6282444,SRA1052323,Sun Yat-sen University|College of Life Sciences,Sun Yat-sen University,2,0.92089,0.91738,0.1584,0.15647,0.68613,0.68925,0.5064,0.50764,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-03-09,Adult,Adult,Brain,Nervous System
57220,SRR11267515,SRX7874139,SRS6282443,SRP252014,PRJNA611476,RNAseq between mutant and wild type zebrafish at different developmental stages,PRJNA611476,Other,,,,,,FB mut 3,,strain:Abtu|ecotype:mutant|dev stage:adult|sex:female|tissue:brain|replicate:biological replicate 3|BioSampleModel:Model organism or animal,,,,,,,,,mutant female brain replicate 3,FB mut 3,FB mut 3,common method,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP252014,,,s-10-MU3FB_RRA121652-V_2.fq.gz s-10-MU3FB_RRA121652-V_1.fq.gz,fastq fastq,7958071500.0,26526905.0,s 10 MU3FB RRA121652 V 1.fq.gz,0:150 1:150,A:2271699105;C:1730786661;G:1720185842;T:2235110285;N:289607,150,150,,,2271699105,1730786661,1720185842,2235110285,289607,SRX7874139,SRS6282443,SRA1052323,Sun Yat-sen University|College of Life Sciences,Sun Yat-sen University,2,0.92007,0.91988,0.14703,0.14667,0.6869,0.68669,0.51161,0.51758,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-03-09,Adult,Adult,Brain,Nervous System
57221,SRR11267516,SRX7874138,SRS6282446,SRP252014,PRJNA611476,RNAseq between mutant and wild type zebrafish at different developmental stages,PRJNA611476,Other,,,,,,FB mut 2,,strain:Abtu|ecotype:mutant|dev stage:adult|sex:female|tissue:brain|replicate:biological replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,mutant female brain replicate 2,FB mut 2,FB mut 2,common method,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP252014,,,s-6-MU2FB_RRA121648-V_1.fq.gz s-6-MU2FB_RRA121648-V_2.fq.gz,fastq fastq,6939368400.0,23131228.0,s 6 MU2FB RRA121648 V 1.fq.gz,0:150 1:150,A:1978515667;C:1512033464;G:1503471960;T:1945092769;N:254540,150,150,,,1978515667,1512033464,1503471960,1945092769,254540,SRX7874138,SRS6282446,SRA1052323,Sun Yat-sen University|College of Life Sciences,Sun Yat-sen University,2,0.91788,0.9148,0.16219,0.16001,0.69238,0.69436,0.50776,0.50757,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-03-09,Adult,Adult,Brain,Nervous System
57222,SRR11267517,SRX7874137,SRS6282442,SRP252014,PRJNA611476,RNAseq between mutant and wild type zebrafish at different developmental stages,PRJNA611476,Other,,,,,,FB mut 1,,strain:Abtu|ecotype:mutant|dev stage:adult|sex:female|tissue:brain|replicate:biological replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,mutant female brain replicate 1,FB mut 1,FB mut 1,common method,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP252014,,,s-2-MU1FB_RRA121644-V_1.fq.gz s-2-MU1FB_RRA121644-V_2.fq.gz,fastq fastq,6850500000.0,22835000.0,s 2 MU1FB RRA121644 V 1.fq.gz,0:150 1:150,A:1930562038;C:1514213507;G:1507784104;T:1897690057;N:250294,150,150,,,1930562038,1514213507,1507784104,1897690057,250294,SRX7874137,SRS6282442,SRA1052323,Sun Yat-sen University|College of Life Sciences,Sun Yat-sen University,2,0.91954,0.91852,0.13805,0.13715,0.68672,0.68773,0.49596,0.49313,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-03-09,Adult,Adult,Brain,Nervous System
69472,SRR18712321,SRX14812930,SRS12569573,SRP369458,PRJNA825495,Regulation of retina microexons by srrm3 in zebrafish,PRJNA825495,Other,To investigate the role of srrm3 as a regulator of retina microexons RetMICs we have sequenced heads from WT animals at 24 hpf and enucleated eyes from 48 hpf 60 hpf and 72 hpf larvae WT and KO for srrm3.,,,,,Head 24hpf WT b,,strain:WT|dev stage:24 hpf|sex:NA|tissue:Head|BioSampleModel:Model organism or animal,,,,,,,,,Heads from 24 hpf larvae WT for the eMIC domain of srrm3.,Head 24hpf WT,Head 24hpf WT,WT and srrm3 mutant zebrafish were grown at 28C 14h light/10h dark cycle. Extract protocol: 24 hpf WT fish heads were removed and pulled for RNA extraction using RNA RNeasy Mini kit QIAGEN. Larvae eyes were removed and from twenty to sixty eyes per genotype were pulled for RNA extraction using RNA RNeasy Micro kit QIAGENLibrary preparation: RNA libraries were prepared for sequencing using standard Illumina protocols; polyA selected stranded RNA seq,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP369458,,,Head_24hpf_WT_b_R1-125.fq.gz Head_24hpf_WT_b_R2-125.fq.gz,fastq fastq,16050157000.0,64200628.0,Head 24hpf WT b R1 125.fq.gz,0:125 1:125,A:4076433263;C:3955246853;G:3964617037;T:4044497256;N:9362591,125,125,,,4076433263,3955246853,3964617037,4044497256,9362591,SRX14812930,SRS12569573,SRA1402039,Centre for Genomic Regulation|Systems Biology,Centre for Genomic Regulation|Systems Biology,2,0.97774,0.97918,0.03623,0.03592,0.71035,0.71474,0.46304,0.46994,125,125,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,Spain,2022-04-11,Pharyngula,Embryo,Head,Nervous System
74405,SRR23816189,SRX19638186,SRS17007061,SRP426733,PRJNA940583,A study of the transcriptome of zebrafish brain tissue,PRJNA940583,Other,Neurobiology of the zebrafish,,,,,C3,,collection date:2022 01|geo loc name:China:Beijing|lat lon:39.56 N 116.20 E|age:missing|breed:missing|cultivar:missing|dev stage:missing|ecotype:missing|isolate:missing|sex:missing|strain:missing|tissue:missing|BioSampleModel:Model organism or animal,,,,,,,,,brain of the zebrafish,C3,C3,Materials and methods,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP426733,,,C3.raw_1.fastq.gz C3.raw_2.fastq.gz,fastq fastq,11050626900.0,36835423.0,C3.raw 1.fastq.gz,0:150 1:150,A:2865145780;C:2642886672;G:2675064008;T:2866540089;N:990351,150,150,,,2865145780,2642886672,2675064008,2866540089,990351,SRX19638186,SRS17007061,SRA1601531,Chinese Academy of Agricultural Sciences|Institute of Quality Standard and Testing Technolo,Chinese Academy of Agricultural Sciences,2,0.9531,0.95272,0.06997,0.07085,0.6634,0.66393,0.48771,0.49045,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2023-03-11,Undetermined,Undetermined,Brain,Nervous System
74406,SRR23816190,SRX19638185,SRS17007060,SRP426733,PRJNA940583,A study of the transcriptome of zebrafish brain tissue,PRJNA940583,Other,Neurobiology of the zebrafish,,,,,C2,,collection date:2022 01|geo loc name:China:Beijing|lat lon:39.56 N 116.20 E|age:missing|breed:missing|cultivar:missing|dev stage:missing|ecotype:missing|isolate:missing|sex:missing|strain:missing|tissue:missing|BioSampleModel:Model organism or animal,,,,,,,,,brain of the zebrafish,C2,C2,Materials and methods,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP426733,,,C2.raw_1.fastq.gz C2.raw_2.fastq.gz,fastq fastq,9161220600.0,30537402.0,C2.raw 1.fastq.gz,0:150 1:150,A:2362480503;C:2178221545;G:2247509752;T:2372225007;N:783793,150,150,,,2362480503,2178221545,2247509752,2372225007,783793,SRX19638185,SRS17007060,SRA1601531,Chinese Academy of Agricultural Sciences|Institute of Quality Standard and Testing Technolo,Chinese Academy of Agricultural Sciences,2,0.95704,0.95351,0.06583,0.06694,0.66951,0.67034,0.50451,0.50466,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2023-03-11,Undetermined,Undetermined,Brain,Nervous System
74407,SRR23816191,SRX19638184,SRS17007059,SRP426733,PRJNA940583,A study of the transcriptome of zebrafish brain tissue,PRJNA940583,Other,Neurobiology of the zebrafish,,,,,C1,,collection date:2022 01|geo loc name:China:Beijing|lat lon:39.56 N 116.20 E|age:missing|breed:missing|cultivar:missing|dev stage:missing|ecotype:missing|isolate:missing|sex:missing|strain:missing|tissue:missing|BioSampleModel:Model organism or animal,,,,,,,,,brain of the zebrafish,C1,C1,Materials and methods,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP426733,,,C1.raw_1.fastq.gz C1.raw_2.fastq.gz,fastq fastq,6557456400.0,21858188.0,C1.raw 1.fastq.gz,0:150 1:150,A:1700751272;C:1563561339;G:1593294702;T:1699335261;N:513826,150,150,,,1700751272,1563561339,1593294702,1699335261,513826,SRX19638184,SRS17007059,SRA1601531,Chinese Academy of Agricultural Sciences|Institute of Quality Standard and Testing Technolo,Chinese Academy of Agricultural Sciences,2,0.9468,0.95291,0.0719,0.07405,0.6706,0.66914,0.46316,0.47396,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2023-03-11,Undetermined,Undetermined,Brain,Nervous System
74408,SRR23816192,SRX19638183,SRS17007058,SRP426733,PRJNA940583,A study of the transcriptome of zebrafish brain tissue,PRJNA940583,Other,Neurobiology of the zebrafish,,,,,C H3,,collection date:2022 01|geo loc name:China:Beijing|lat lon:39.56 N 116.20 E|age:missing|breed:missing|cultivar:missing|dev stage:missing|ecotype:missing|isolate:missing|sex:missing|strain:missing|tissue:missing|BioSampleModel:Model organism or animal,,,,,,,,,brain of the zebrafish,C H3,C H3,Materials and methods,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP426733,,,C_H3.raw_1.fastq.gz C_H3.raw_2.fastq.gz,fastq fastq,9295081800.0,30983606.0,C H3.raw 1.fastq.gz,0:150 1:150,A:2420308728;C:2209690139;G:2245386913;T:2418963797;N:732223,150,150,,,2420308728,2209690139,2245386913,2418963797,732223,SRX19638183,SRS17007058,SRA1601531,Chinese Academy of Agricultural Sciences|Institute of Quality Standard and Testing Technolo,Chinese Academy of Agricultural Sciences,2,0.94656,0.9521,0.07155,0.07386,0.66383,0.66391,0.48502,0.48282,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2023-03-11,Undetermined,Undetermined,Brain,Nervous System
74409,SRR23816193,SRX19638182,SRS17007057,SRP426733,PRJNA940583,A study of the transcriptome of zebrafish brain tissue,PRJNA940583,Other,Neurobiology of the zebrafish,,,,,C H2,,collection date:2022 01|geo loc name:China:Beijing|lat lon:39.56 N 116.20 E|age:missing|breed:missing|cultivar:missing|dev stage:missing|ecotype:missing|isolate:missing|sex:missing|strain:missing|tissue:missing|BioSampleModel:Model organism or animal,,,,,,,,,brain of the zebrafish,C H2,C H2,Materials and methods,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP426733,,,C_H2.raw_1.fastq.gz C_H2.raw_2.fastq.gz,fastq fastq,10811531700.0,36038439.0,C H2.raw 1.fastq.gz,0:150 1:150,A:2802038157;C:2586697803;G:2620325966;T:2801538702;N:931072,150,150,,,2802038157,2586697803,2620325966,2801538702,931072,SRX19638182,SRS17007057,SRA1601531,Chinese Academy of Agricultural Sciences|Institute of Quality Standard and Testing Technolo,Chinese Academy of Agricultural Sciences,2,0.95404,0.95031,0.06755,0.06783,0.66703,0.66766,0.48371,0.48209,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2023-03-11,Undetermined,Undetermined,Brain,Nervous System
74410,SRR23816194,SRX19638181,SRS17007056,SRP426733,PRJNA940583,A study of the transcriptome of zebrafish brain tissue,PRJNA940583,Other,Neurobiology of the zebrafish,,,,,C H1,,collection date:2022 01|geo loc name:China:Beijing|lat lon:39.56 N 116.20 E|age:missing|breed:missing|cultivar:missing|dev stage:missing|ecotype:missing|isolate:missing|sex:missing|strain:missing|tissue:missing|BioSampleModel:Model organism or animal,,,,,,,,,brain of the zebrafish,C H1,C H1,Materials and methods,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP426733,,,C_H1.raw_1.fastq.gz C_H1.raw_2.fastq.gz,fastq fastq,7084951800.0,23616506.0,C H1.raw 1.fastq.gz,0:150 1:150,A:1848926248;C:1674901289;G:1707752429;T:1852765799;N:606035,150,150,,,1848926248,1674901289,1707752429,1852765799,606035,SRX19638181,SRS17007056,SRA1601531,Chinese Academy of Agricultural Sciences|Institute of Quality Standard and Testing Technolo,Chinese Academy of Agricultural Sciences,2,0.95273,0.94995,0.07309,0.07329,0.66576,0.66616,0.48159,0.47398,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2023-03-11,Undetermined,Undetermined,Brain,Nervous System