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84 rows where experiment.library_selection = "RANDOM", experiment.platform = "ILLUMINA" and tissue_curation = "Brain"

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devstage_curation 5

devstage_curation_coarse 4

technology 3

experiment.library_source 2

experiment.library_layout 2

tissue_curation_coarse 1

tissue_curation 1

  • Brain · 84 ✖

experiment.platform 1

  • ILLUMINA · 84 ✖

experiment.library_strategy 1

experiment.library_selection 1

  • RANDOM · 84 ✖
Link rowid ▼ run.accession experiment.accession sample.accession study.accession bioproject study.title study.alias study.type study.abstract study.attributes study.PMIDs sample.description sample.title sample.alias sample.centername sample.attributes GEOsample.title GEOsample.dataprocessing GEOsample.source GEOsample.treatmentprotocol GEOsample.extractprotocol GEOsample.growthprotocol GEOsample.characteristics GEOsample.accession experiment.title experiment.alias experiment.library_name experiment.design_description experiment.library_construction_protocol experiment.attributes experiment.library_strategy experiment.library_source experiment.library_selection experiment.library_layout experiment.platform experiment.instrument_model experiment.spot_descriptor experiment.study_ref run.title run.attributes run.filename run.semantic_name run.total_bases run.total_spots run.alias run.read_lengths run.base_counts run.r1_length run.r2_length run.r3_length run.r4_length run.Acount run.Ccount run.Gcount run.Tcount run.Ncount run.experiment run.pool_member submission.accession submission.srasource submission.bioprojectsource seqdetective.n_mates seqdetective.mapping_rate.mate1 seqdetective.mapping_rate.mate2 seqdetective.nofeature_rate.mate1 seqdetective.nofeature_rate.mate2 seqdetective.sparsity.mate1 seqdetective.sparsity.mate2 seqdetective.pos_strand_rate.mate1 seqdetective.pos_strand_rate.mate2 seqdetective.readlen.mate1 seqdetective.readlen.mate2 seqdetective.judgement.mate1 seqdetective.judgement.mate2 seqdetective.judgement.reason platform_family instrument_generation read_bias selection_class prep_kit sc_or_bulk tech_class technology tech_variant submission.bioprojectsource.country earliest_date devstage_curation devstage_curation_coarse tissue_curation tissue_curation_coarse
38 38 DRR408248 DRX393854 DRS407179 DRP012042 PRJDB14275 Zebrafish EN/ENCDC RNA seq DRP012042 Transcriptome Analysis A project to find differential expressed genes between enteric neurons ENs and enteric neural crest derived cells ENCDCs in larval zebrafish gut. We dissected guts of transgenic line TgSAGFFLF217B; uas:gfp for ENs and Tgsox10:cre; EF1alpha:loxP gfp loxP dsred for ENCDCs and isolated GFP+ ENs and dsRed+ ENCDCs. Three duplicates for each of ENs and ENCDCs are prepared. Libraries for NGS are prepared using SMART Seq V4 Ultra Low Input RNA Kit.     zebrafish 5 day DsRed positive enteric neural crest derived cells replicate 3 zebrafish ENCDC replicate 3 SAMD00529468   sample name:zebrafish ENCDC replicate 3|biological replicate:enteric neural crest derived cells 3|strain:Tgsox10:cre; EF3alpha:loxP gfp loxP dsred                 NextSeq 550 paired end sequencing of SAMD00529468 DRX393854 190326ENvsNC N706 5day;NeuralCrestDerivedCell;rep3 1 1   RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA NextSeq 550 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>160</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>81</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP012042 NextSeq 550 paired end sequencing of SAMD00529468       3803721121.0 24526633.0 DRR408248 0:77.54 1:77.54 A:999106107;C:897663781;G:921501114;T:979486853;N:5963266 77 77     999106107 897663781 921501114 979486853 5963266 DRX393854 DRS407179 DRA014886 NIBB|NIBB core research facilities, National Institute for Basic Biology University of Hyogo                       B B biological fallback assumption illumina nextseq unknown random_priming unknown bulk unknown unknown   Japan 2024-09-22 Undetermined Larval Brain Nervous System
39 39 DRR408247 DRX393853 DRS407178 DRP012042 PRJDB14275 Zebrafish EN/ENCDC RNA seq DRP012042 Transcriptome Analysis A project to find differential expressed genes between enteric neurons ENs and enteric neural crest derived cells ENCDCs in larval zebrafish gut. We dissected guts of transgenic line TgSAGFFLF217B; uas:gfp for ENs and Tgsox10:cre; EF1alpha:loxP gfp loxP dsred for ENCDCs and isolated GFP+ ENs and dsRed+ ENCDCs. Three duplicates for each of ENs and ENCDCs are prepared. Libraries for NGS are prepared using SMART Seq V4 Ultra Low Input RNA Kit.     zebrafish 5 day DsRed positive enteric neural crest derived cells replicate 2 zebrafish ENCDC replicate 2 SAMD00529467   sample name:zebrafish ENCDC replicate 2|biological replicate:enteric neural crest derived cells 2|strain:Tgsox10:cre; EF2alpha:loxP gfp loxP dsred                 NextSeq 550 paired end sequencing of SAMD00529467 DRX393853 190326ENvsNC N705 5day;NeuralCrestDerivedCell;rep2 1 1   RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA NextSeq 550 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>160</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>81</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP012042 NextSeq 550 paired end sequencing of SAMD00529467       3436798274.0 22156202.0 DRR408247 0:77.56 1:77.56 A:900848174;C:812031426;G:832960423;T:885671203;N:5287048 77 77     900848174 812031426 832960423 885671203 5287048 DRX393853 DRS407178 DRA014886 NIBB|NIBB core research facilities, National Institute for Basic Biology University of Hyogo                       B B biological fallback assumption illumina nextseq unknown random_priming unknown bulk unknown unknown   Japan 2024-09-22 Undetermined Larval Brain Nervous System
40 40 DRR408246 DRX393852 DRS407177 DRP012042 PRJDB14275 Zebrafish EN/ENCDC RNA seq DRP012042 Transcriptome Analysis A project to find differential expressed genes between enteric neurons ENs and enteric neural crest derived cells ENCDCs in larval zebrafish gut. We dissected guts of transgenic line TgSAGFFLF217B; uas:gfp for ENs and Tgsox10:cre; EF1alpha:loxP gfp loxP dsred for ENCDCs and isolated GFP+ ENs and dsRed+ ENCDCs. Three duplicates for each of ENs and ENCDCs are prepared. Libraries for NGS are prepared using SMART Seq V4 Ultra Low Input RNA Kit.     zebrafish 5 day DsRed positive enteric neural crest derived cells replicate 1 zebrafish ENCDC replicate 1 SAMD00529466   sample name:zebrafish ENCDC replicate 1|biological replicate:enteric neural crest derived cells 1|strain:Tgsox10:cre; EF1alpha:loxP gfp loxP dsred                 NextSeq 550 paired end sequencing of SAMD00529466 DRX393852 190326ENvsNC N704 5day;NeuralCrestDerivedCell;rep1 1 1   RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA NextSeq 550 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>160</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>81</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP012042 NextSeq 550 paired end sequencing of SAMD00529466       3582073512.0 23135170.0 DRR408246 0:77.41 1:77.42 A:943152815;C:841972211;G:863627245;T:927361159;N:5960082 77 77     943152815 841972211 863627245 927361159 5960082 DRX393852 DRS407177 DRA014886 NIBB|NIBB core research facilities, National Institute for Basic Biology University of Hyogo                       B B biological fallback assumption illumina nextseq unknown random_priming unknown bulk unknown unknown   Japan 2024-09-22 Undetermined Larval Brain Nervous System
9331 9331 ERR2862354 ERX2868592 ERS2866329 ERP111743 PRJEB29441 Receptor Tyrosine Kinase pathway activation is sufficient to trigger chordoma in zebrafish E-MTAB-7349 Transcriptome Analysis Oncogenic transformation of individual cell fates by developmental signaling cascades and transcription factors triggers diverse cancer types. Chordoma is a rare aggressive tumor arising from transformed notochord remnants. Various potentially oncogenic factors have been found deregulated in chordoma and its metastases yet clear causation remains uncertain. In particular expression of the notochord controlling transcription factor Brachyury is hypothesized as key molecular driver in chordoma formation yet an in vivo model to causally test its oncogenic potential in the notochord is missing. Here we apply a zebrafish model of chordoma onset to identify the notochord transforming potential of tumor implicated candidate genes in vivo. We find that overexpression of human and zebrafish Brachyury including a version with augmented transcriptional activity is insufficient to initiate notochord hyperplasia in vivo. In contrast the repeatedly chordoma implicated receptor tyrosine kinase RTK genes EGFR and KDR/VEGFR2 are sufficient to transform developmental notochord cells akin to direct activation of Ras. Analysis of transcriptome and sub cellular organization from transformed notochords suggests that aberrant activation of RTK/Ras signaling attenuates processes required for the differentiation of notochord cells. Taken together our results provide first in vivo indication for a lack of tumor initiating potential of Brachyury expression in the notochord and suggest activated RTK signaling as potent hyperplasia initiating event in chordoma. ENA FIRST PUBLIC:2018 12 01|ENA LAST UPDATE:2018 10 30   Protocols: 8 dpf wildtype and Tgtwhh:Gal4;TgUAS:EGFP HRASV12 were euthanized with 3% Tricaine methanesulfonate Sigma. Embryos were decapitated and incubated in Tripsin EDTA Sigma for 30 minutes to facilitate tissue dissociation. Notochords were then dissected using tungsten needles and immediately transferred to Trizol LS Ambion. We isolated 30 50 notochords per replicate with a total of 3 replicates per condition 3x wildtype 3x HRASV12. Notochord RNA was extracted following the manufacturer's protocol using Trizol LS. RNA seq libraries were constructed using the Truseq stranded total RNA kit. TUC SAMEA5055152 UZH ENA FIRST PUBLIC:2018 12 01T17:03:21Z|ENA LAST UPDATE:2018 10 30T13:30:13Z|External Id:SAMEA5055152|INSDC center name:UZH|INSDC first public:2018 12 01T17:03:21Z|INSDC last update:2018 10 30T13:30:13Z|INSDC status:public|Submitter Id:E MTAB 7349:TUC|age:8|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:wild type genotype|individual:mixed pool of 30 to 50 embryos|organism part:notochord|sample name:E MTAB 7349:TUC|scientific name:Danio rerio|sex:mixed                 Illumina HiSeq 2500 paired end sequencing; Receptor Tyrosine Kinase pathway activation is sufficient to trigger chordoma in zebrafish E MTAB 7349:TUC p TUC p Receptor Tyrosine Kinase pathway activation is sufficient to trigger chordoma in zebrafish 8 dpf wildtype and Tgtwhh:Gal4;TgUAS:EGFP HRASV12 were euthanized with 3% Tricaine methanesulfonate Sigma. Embryos were decapitated and incubated in Tripsin EDTA Sigma for 30 minutes to facilitate tissue dissociation. Notochords were then dissected using tungsten needles and immediately transferred to Trizol LS Ambion. We isolated 30 50 notochords per replicate with a total of 3 replicates per condition 3x wildtype 3x HRASV12. Notochord RNA was extracted following the manufacturer's protocol using Trizol LS. RNA seq libraries were constructed using the Truseq stranded total RNA kit. Experimental Factor: genotype:wild type genotype RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP111743 Illumina HiSeq 2500 paired end sequencing; Receptor Tyrosine Kinase pathway activation is sufficient to trigger chordoma in zebrafish ENA FIRST PUBLIC:2018 12 01|ENA LAST UPDATE:2018 11 16 AGCGATAG_AGGCTATA__160520_I127_FCH732GBBXX_L8_CDKPEI160513002_1.fq.gz AGCGATAG_AGGCTATA__160520_I127_FCH732GBBXX_L8_CDKPEI160513002_2.fq.gz fastq fastq 12890102400.0 64450512.0 E MTAB 7349:AGCGATAG AGGCTATA 160520 I127 FCH732GBBXX L8 CDKPEI160513002 0:100 1:100 A:3347844573;C:3078635366;G:3118813009;T:3343385073;N:1424379 100 100     3347844573 3078635366 3118813009 3343385073 1424379 ERX2868592 ERS2866329 ERA1640550 European Nucleotide Archive European Nucleotide Archive 2 0.89165 0.8896 0.26768 0.26518 0.75142 0.75459 0.60855 0.6105 100 100 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   Unknown 2018-10-30 Larval Larval Brain Nervous System
9332 9332 ERR2862353 ERX2868591 ERS2866328 ERP111743 PRJEB29441 Receptor Tyrosine Kinase pathway activation is sufficient to trigger chordoma in zebrafish E-MTAB-7349 Transcriptome Analysis Oncogenic transformation of individual cell fates by developmental signaling cascades and transcription factors triggers diverse cancer types. Chordoma is a rare aggressive tumor arising from transformed notochord remnants. Various potentially oncogenic factors have been found deregulated in chordoma and its metastases yet clear causation remains uncertain. In particular expression of the notochord controlling transcription factor Brachyury is hypothesized as key molecular driver in chordoma formation yet an in vivo model to causally test its oncogenic potential in the notochord is missing. Here we apply a zebrafish model of chordoma onset to identify the notochord transforming potential of tumor implicated candidate genes in vivo. We find that overexpression of human and zebrafish Brachyury including a version with augmented transcriptional activity is insufficient to initiate notochord hyperplasia in vivo. In contrast the repeatedly chordoma implicated receptor tyrosine kinase RTK genes EGFR and KDR/VEGFR2 are sufficient to transform developmental notochord cells akin to direct activation of Ras. Analysis of transcriptome and sub cellular organization from transformed notochords suggests that aberrant activation of RTK/Ras signaling attenuates processes required for the differentiation of notochord cells. Taken together our results provide first in vivo indication for a lack of tumor initiating potential of Brachyury expression in the notochord and suggest activated RTK signaling as potent hyperplasia initiating event in chordoma. ENA FIRST PUBLIC:2018 12 01|ENA LAST UPDATE:2018 10 30   Protocols: 8 dpf wildtype and Tgtwhh:Gal4;TgUAS:EGFP HRASV12 were euthanized with 3% Tricaine methanesulfonate Sigma. Embryos were decapitated and incubated in Tripsin EDTA Sigma for 30 minutes to facilitate tissue dissociation. Notochords were then dissected using tungsten needles and immediately transferred to Trizol LS Ambion. We isolated 30 50 notochords per replicate with a total of 3 replicates per condition 3x wildtype 3x HRASV12. Notochord RNA was extracted following the manufacturer's protocol using Trizol LS. RNA seq libraries were constructed using the Truseq stranded total RNA kit. TUB SAMEA5055151 UZH ENA FIRST PUBLIC:2018 12 01T17:03:21Z|ENA LAST UPDATE:2018 10 30T13:30:13Z|External Id:SAMEA5055151|INSDC center name:UZH|INSDC first public:2018 12 01T17:03:21Z|INSDC last update:2018 10 30T13:30:13Z|INSDC status:public|Submitter Id:E MTAB 7349:TUB|age:8|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:wild type genotype|individual:mixed pool of 30 to 50 embryos|organism part:notochord|sample name:E MTAB 7349:TUB|scientific name:Danio rerio|sex:mixed                 Illumina HiSeq 2500 paired end sequencing; Receptor Tyrosine Kinase pathway activation is sufficient to trigger chordoma in zebrafish E MTAB 7349:TUB p TUB p Receptor Tyrosine Kinase pathway activation is sufficient to trigger chordoma in zebrafish 8 dpf wildtype and Tgtwhh:Gal4;TgUAS:EGFP HRASV12 were euthanized with 3% Tricaine methanesulfonate Sigma. Embryos were decapitated and incubated in Tripsin EDTA Sigma for 30 minutes to facilitate tissue dissociation. Notochords were then dissected using tungsten needles and immediately transferred to Trizol LS Ambion. We isolated 30 50 notochords per replicate with a total of 3 replicates per condition 3x wildtype 3x HRASV12. Notochord RNA was extracted following the manufacturer's protocol using Trizol LS. RNA seq libraries were constructed using the Truseq stranded total RNA kit. Experimental Factor: genotype:wild type genotype RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP111743 Illumina HiSeq 2500 paired end sequencing; Receptor Tyrosine Kinase pathway activation is sufficient to trigger chordoma in zebrafish ENA FIRST PUBLIC:2018 12 01|ENA LAST UPDATE:2018 11 16 TCTCGCGC_AGGCTATA__160520_I127_FCH732GBBXX_L8_CDKPEI160513002_2.fq.gz TCTCGCGC_AGGCTATA__160520_I127_FCH732GBBXX_L8_CDKPEI160513002_1.fq.gz fastq fastq 15345882200.0 76729411.0 E MTAB 7349:TCTCGCGC AGGCTATA 160520 I127 FCH732GBBXX L8 CDKPEI160513002 0:100 1:100 A:4257362303;C:3394893224;G:3451042837;T:4240872487;N:1711349 100 100     4257362303 3394893224 3451042837 4240872487 1711349 ERX2868591 ERS2866328 ERA1640550 European Nucleotide Archive European Nucleotide Archive 2 0.86888 0.86735 0.45025 0.44476 0.72036 0.72529 0.56048 0.56274 100 100 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   Unknown 2018-10-30 Larval Larval Brain Nervous System
9333 9333 ERR2862352 ERX2868590 ERS2866327 ERP111743 PRJEB29441 Receptor Tyrosine Kinase pathway activation is sufficient to trigger chordoma in zebrafish E-MTAB-7349 Transcriptome Analysis Oncogenic transformation of individual cell fates by developmental signaling cascades and transcription factors triggers diverse cancer types. Chordoma is a rare aggressive tumor arising from transformed notochord remnants. Various potentially oncogenic factors have been found deregulated in chordoma and its metastases yet clear causation remains uncertain. In particular expression of the notochord controlling transcription factor Brachyury is hypothesized as key molecular driver in chordoma formation yet an in vivo model to causally test its oncogenic potential in the notochord is missing. Here we apply a zebrafish model of chordoma onset to identify the notochord transforming potential of tumor implicated candidate genes in vivo. We find that overexpression of human and zebrafish Brachyury including a version with augmented transcriptional activity is insufficient to initiate notochord hyperplasia in vivo. In contrast the repeatedly chordoma implicated receptor tyrosine kinase RTK genes EGFR and KDR/VEGFR2 are sufficient to transform developmental notochord cells akin to direct activation of Ras. Analysis of transcriptome and sub cellular organization from transformed notochords suggests that aberrant activation of RTK/Ras signaling attenuates processes required for the differentiation of notochord cells. Taken together our results provide first in vivo indication for a lack of tumor initiating potential of Brachyury expression in the notochord and suggest activated RTK signaling as potent hyperplasia initiating event in chordoma. ENA FIRST PUBLIC:2018 12 01|ENA LAST UPDATE:2018 10 30   Protocols: 8 dpf wildtype and Tgtwhh:Gal4;TgUAS:EGFP HRASV12 were euthanized with 3% Tricaine methanesulfonate Sigma. Embryos were decapitated and incubated in Tripsin EDTA Sigma for 30 minutes to facilitate tissue dissociation. Notochords were then dissected using tungsten needles and immediately transferred to Trizol LS Ambion. We isolated 30 50 notochords per replicate with a total of 3 replicates per condition 3x wildtype 3x HRASV12. Notochord RNA was extracted following the manufacturer's protocol using Trizol LS. RNA seq libraries were constructed using the Truseq stranded total RNA kit. TUA SAMEA5055150 UZH ENA FIRST PUBLIC:2018 12 01T17:03:21Z|ENA LAST UPDATE:2018 10 30T13:30:13Z|External Id:SAMEA5055150|INSDC center name:UZH|INSDC first public:2018 12 01T17:03:21Z|INSDC last update:2018 10 30T13:30:13Z|INSDC status:public|Submitter Id:E MTAB 7349:TUA|age:8|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:wild type genotype|individual:mixed pool of 30 to 50 embryos|organism part:notochord|sample name:E MTAB 7349:TUA|scientific name:Danio rerio|sex:mixed                 Illumina HiSeq 2500 paired end sequencing; Receptor Tyrosine Kinase pathway activation is sufficient to trigger chordoma in zebrafish E MTAB 7349:TUA p TUA p Receptor Tyrosine Kinase pathway activation is sufficient to trigger chordoma in zebrafish 8 dpf wildtype and Tgtwhh:Gal4;TgUAS:EGFP HRASV12 were euthanized with 3% Tricaine methanesulfonate Sigma. Embryos were decapitated and incubated in Tripsin EDTA Sigma for 30 minutes to facilitate tissue dissociation. Notochords were then dissected using tungsten needles and immediately transferred to Trizol LS Ambion. We isolated 30 50 notochords per replicate with a total of 3 replicates per condition 3x wildtype 3x HRASV12. Notochord RNA was extracted following the manufacturer's protocol using Trizol LS. RNA seq libraries were constructed using the Truseq stranded total RNA kit. Experimental Factor: genotype:wild type genotype RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP111743 Illumina HiSeq 2500 paired end sequencing; Receptor Tyrosine Kinase pathway activation is sufficient to trigger chordoma in zebrafish ENA FIRST PUBLIC:2018 12 01|ENA LAST UPDATE:2018 11 16 TCCGCGAA_AGGCTATA__160520_I127_FCH732GBBXX_L8_CDKPEI160513002_1.fq.gz TCCGCGAA_AGGCTATA__160520_I127_FCH732GBBXX_L8_CDKPEI160513002_2.fq.gz fastq fastq 11985547000.0 59927735.0 E MTAB 7349:TCCGCGAA AGGCTATA 160520 I127 FCH732GBBXX L8 CDKPEI160513002 0:100 1:100 A:3239652711;C:2732996991;G:2737809176;T:3273773368;N:1314754 100 100     3239652711 2732996991 2737809176 3273773368 1314754 ERX2868590 ERS2866327 ERA1640550 European Nucleotide Archive European Nucleotide Archive 2 0.91524 0.91585 0.32418 0.32053 0.72616 0.72671 0.59362 0.42478 100 100 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   Unknown 2018-10-30 Larval Larval Brain Nervous System
9334 9334 ERR2862351 ERX2868589 ERS2866326 ERP111743 PRJEB29441 Receptor Tyrosine Kinase pathway activation is sufficient to trigger chordoma in zebrafish E-MTAB-7349 Transcriptome Analysis Oncogenic transformation of individual cell fates by developmental signaling cascades and transcription factors triggers diverse cancer types. Chordoma is a rare aggressive tumor arising from transformed notochord remnants. Various potentially oncogenic factors have been found deregulated in chordoma and its metastases yet clear causation remains uncertain. In particular expression of the notochord controlling transcription factor Brachyury is hypothesized as key molecular driver in chordoma formation yet an in vivo model to causally test its oncogenic potential in the notochord is missing. Here we apply a zebrafish model of chordoma onset to identify the notochord transforming potential of tumor implicated candidate genes in vivo. We find that overexpression of human and zebrafish Brachyury including a version with augmented transcriptional activity is insufficient to initiate notochord hyperplasia in vivo. In contrast the repeatedly chordoma implicated receptor tyrosine kinase RTK genes EGFR and KDR/VEGFR2 are sufficient to transform developmental notochord cells akin to direct activation of Ras. Analysis of transcriptome and sub cellular organization from transformed notochords suggests that aberrant activation of RTK/Ras signaling attenuates processes required for the differentiation of notochord cells. Taken together our results provide first in vivo indication for a lack of tumor initiating potential of Brachyury expression in the notochord and suggest activated RTK signaling as potent hyperplasia initiating event in chordoma. ENA FIRST PUBLIC:2018 12 01|ENA LAST UPDATE:2018 10 30   Protocols: 8 dpf wildtype and Tgtwhh:Gal4;TgUAS:EGFP HRASV12 were euthanized with 3% Tricaine methanesulfonate Sigma. Embryos were decapitated and incubated in Tripsin EDTA Sigma for 30 minutes to facilitate tissue dissociation. Notochords were then dissected using tungsten needles and immediately transferred to Trizol LS Ambion. We isolated 30 50 notochords per replicate with a total of 3 replicates per condition 3x wildtype 3x HRASV12. Notochord RNA was extracted following the manufacturer's protocol using Trizol LS. RNA seq libraries were constructed using the Truseq stranded total RNA kit. HRASC SAMEA5055149 UZH ENA FIRST PUBLIC:2018 12 01T17:03:21Z|ENA LAST UPDATE:2018 10 30T13:30:13Z|External Id:SAMEA5055149|INSDC center name:UZH|INSDC first public:2018 12 01T17:03:21Z|INSDC last update:2018 10 30T13:30:13Z|INSDC status:public|Submitter Id:E MTAB 7349:HRASC|age:8|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:Tgtwhh:Gal4;TgUAS:EGFP HRASV12|individual:mixed pool of 30 to 50 embryos|organism part:notochord|sample name:E MTAB 7349:HRASC|scientific name:Danio rerio|sex:mixed                 Illumina HiSeq 2500 paired end sequencing; Receptor Tyrosine Kinase pathway activation is sufficient to trigger chordoma in zebrafish E MTAB 7349:HRASC p HRASC p Receptor Tyrosine Kinase pathway activation is sufficient to trigger chordoma in zebrafish 8 dpf wildtype and Tgtwhh:Gal4;TgUAS:EGFP HRASV12 were euthanized with 3% Tricaine methanesulfonate Sigma. Embryos were decapitated and incubated in Tripsin EDTA Sigma for 30 minutes to facilitate tissue dissociation. Notochords were then dissected using tungsten needles and immediately transferred to Trizol LS Ambion. We isolated 30 50 notochords per replicate with a total of 3 replicates per condition 3x wildtype 3x HRASV12. Notochord RNA was extracted following the manufacturer's protocol using Trizol LS. RNA seq libraries were constructed using the Truseq stranded total RNA kit. Experimental Factor: genotype:Tgtwhh:Gal4;TgUAS:EGFP HRASV12 RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP111743 Illumina HiSeq 2500 paired end sequencing; Receptor Tyrosine Kinase pathway activation is sufficient to trigger chordoma in zebrafish ENA FIRST PUBLIC:2018 12 01|ENA LAST UPDATE:2018 11 16 CGGCTATG_GTCAGTAC__160520_I127_FCH732GBBXX_L8_CDKPEI160513002_1.fq.gz CGGCTATG_GTCAGTAC__160520_I127_FCH732GBBXX_L8_CDKPEI160513002_2.fq.gz fastq fastq 11297151800.0 56485759.0 E MTAB 7349:CGGCTATG GTCAGTAC 160520 I127 FCH732GBBXX L8 CDKPEI160513002 0:100 1:100 A:3202944476;C:2429970659;G:2461948398;T:3201079699;N:1208568 100 100     3202944476 2429970659 2461948398 3201079699 1208568 ERX2868589 ERS2866326 ERA1640550 European Nucleotide Archive European Nucleotide Archive 2 0.89842 0.86269 0.32455 0.30708 0.74245 0.75191 0.7454 0.74185 100 100 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   Unknown 2018-10-30 Larval Larval Brain Nervous System
9335 9335 ERR2862350 ERX2868588 ERS2866325 ERP111743 PRJEB29441 Receptor Tyrosine Kinase pathway activation is sufficient to trigger chordoma in zebrafish E-MTAB-7349 Transcriptome Analysis Oncogenic transformation of individual cell fates by developmental signaling cascades and transcription factors triggers diverse cancer types. Chordoma is a rare aggressive tumor arising from transformed notochord remnants. Various potentially oncogenic factors have been found deregulated in chordoma and its metastases yet clear causation remains uncertain. In particular expression of the notochord controlling transcription factor Brachyury is hypothesized as key molecular driver in chordoma formation yet an in vivo model to causally test its oncogenic potential in the notochord is missing. Here we apply a zebrafish model of chordoma onset to identify the notochord transforming potential of tumor implicated candidate genes in vivo. We find that overexpression of human and zebrafish Brachyury including a version with augmented transcriptional activity is insufficient to initiate notochord hyperplasia in vivo. In contrast the repeatedly chordoma implicated receptor tyrosine kinase RTK genes EGFR and KDR/VEGFR2 are sufficient to transform developmental notochord cells akin to direct activation of Ras. Analysis of transcriptome and sub cellular organization from transformed notochords suggests that aberrant activation of RTK/Ras signaling attenuates processes required for the differentiation of notochord cells. Taken together our results provide first in vivo indication for a lack of tumor initiating potential of Brachyury expression in the notochord and suggest activated RTK signaling as potent hyperplasia initiating event in chordoma. ENA FIRST PUBLIC:2018 12 01|ENA LAST UPDATE:2018 10 30   Protocols: 8 dpf wildtype and Tgtwhh:Gal4;TgUAS:EGFP HRASV12 were euthanized with 3% Tricaine methanesulfonate Sigma. Embryos were decapitated and incubated in Tripsin EDTA Sigma for 30 minutes to facilitate tissue dissociation. Notochords were then dissected using tungsten needles and immediately transferred to Trizol LS Ambion. We isolated 30 50 notochords per replicate with a total of 3 replicates per condition 3x wildtype 3x HRASV12. Notochord RNA was extracted following the manufacturer's protocol using Trizol LS. RNA seq libraries were constructed using the Truseq stranded total RNA kit. HRASB 1A SAMEA5055148 UZH ENA FIRST PUBLIC:2018 12 01T17:03:21Z|ENA LAST UPDATE:2018 10 30T13:30:13Z|External Id:SAMEA5055148|INSDC center name:UZH|INSDC first public:2018 12 01T17:03:21Z|INSDC last update:2018 10 30T13:30:13Z|INSDC status:public|Submitter Id:E MTAB 7349:HRASB 1A|age:8|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:Tgtwhh:Gal4;TgUAS:EGFP HRASV12|individual:mixed pool of 30 to 50 embryos|organism part:notochord|sample name:E MTAB 7349:HRASB 1A|scientific name:Danio rerio|sex:mixed                 Illumina HiSeq 2500 paired end sequencing; Receptor Tyrosine Kinase pathway activation is sufficient to trigger chordoma in zebrafish E MTAB 7349:HRASB 1A p HRASB 1A p Receptor Tyrosine Kinase pathway activation is sufficient to trigger chordoma in zebrafish 8 dpf wildtype and Tgtwhh:Gal4;TgUAS:EGFP HRASV12 were euthanized with 3% Tricaine methanesulfonate Sigma. Embryos were decapitated and incubated in Tripsin EDTA Sigma for 30 minutes to facilitate tissue dissociation. Notochords were then dissected using tungsten needles and immediately transferred to Trizol LS Ambion. We isolated 30 50 notochords per replicate with a total of 3 replicates per condition 3x wildtype 3x HRASV12. Notochord RNA was extracted following the manufacturer's protocol using Trizol LS. RNA seq libraries were constructed using the Truseq stranded total RNA kit. Experimental Factor: genotype:Tgtwhh:Gal4;TgUAS:EGFP HRASV12 RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP111743 Illumina HiSeq 2500 paired end sequencing; Receptor Tyrosine Kinase pathway activation is sufficient to trigger chordoma in zebrafish ENA FIRST PUBLIC:2018 12 01|ENA LAST UPDATE:2018 11 16 TCTCGCGC_GTCAGTAC__160520_I127_FCH732GBBXX_L8_CDKPEI160513002_1.fq.gz TCTCGCGC_GTCAGTAC__160520_I127_FCH732GBBXX_L8_CDKPEI160513002_2.fq.gz fastq fastq 13035635000.0 65178175.0 E MTAB 7349:TCTCGCGC GTCAGTAC 160520 I127 FCH732GBBXX L8 CDKPEI160513002 0:100 1:100 A:3518767071;C:2991842048;G:3005014068;T:3518541297;N:1470516 100 100     3518767071 2991842048 3005014068 3518541297 1470516 ERX2868588 ERS2866325 ERA1640550 European Nucleotide Archive European Nucleotide Archive 2 0.89434 0.89384 0.28234 0.28093 0.7274 0.72813 0.6198 0.62424 100 100 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   Unknown 2018-10-30 Larval Larval Brain Nervous System
9336 9336 ERR2862349 ERX2868587 ERS2866324 ERP111743 PRJEB29441 Receptor Tyrosine Kinase pathway activation is sufficient to trigger chordoma in zebrafish E-MTAB-7349 Transcriptome Analysis Oncogenic transformation of individual cell fates by developmental signaling cascades and transcription factors triggers diverse cancer types. Chordoma is a rare aggressive tumor arising from transformed notochord remnants. Various potentially oncogenic factors have been found deregulated in chordoma and its metastases yet clear causation remains uncertain. In particular expression of the notochord controlling transcription factor Brachyury is hypothesized as key molecular driver in chordoma formation yet an in vivo model to causally test its oncogenic potential in the notochord is missing. Here we apply a zebrafish model of chordoma onset to identify the notochord transforming potential of tumor implicated candidate genes in vivo. We find that overexpression of human and zebrafish Brachyury including a version with augmented transcriptional activity is insufficient to initiate notochord hyperplasia in vivo. In contrast the repeatedly chordoma implicated receptor tyrosine kinase RTK genes EGFR and KDR/VEGFR2 are sufficient to transform developmental notochord cells akin to direct activation of Ras. Analysis of transcriptome and sub cellular organization from transformed notochords suggests that aberrant activation of RTK/Ras signaling attenuates processes required for the differentiation of notochord cells. Taken together our results provide first in vivo indication for a lack of tumor initiating potential of Brachyury expression in the notochord and suggest activated RTK signaling as potent hyperplasia initiating event in chordoma. ENA FIRST PUBLIC:2018 12 01|ENA LAST UPDATE:2018 10 30   Protocols: 8 dpf wildtype and Tgtwhh:Gal4;TgUAS:EGFP HRASV12 were euthanized with 3% Tricaine methanesulfonate Sigma. Embryos were decapitated and incubated in Tripsin EDTA Sigma for 30 minutes to facilitate tissue dissociation. Notochords were then dissected using tungsten needles and immediately transferred to Trizol LS Ambion. We isolated 30 50 notochords per replicate with a total of 3 replicates per condition 3x wildtype 3x HRASV12. Notochord RNA was extracted following the manufacturer's protocol using Trizol LS. RNA seq libraries were constructed using the Truseq stranded total RNA kit. 2A SAMEA5055147 UZH ENA FIRST PUBLIC:2018 12 01T17:03:21Z|ENA LAST UPDATE:2018 10 30T13:30:13Z|External Id:SAMEA5055147|INSDC center name:UZH|INSDC first public:2018 12 01T17:03:21Z|INSDC last update:2018 10 30T13:30:13Z|INSDC status:public|Submitter Id:E MTAB 7349:2A|age:8|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:Tgtwhh:Gal4;TgUAS:EGFP HRASV12|individual:mixed pool of 30 to 50 embryos|organism part:notochord|sample name:E MTAB 7349:2A|scientific name:Danio rerio|sex:mixed                 Illumina HiSeq 2500 paired end sequencing; Receptor Tyrosine Kinase pathway activation is sufficient to trigger chordoma in zebrafish E MTAB 7349:2A p 2A p Receptor Tyrosine Kinase pathway activation is sufficient to trigger chordoma in zebrafish 8 dpf wildtype and Tgtwhh:Gal4;TgUAS:EGFP HRASV12 were euthanized with 3% Tricaine methanesulfonate Sigma. Embryos were decapitated and incubated in Tripsin EDTA Sigma for 30 minutes to facilitate tissue dissociation. Notochords were then dissected using tungsten needles and immediately transferred to Trizol LS Ambion. We isolated 30 50 notochords per replicate with a total of 3 replicates per condition 3x wildtype 3x HRASV12. Notochord RNA was extracted following the manufacturer's protocol using Trizol LS. RNA seq libraries were constructed using the Truseq stranded total RNA kit. Experimental Factor: genotype:Tgtwhh:Gal4;TgUAS:EGFP HRASV12 RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP111743 Illumina HiSeq 2500 paired end sequencing; Receptor Tyrosine Kinase pathway activation is sufficient to trigger chordoma in zebrafish ENA FIRST PUBLIC:2018 12 01|ENA LAST UPDATE:2018 11 16 TCCGCGAA_GTCAGTAC__160520_I127_FCH732GBBXX_L8_CDKPEI160513002_2.fq.gz TCCGCGAA_GTCAGTAC__160520_I127_FCH732GBBXX_L8_CDKPEI160513002_1.fq.gz fastq fastq 11671772800.0 58358864.0 E MTAB 7349:TCCGCGAA GTCAGTAC 160520 I127 FCH732GBBXX L8 CDKPEI160513002 0:100 1:100 A:3164806186;C:2661342106;G:2677258036;T:3167072669;N:1293803 100 100     3164806186 2661342106 2677258036 3167072669 1293803 ERX2868587 ERS2866324 ERA1640550 European Nucleotide Archive European Nucleotide Archive 2 0.89879 0.89878 0.28162 0.28061 0.73212 0.73452 0.59632 0.60115 100 100 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   Unknown 2018-10-30 Larval Larval Brain Nervous System
10391 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>102</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>52</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> 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 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 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP062493     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 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 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP062493     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 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 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP062493     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 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 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP062493     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 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 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP062493     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 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 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP062493     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 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 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP062493     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 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 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP062493     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 39835 SRR2382596 SRX1321825 SRS1109647 SRP062493 PRJNA293106 Danio rerio Raw sequence reads PRJNA293106 Metagenomics Zebrafish Hypoxia RNAseq     RNAseq at 72hpf following normoxia   72hpf normoxia   strain:TU|age:72hpf|sex:not determined|tissue:brain|treatment:normoxia|BioSampleModel:Model organism or animal                 Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample 72hpf normoxia 72hpf.normoxia.3.10329X30 72hpf.normoxia.3.10329X30 We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition. For hypoxia we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected. We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages. At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation. RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer. The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides single end stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.     RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP062493     10329X30_130822_SN141_0719_AD2CK5ACXX_8.txt.gz fastq 1202543000.0 24050860.0 72hpf.normoxia.3.10329X30 0:50 A:317814132;C:265339479;G:263354488;T:356015292;N:19609 50       317814132 265339479 263354488 356015292 19609 SRX1321825 SRS1109647 SRA289450 University of Utah|Bonkowsky University of Utah 1 0.94396   0.39792   0.68592   0.51696   50   B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   United States 2015-10-10 Larval Larval Brain Nervous System
39836 39836 SRR2346975 SRX1321824 SRS1109649 SRP062493 PRJNA293106 Danio rerio Raw sequence reads PRJNA293106 Metagenomics Zebrafish Hypoxia RNAseq     RNAseq at 72hpf following hypoxia   72hpf hypoxia   strain:TU|age:72hpf|sex:not determined|tissue:brain|treatment:hypoxia|BioSampleModel:Model organism or animal                 Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample 72hpf hypoxia 72hpf.hypoxia.3.10329X29 72hpf.hypoxia.3.10329X29 We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition. For hypoxia we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected. We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages. At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation. RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer. The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides single end stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.     RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP062493     10329X29_130822_SN141_0719_AD2CK5ACXX_8.txt.gz fastq 977694000.0 19553880.0 72hpf.hypoxia.3.10329X29 0:50 A:252845467;C:218082615;G:213237499;T:293512810;N:15609 50       252845467 218082615 213237499 293512810 15609 SRX1321824 SRS1109649 SRA289450 University of Utah|Bonkowsky University of Utah 1 0.94858   0.35206   0.68889   0.53177   50   B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   United States 2015-09-10 Larval Larval Brain Nervous System
39837 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 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP062493     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 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 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP062493     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 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 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP062493     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 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 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP062493     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 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 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP062493     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 39842 SRR2243358 SRX1321818 SRS1109647 SRP062493 PRJNA293106 Danio rerio Raw sequence reads PRJNA293106 Metagenomics Zebrafish Hypoxia RNAseq     RNAseq at 72hpf following normoxia   72hpf normoxia   strain:TU|age:72hpf|sex:not determined|tissue:brain|treatment:normoxia|BioSampleModel:Model organism or animal                 Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample 72hpf normoxia 72hpf.normoxia.2.10329X20 72hpf.normoxia.2.10329X20 We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition. For hypoxia we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected. We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages. At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation. RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer. The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides single end stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.     RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP062493     10329X20_130822_SN141_0719_AD2CK5ACXX_7.txt.gz fastq 1530276050.0 30605521.0 72hpf.normoxia.2.10329X20 0:50 A:387360143;C:340062704;G:324515181;T:458965961;N:19372061 50       387360143 340062704 324515181 458965961 19372061 SRX1321818 SRS1109647 SRA289450 University of Utah|Bonkowsky University of Utah 1 0.8774   0.25469   0.68799   0.52777   50   B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   United States 2015-10-10 Larval Larval Brain Nervous System
39843 39843 SRR2243161 SRX1321817 SRS1109649 SRP062493 PRJNA293106 Danio rerio Raw sequence reads PRJNA293106 Metagenomics Zebrafish Hypoxia RNAseq     RNAseq at 72hpf following hypoxia   72hpf hypoxia   strain:TU|age:72hpf|sex:not determined|tissue:brain|treatment:hypoxia|BioSampleModel:Model organism or animal                 Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample 72hpf hypoxia 72hpf.hypoxia.2.10329X19 72hpf.hypoxia.2.10329X19 We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition. For hypoxia we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected. We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages. At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation. RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer. The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides single end stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.     RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP062493     10329X19_130822_SN141_0719_AD2CK5ACXX_7.txt.gz fastq 1866619850.0 37332397.0 72hpf.hypoxia.2.10329X19 0:50 A:465524152;C:423400277;G:418937882;T:535202326;N:23555213 50       465524152 423400277 418937882 535202326 23555213 SRX1321817 SRS1109649 SRA289450 University of Utah|Bonkowsky University of Utah 1 0.85514   0.26828   0.7041   0.54006   50   B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   United States 2015-10-10 Larval Larval Brain Nervous System
39844 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 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP062493     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 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 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP062493     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 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 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP062493     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 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 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP062493     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 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 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP062493     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 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 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP062493     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 39850 SRR2227378 SRX1321810 SRS1109647 SRP062493 PRJNA293106 Danio rerio Raw sequence reads PRJNA293106 Metagenomics Zebrafish Hypoxia RNAseq     RNAseq at 72hpf following normoxia   72hpf normoxia   strain:TU|age:72hpf|sex:not determined|tissue:brain|treatment:normoxia|BioSampleModel:Model organism or animal                 Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample 72hpf normoxia 72hpf.normoxia.1.10329X10 72hpf.normoxia.1.10329X10 We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition. For hypoxia we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected. We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages. At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation. RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer. The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides single end stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.     RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP062493     10329X10_130822_SN141_0719_AD2CK5ACXX_5.txt.gz fastq 1268552500.0 25371050.0 72hpf.normoxia.1.10329X10 0:50 A:334230065;C:286785060;G:271795849;T:375668734;N:72792 50       334230065 286785060 271795849 375668734 72792 SRX1321810 SRS1109647 SRA289450 University of Utah|Bonkowsky University of Utah 1 0.94017   0.34471   0.67109   0.5244   50   B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   United States 2015-09-18 Larval Larval Brain Nervous System
39851 39851 SRR2226742 SRX1321809 SRS1109649 SRP062493 PRJNA293106 Danio rerio Raw sequence reads PRJNA293106 Metagenomics Zebrafish Hypoxia RNAseq     RNAseq at 72hpf following hypoxia   72hpf hypoxia   strain:TU|age:72hpf|sex:not determined|tissue:brain|treatment:hypoxia|BioSampleModel:Model organism or animal                 Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample 72hpf hypoxia 72hpf.hypoxia.1.10329X9 72hpf.hypoxia.1.10329X9 We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition. For hypoxia we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected. We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages. At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation. RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer. The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides single end stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.     RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP062493     10329X9_130822_SN141_0719_AD2CK5ACXX_5.txt.gz fastq 1625518100.0 32510362.0 72hpf.hypoxia.1.10329X9 0:50 A:428393257;C:366720934;G:349089971;T:481221434;N:92504 50       428393257 366720934 349089971 481221434 92504 SRX1321809 SRS1109649 SRA289450 University of Utah|Bonkowsky University of Utah 1 0.9444   0.36232   0.67503   0.53278   50   B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   United States 2015-10-10 Larval Larval Brain Nervous System
39852 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 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP062493     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 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 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP062493     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 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 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP062493     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 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 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP062493     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 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 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP062493     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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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
74405 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 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 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 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 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 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

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;