RNAquarium Metadata Server
Institute Website Terms of Use Privacy Policy

run_metadata

92 rows where experiment.library_selection = "RANDOM" and tissue_curation_coarse = "Surface Structure"

✎ View and edit SQL

This data as json, CSV (advanced)

tissue_curation 4

devstage_curation_coarse 3

devstage_curation 3

technology 2

experiment.platform 2

experiment.library_strategy 2

experiment.library_source 2

experiment.library_layout 2

tissue_curation_coarse 1

  • Surface Structure · 92 ✖

experiment.library_selection 1

  • RANDOM · 92 ✖
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
28383 28383 SRR26319642 SRX22027776 SRS19100884 SRP463771 PRJNA1022139 Danio rerio strain:AB Transcriptome or Gene expression PRJNA1022139 Other Effects and Mechanisms of Porphyromonas gingivalis Outer Membrane Vesicles Induced Cardiovascular Injury         WT 3   strain:AB|age:larvae|dev stage:48 hpi|collection date:2022 11 06|geo loc name:China:Fujian|sex:not applicable|tissue:Whole body|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio:PBS treated WT 3 WT 3 PBS treated     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   SRP463771     WT_3_1.fq.gz WT_3_2.fq.gz fastq fastq 6638052600.0 22126842.0 WT 3 1.fq.gz 0:150 1:150 A:1795389898;C:1548955123;G:1524873816;T:1768758791;N:74972 150 150     1795389898 1548955123 1524873816 1768758791 74972 SRX22027776 SRS19100884 SRA1727571 Hospital of Stomatology, Fujian Medical University|Department of Orthodontics Hospital of Stomatology, Fujian Medical University 2 0.94512 0.94441 0.0675 0.06744 0.69457 0.69353 0.47279 0.46651 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2023-10-11 Larval Larval Trunk Surface Structure
28384 28384 SRR26316552 SRX22024811 SRS19097993 SRP463771 PRJNA1022139 Danio rerio strain:AB Transcriptome or Gene expression PRJNA1022139 Other Effects and Mechanisms of Porphyromonas gingivalis Outer Membrane Vesicles Induced Cardiovascular Injury       WT 1 WT 1   strain:AB|age:larvae|dev stage:48 hpi|collection date:2022 11 06|geo loc name:China:Fujian|sex:not applicable|tissue:Whole body|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio:PBS treated WT 1 WT 1 PBS treated     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   SRP463771     WT_1_1.fq.gz WT_1_2.fq.gz fastq fastq 6806096700.0 22686989.0 WT 1 1.fq.gz 0:150 1:150 A:1824700900;C:1607509679;G:1583685250;T:1790098957;N:101914 150 150     1824700900 1607509679 1583685250 1790098957 101914 SRX22024811 SRS19097993 SRA1727466 Hospital of Stomatology, Fujian Medical University|Department of Orthodontics Hospital of Stomatology, Fujian Medical University 2 0.94441 0.94413 0.0633 0.06243 0.69589 0.69603 0.47278 0.46311 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2023-10-11 Larval Larval Trunk Surface Structure
28385 28385 SRR26298124 SRX22006623 SRS19081287 SRP463771 PRJNA1022139 Danio rerio strain:AB Transcriptome or Gene expression PRJNA1022139 Other Effects and Mechanisms of Porphyromonas gingivalis Outer Membrane Vesicles Induced Cardiovascular Injury       Pg OMVs 3 Pg OMVs 3   strain:AB|age:larvae|dev stage:48 hpi|collection date:2022 11 06|geo loc name:China:Fujian|sex:not applicable|tissue:whole body|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio:Pg OMVs treated Pg OMVs 3 Pg OMVs 3 Pg OMVs treated     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   SRP463771     Pgom_3_1.fq.gz Pgom_3_2.fq.gz fastq fastq 6799556700.0 22665189.0 Pgom 3 1.fq.gz 0:150 1:150 A:1841955583;C:1578686846;G:1566584129;T:1812024582;N:305560 150 150     1841955583 1578686846 1566584129 1812024582 305560 SRX22006623 SRS19081287 SRA1726653 Hospital of Stomatology, Fujian Medical University|Department of Orthodontics Hospital of Stomatology, Fujian Medical University 2 0.93679 0.93643 0.0705 0.07046 0.69522 0.69572 0.46657 0.46769 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2023-10-09 Larval Larval Trunk Surface Structure
28386 28386 SRR26284600 SRX21993532 SRS19068394 SRP463771 PRJNA1022139 Danio rerio strain:AB Transcriptome or Gene expression PRJNA1022139 Other Effects and Mechanisms of Porphyromonas gingivalis Outer Membrane Vesicles Induced Cardiovascular Injury       Pg OMVs 2 Pg OMVs 2   strain:AB|age:larvae|dev stage:48 hpi|collection date:2022 11 06|geo loc name:China:Fujian|sex:not applicable|tissue:whole body|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio:Pg OMVs treated Pg OMVs 2 Pg OMVs 2 Pg OMVs treated     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   SRP463771     Pgom_2_2.fq.gz Pgom_2_1.fq.gz fastq fastq 6873087300.0 22910291.0 Pgom 2 1.fq.gz 0:150 1:150 A:1852244290;C:1608380801;G:1593161224;T:1819219541;N:81444 150 150     1852244290 1608380801 1593161224 1819219541 81444 SRX21993532 SRS19068394 SRA1726180 Hospital of Stomatology, Fujian Medical University|Department of Orthodontics Hospital of Stomatology, Fujian Medical University 2 0.93991 0.93977 0.06917 0.06976 0.68883 0.68931 0.47575 0.45981 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2023-10-06 Larval Larval Trunk Surface Structure
28387 28387 SRR26283523 SRX21992473 SRS19067399 SRP463771 PRJNA1022139 Danio rerio strain:AB Transcriptome or Gene expression PRJNA1022139 Other Effects and Mechanisms of Porphyromonas gingivalis Outer Membrane Vesicles Induced Cardiovascular Injury         WT 2   strain:AB|age:larvae|dev stage:48 hpi|collection date:2022 11 06|geo loc name:China:Fujian|sex:not applicable|tissue:whole body|BioSampleModel:Model organism or animal                 not applicable not applicable not applicable wild type     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   SRP463771     WT_2_1.fq.gz WT_2_2.fq.gz fastq fastq 6662879700.0 22209599.0 WT 2 1.fq.gz 0:150 1:150 A:1793163738;C:1560948295;G:1543048656;T:1765563975;N:155036 150 150     1793163738 1560948295 1543048656 1765563975 155036 SRX21992473 SRS19067399 SRA1726064 Hospital of Stomatology, Fujian Medical University|Department of Orthodontics Hospital of Stomatology, Fujian Medical University 2 0.94479 0.94546 0.06315 0.06307 0.69751 0.69627 0.46332 0.45959 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2023-10-06 Larval Larval Trunk Surface Structure
28388 28388 SRR26213372 SRX21923899 SRS19008410 SRP463771 PRJNA1022139 Danio rerio strain:AB Transcriptome or Gene expression PRJNA1022139 Other Effects and Mechanisms of Porphyromonas gingivalis Outer Membrane Vesicles Induced Cardiovascular Injury       Model organism or animal sample from Danio rerio Pg OMVs 1 a   strain:AB|dev stage:larvae|collection date:2022 11 06|geo loc name:China:Fujian|sex:not applicable|tissue:whole body|treatment:Pg OMVs injected|BioSampleModel:Model organism or animal                 RNA seq of zebrafish:48 hpi Pg OMVs group1a Pg OMVs group1a Pg OMVs injected     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   SRP463771     Pgom_1_1.fq.gz Pgom_1_2.fq.gz fastq fastq 6768097800.0 22560326.0 Pgom 1 1.fq.gz 0:150 1:150 A:1807197563;C:1591333381;G:1591884474;T:1777600011;N:82371 150 150     1807197563 1591333381 1591884474 1777600011 82371 SRX21923899 SRS19008410 SRA1722765 Hospital of Stomatology, Fujian Medical University|Department of Orthodontics Hospital of Stomatology, Fujian Medical University 2 0.93975 0.93898 0.05827 0.05801 0.68521 0.68517 0.46882 0.46802 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2023-09-28 Larval Larval Trunk Surface Structure
31473 31473 SRR28362822 SRX23967985 SRS20767216 SRP495638 PRJNA1088730 Effects of noxo1a deficiency on gene expression in zebrafish larvae upon exposure to cold warm stress PRJNA1088730 Other Exposure of fish to cold warm stress was reported to elicit ROS generation and subsequent tissue damage. On the other hand ROS signaling is essential for many physiological functions of the organism. As a NADPH oxidase NOX organizer deficiency of Noxo1a is expected to decrease the content of hydrogen peroxide in fish tissue upon exposure to cold warm stress. In this study the effect on Noxo1a deficiency on gene expression in zebrafish larvae under cold warm stress was characterized by RNA sequencing.       WT re#2 WT re#2   strain:AB strain|dev stage:Larvae|collection date:2023 03 05|geo loc name:China: Wuhan|sex:not determined|tissue:Whole body|genotype:Wild type|treatment:Exposed to 10 °C for 12 h followed by recovery at 28 °C for 6 h|replicate:replicate = biological replicate 2|BioSampleModel:Model organism or animal                 WT re#2 WT re#2 WT re#2 One microgram total RNA from each sample was used as the beginning material for sequencing library construction. Each treatment included 4 biological replicates. The NEBNext rRNA Depletion Kit was used for rRNA depletion. post rRNA depletion Agencourt RNAClean XP Beads from Beckman Coulter were used for RNA purification. Then the NEBNext Ultra Directional RNA Library Prep Kit for Illumina was used for RNA fragmentation first and second strand cDNA synthesis double stranded cDNA end repair. Double strand cDNAs were purified using the Agencourt AMPure XP from Beckman Coulter and ligated to adaptors of NEBNext Multiplex Oligos for Illumina. Finally the Q5 Hot Start HiFi PCR Master Mix was used for PCR enrichment of the adaptor ligated DNA. The concentration and quality of the constructed sequencing libraries were measured by using the Agilent High Sensitivity DNA Kit and a Bioanalyzer 2100 from Agilent Technologies. The libraries were submitted to 51 bp single end high throughput sequencing by the Center for Advanced Technology CAT of the University of California San Francisco using Hiseq 3000.     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   SRP495638     wt-re-2_S42_L004_R1_001.fastq.gz wt-re-2_S42_L004_R2_001.fastq.gz fastq fastq 7360107300.0 24533691.0 wt re 2 S42 L004 R1 001.fastq.gz 0:150 1:150 A:1953410192;C:1717566713;G:1749971750;T:1938773172;N:385473 150 150     1953410192 1717566713 1749971750 1938773172 385473 SRX23967985 SRS20767216 SRA1825819 Chinese Academy of Sciences|Institute of Hydrobiology Chinese Academy of Sciences                       B B biological fallback assumption illumina novaseq_era unknown random_priming nebnext bulk unknown unknown   China 2024-03-16 Larval Larval Trunk Surface Structure
31474 31474 SRR28362829 SRX23967984 SRS20767215 SRP495638 PRJNA1088730 Effects of noxo1a deficiency on gene expression in zebrafish larvae upon exposure to cold warm stress PRJNA1088730 Other Exposure of fish to cold warm stress was reported to elicit ROS generation and subsequent tissue damage. On the other hand ROS signaling is essential for many physiological functions of the organism. As a NADPH oxidase NOX organizer deficiency of Noxo1a is expected to decrease the content of hydrogen peroxide in fish tissue upon exposure to cold warm stress. In this study the effect on Noxo1a deficiency on gene expression in zebrafish larvae under cold warm stress was characterized by RNA sequencing.       WT re#1 WT re#1   strain:AB strain|dev stage:Larvae|collection date:2023 03 05|geo loc name:China: Wuhan|sex:not determined|tissue:Whole body|genotype:Wild type|treatment:Exposed to 10 °C for 12 h followed by recovery at 28 °C for 6 h|replicate:replicate = biological replicate 1|BioSampleModel:Model organism or animal                 WT re#1 WT re#1 WT re#1 One microgram total RNA from each sample was used as the beginning material for sequencing library construction. Each treatment included 4 biological replicates. The NEBNext rRNA Depletion Kit was used for rRNA depletion. post rRNA depletion Agencourt RNAClean XP Beads from Beckman Coulter were used for RNA purification. Then the NEBNext Ultra Directional RNA Library Prep Kit for Illumina was used for RNA fragmentation first and second strand cDNA synthesis double stranded cDNA end repair. Double strand cDNAs were purified using the Agencourt AMPure XP from Beckman Coulter and ligated to adaptors of NEBNext Multiplex Oligos for Illumina. Finally the Q5 Hot Start HiFi PCR Master Mix was used for PCR enrichment of the adaptor ligated DNA. The concentration and quality of the constructed sequencing libraries were measured by using the Agilent High Sensitivity DNA Kit and a Bioanalyzer 2100 from Agilent Technologies. The libraries were submitted to 51 bp single end high throughput sequencing by the Center for Advanced Technology CAT of the University of California San Francisco using Hiseq 3000.     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   SRP495638     wt-re-1_S41_L004_R1_001.fastq.gz wt-re-1_S41_L004_R2_001.fastq.gz wt-re-1_S6_L002_R1_001.fastq.gz wt-re-1_S6_L002_R2_001.fastq.gz fastq fastq fastq fastq 7304976300.0 24349921.0 wt re 1 S41 L004 R1 001.fastq.gz 0:150 1:150 A:1931654450;C:1711483982;G:1750280300;T:1911082544;N:475024 150 150     1931654450 1711483982 1750280300 1911082544 475024 SRX23967984 SRS20767215 SRA1825819 Chinese Academy of Sciences|Institute of Hydrobiology Chinese Academy of Sciences                       B B biological fallback assumption illumina novaseq_era unknown random_priming nebnext bulk unknown unknown   China 2024-03-16 Larval Larval Trunk Surface Structure
31475 31475 SRR28362823 SRX23967983 SRS20767214 SRP495638 PRJNA1088730 Effects of noxo1a deficiency on gene expression in zebrafish larvae upon exposure to cold warm stress PRJNA1088730 Other Exposure of fish to cold warm stress was reported to elicit ROS generation and subsequent tissue damage. On the other hand ROS signaling is essential for many physiological functions of the organism. As a NADPH oxidase NOX organizer deficiency of Noxo1a is expected to decrease the content of hydrogen peroxide in fish tissue upon exposure to cold warm stress. In this study the effect on Noxo1a deficiency on gene expression in zebrafish larvae under cold warm stress was characterized by RNA sequencing.       WT cs#4 WT cs#4   strain:AB strain|dev stage:Larvae|collection date:2023 03 05|geo loc name:China: Wuhan|sex:not determined|tissue:Whole body|genotype:Wild type|treatment:Exposed to 10 °C for 12 h|replicate:replicate = biological replicate 4|BioSampleModel:Model organism or animal                 WT cs#4 WT cs#4 WT cs#4 One microgram total RNA from each sample was used as the beginning material for sequencing library construction. Each treatment included 4 biological replicates. The NEBNext rRNA Depletion Kit was used for rRNA depletion. post rRNA depletion Agencourt RNAClean XP Beads from Beckman Coulter were used for RNA purification. Then the NEBNext Ultra Directional RNA Library Prep Kit for Illumina was used for RNA fragmentation first and second strand cDNA synthesis double stranded cDNA end repair. Double strand cDNAs were purified using the Agencourt AMPure XP from Beckman Coulter and ligated to adaptors of NEBNext Multiplex Oligos for Illumina. Finally the Q5 Hot Start HiFi PCR Master Mix was used for PCR enrichment of the adaptor ligated DNA. The concentration and quality of the constructed sequencing libraries were measured by using the Agilent High Sensitivity DNA Kit and a Bioanalyzer 2100 from Agilent Technologies. The libraries were submitted to 51 bp single end high throughput sequencing by the Center for Advanced Technology CAT of the University of California San Francisco using Hiseq 3000.     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   SRP495638     wt-cs-4_S38_L004_R1_001.fastq.gz wt-cs-4_S38_L004_R2_001.fastq.gz fastq fastq 7117266300.0 23724221.0 wt cs 4 S38 L004 R1 001.fastq.gz 0:150 1:150 A:1893835105;C:1654405982;G:1690442550;T:1878207126;N:375537 150 150     1893835105 1654405982 1690442550 1878207126 375537 SRX23967983 SRS20767214 SRA1825819 Chinese Academy of Sciences|Institute of Hydrobiology Chinese Academy of Sciences                       B B biological fallback assumption illumina novaseq_era unknown random_priming nebnext bulk unknown unknown   China 2024-03-16 Larval Larval Trunk Surface Structure
31476 31476 SRR28362824 SRX23967982 SRS20767213 SRP495638 PRJNA1088730 Effects of noxo1a deficiency on gene expression in zebrafish larvae upon exposure to cold warm stress PRJNA1088730 Other Exposure of fish to cold warm stress was reported to elicit ROS generation and subsequent tissue damage. On the other hand ROS signaling is essential for many physiological functions of the organism. As a NADPH oxidase NOX organizer deficiency of Noxo1a is expected to decrease the content of hydrogen peroxide in fish tissue upon exposure to cold warm stress. In this study the effect on Noxo1a deficiency on gene expression in zebrafish larvae under cold warm stress was characterized by RNA sequencing.       WT cs#3 WT cs#3   strain:AB strain|dev stage:Larvae|collection date:2023 03 05|geo loc name:China: Wuhan|sex:not determined|tissue:Whole body|genotype:Wild type|treatment:Exposed to 10 °C for 12 h|replicate:replicate = biological replicate 3|BioSampleModel:Model organism or animal                 WT cs#3 WT cs#3 WT cs#3 One microgram total RNA from each sample was used as the beginning material for sequencing library construction. Each treatment included 4 biological replicates. The NEBNext rRNA Depletion Kit was used for rRNA depletion. post rRNA depletion Agencourt RNAClean XP Beads from Beckman Coulter were used for RNA purification. Then the NEBNext Ultra Directional RNA Library Prep Kit for Illumina was used for RNA fragmentation first and second strand cDNA synthesis double stranded cDNA end repair. Double strand cDNAs were purified using the Agencourt AMPure XP from Beckman Coulter and ligated to adaptors of NEBNext Multiplex Oligos for Illumina. Finally the Q5 Hot Start HiFi PCR Master Mix was used for PCR enrichment of the adaptor ligated DNA. The concentration and quality of the constructed sequencing libraries were measured by using the Agilent High Sensitivity DNA Kit and a Bioanalyzer 2100 from Agilent Technologies. The libraries were submitted to 51 bp single end high throughput sequencing by the Center for Advanced Technology CAT of the University of California San Francisco using Hiseq 3000.     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   SRP495638     wt-cs-3_S37_L004_R1_001.fastq.gz wt-cs-3_S37_L004_R2_001.fastq.gz fastq fastq 7766755500.0 25889185.0 wt cs 3 S37 L004 R1 001.fastq.gz 0:150 1:150 A:2066456864;C:1808454260;G:1837135016;T:2054303347;N:406013 150 150     2066456864 1808454260 1837135016 2054303347 406013 SRX23967982 SRS20767213 SRA1825819 Chinese Academy of Sciences|Institute of Hydrobiology Chinese Academy of Sciences                       B B biological fallback assumption illumina novaseq_era unknown random_priming nebnext bulk unknown unknown   China 2024-03-16 Larval Larval Trunk Surface Structure
31477 31477 SRR28362825 SRX23967981 SRS20767212 SRP495638 PRJNA1088730 Effects of noxo1a deficiency on gene expression in zebrafish larvae upon exposure to cold warm stress PRJNA1088730 Other Exposure of fish to cold warm stress was reported to elicit ROS generation and subsequent tissue damage. On the other hand ROS signaling is essential for many physiological functions of the organism. As a NADPH oxidase NOX organizer deficiency of Noxo1a is expected to decrease the content of hydrogen peroxide in fish tissue upon exposure to cold warm stress. In this study the effect on Noxo1a deficiency on gene expression in zebrafish larvae under cold warm stress was characterized by RNA sequencing.       WT cs#2 WT cs#2   strain:AB strain|dev stage:Larvae|collection date:2023 03 05|geo loc name:China: Wuhan|sex:not determined|tissue:Whole body|genotype:Wild type|treatment:Exposed to 10 °C for 12 h|replicate:replicate = biological replicate 2|BioSampleModel:Model organism or animal                 WT cs#2 WT cs#2 WT cs#2 One microgram total RNA from each sample was used as the beginning material for sequencing library construction. Each treatment included 4 biological replicates. The NEBNext rRNA Depletion Kit was used for rRNA depletion. post rRNA depletion Agencourt RNAClean XP Beads from Beckman Coulter were used for RNA purification. Then the NEBNext Ultra Directional RNA Library Prep Kit for Illumina was used for RNA fragmentation first and second strand cDNA synthesis double stranded cDNA end repair. Double strand cDNAs were purified using the Agencourt AMPure XP from Beckman Coulter and ligated to adaptors of NEBNext Multiplex Oligos for Illumina. Finally the Q5 Hot Start HiFi PCR Master Mix was used for PCR enrichment of the adaptor ligated DNA. The concentration and quality of the constructed sequencing libraries were measured by using the Agilent High Sensitivity DNA Kit and a Bioanalyzer 2100 from Agilent Technologies. The libraries were submitted to 51 bp single end high throughput sequencing by the Center for Advanced Technology CAT of the University of California San Francisco using Hiseq 3000.     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   SRP495638     wt-cs-2_S36_L004_R1_001.fastq.gz wt-cs-2_S36_L004_R2_001.fastq.gz fastq fastq 7863905100.0 26213017.0 wt cs 2 S36 L004 R1 001.fastq.gz 0:150 1:150 A:2095810379;C:1826144395;G:1861582031;T:2079957538;N:410757 150 150     2095810379 1826144395 1861582031 2079957538 410757 SRX23967981 SRS20767212 SRA1825819 Chinese Academy of Sciences|Institute of Hydrobiology Chinese Academy of Sciences                       B B biological fallback assumption illumina novaseq_era unknown random_priming nebnext bulk unknown unknown   China 2024-03-16 Larval Larval Trunk Surface Structure
31478 31478 SRR28362826 SRX23967980 SRS20767211 SRP495638 PRJNA1088730 Effects of noxo1a deficiency on gene expression in zebrafish larvae upon exposure to cold warm stress PRJNA1088730 Other Exposure of fish to cold warm stress was reported to elicit ROS generation and subsequent tissue damage. On the other hand ROS signaling is essential for many physiological functions of the organism. As a NADPH oxidase NOX organizer deficiency of Noxo1a is expected to decrease the content of hydrogen peroxide in fish tissue upon exposure to cold warm stress. In this study the effect on Noxo1a deficiency on gene expression in zebrafish larvae under cold warm stress was characterized by RNA sequencing.       WT cs#1 WT cs#1   strain:AB strain|dev stage:Larvae|collection date:2023 03 05|geo loc name:China: Wuhan|sex:not determined|tissue:Whole body|genotype:Wild type|treatment:Exposed to 10 °C for 12 h|replicate:replicate = biological replicate 1|BioSampleModel:Model organism or animal                 WT cs#1 WT cs#1 WT cs#1 One microgram total RNA from each sample was used as the beginning material for sequencing library construction. Each treatment included 4 biological replicates. The NEBNext rRNA Depletion Kit was used for rRNA depletion. post rRNA depletion Agencourt RNAClean XP Beads from Beckman Coulter were used for RNA purification. Then the NEBNext Ultra Directional RNA Library Prep Kit for Illumina was used for RNA fragmentation first and second strand cDNA synthesis double stranded cDNA end repair. Double strand cDNAs were purified using the Agencourt AMPure XP from Beckman Coulter and ligated to adaptors of NEBNext Multiplex Oligos for Illumina. Finally the Q5 Hot Start HiFi PCR Master Mix was used for PCR enrichment of the adaptor ligated DNA. The concentration and quality of the constructed sequencing libraries were measured by using the Agilent High Sensitivity DNA Kit and a Bioanalyzer 2100 from Agilent Technologies. The libraries were submitted to 51 bp single end high throughput sequencing by the Center for Advanced Technology CAT of the University of California San Francisco using Hiseq 3000.     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   SRP495638     wt-cs-1_S35_L004_R1_001.fastq.gz wt-cs-1_S35_L004_R2_001.fastq.gz fastq fastq 6904903200.0 23016344.0 wt cs 1 S35 L004 R1 001.fastq.gz 0:150 1:150 A:1837602528;C:1605156041;G:1638534027;T:1823249554;N:361050 150 150     1837602528 1605156041 1638534027 1823249554 361050 SRX23967980 SRS20767211 SRA1825819 Chinese Academy of Sciences|Institute of Hydrobiology Chinese Academy of Sciences                       B B biological fallback assumption illumina novaseq_era unknown random_priming nebnext bulk unknown unknown   China 2024-03-16 Larval Larval Trunk Surface Structure
31479 31479 SRR28362827 SRX23967979 SRS20767210 SRP495638 PRJNA1088730 Effects of noxo1a deficiency on gene expression in zebrafish larvae upon exposure to cold warm stress PRJNA1088730 Other Exposure of fish to cold warm stress was reported to elicit ROS generation and subsequent tissue damage. On the other hand ROS signaling is essential for many physiological functions of the organism. As a NADPH oxidase NOX organizer deficiency of Noxo1a is expected to decrease the content of hydrogen peroxide in fish tissue upon exposure to cold warm stress. In this study the effect on Noxo1a deficiency on gene expression in zebrafish larvae under cold warm stress was characterized by RNA sequencing.       WT ctrl#4 WT ctrl#4   strain:AB strain|dev stage:Larvae|collection date:2023 03 05|geo loc name:China: Wuhan|sex:not determined|tissue:Whole body|genotype:Wild type|treatment:Collected at 96 hpf|replicate:replicate = biological replicate 4|BioSampleModel:Model organism or animal                 WT ctrl#4 WT ctrl#4 WT ctrl#4 One microgram total RNA from each sample was used as the beginning material for sequencing library construction. Each treatment included 4 biological replicates. The NEBNext rRNA Depletion Kit was used for rRNA depletion. post rRNA depletion Agencourt RNAClean XP Beads from Beckman Coulter were used for RNA purification. Then the NEBNext Ultra Directional RNA Library Prep Kit for Illumina was used for RNA fragmentation first and second strand cDNA synthesis double stranded cDNA end repair. Double strand cDNAs were purified using the Agencourt AMPure XP from Beckman Coulter and ligated to adaptors of NEBNext Multiplex Oligos for Illumina. Finally the Q5 Hot Start HiFi PCR Master Mix was used for PCR enrichment of the adaptor ligated DNA. The concentration and quality of the constructed sequencing libraries were measured by using the Agilent High Sensitivity DNA Kit and a Bioanalyzer 2100 from Agilent Technologies. The libraries were submitted to 51 bp single end high throughput sequencing by the Center for Advanced Technology CAT of the University of California San Francisco using Hiseq 3000.     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   SRP495638     wt-ctrl-4_S20_L004_R1_001.fastq.gz wt-ctrl-4_S20_L004_R2_001.fastq.gz fastq fastq 6576597600.0 21921992.0 wt ctrl 4 S20 L004 R1 001.fastq.gz 0:150 1:150 A:1706071185;C:1570838977;G:1609917484;T:1689461796;N:308158 150 150     1706071185 1570838977 1609917484 1689461796 308158 SRX23967979 SRS20767210 SRA1825819 Chinese Academy of Sciences|Institute of Hydrobiology Chinese Academy of Sciences                       B B biological fallback assumption illumina novaseq_era unknown random_priming nebnext bulk unknown unknown   China 2024-03-16 Larval Larval Trunk Surface Structure
31480 31480 SRR28362828 SRX23967978 SRS20767209 SRP495638 PRJNA1088730 Effects of noxo1a deficiency on gene expression in zebrafish larvae upon exposure to cold warm stress PRJNA1088730 Other Exposure of fish to cold warm stress was reported to elicit ROS generation and subsequent tissue damage. On the other hand ROS signaling is essential for many physiological functions of the organism. As a NADPH oxidase NOX organizer deficiency of Noxo1a is expected to decrease the content of hydrogen peroxide in fish tissue upon exposure to cold warm stress. In this study the effect on Noxo1a deficiency on gene expression in zebrafish larvae under cold warm stress was characterized by RNA sequencing.       noxo1a re#4 noxo1a re#4   strain:AB strain|dev stage:Larvae|collection date:2023 03 05|geo loc name:China: Wuhan|sex:not determined|tissue:Whole body|genotype:noxo1a mutant with indel|treatment:Exposed to 10 °C for 12 h followed by recovery at 28 °C for 6 h|replicate:replicate = biological replicate 4|BioSampleModel:Model organism or animal                 noxo1a re#4 noxo1a re#4 noxo1a re#4 One microgram total RNA from each sample was used as the beginning material for sequencing library construction. Each treatment included 4 biological replicates. The NEBNext rRNA Depletion Kit was used for rRNA depletion. post rRNA depletion Agencourt RNAClean XP Beads from Beckman Coulter were used for RNA purification. Then the NEBNext Ultra Directional RNA Library Prep Kit for Illumina was used for RNA fragmentation first and second strand cDNA synthesis double stranded cDNA end repair. Double strand cDNAs were purified using the Agencourt AMPure XP from Beckman Coulter and ligated to adaptors of NEBNext Multiplex Oligos for Illumina. Finally the Q5 Hot Start HiFi PCR Master Mix was used for PCR enrichment of the adaptor ligated DNA. The concentration and quality of the constructed sequencing libraries were measured by using the Agilent High Sensitivity DNA Kit and a Bioanalyzer 2100 from Agilent Technologies. The libraries were submitted to 51 bp single end high throughput sequencing by the Center for Advanced Technology CAT of the University of California San Francisco using Hiseq 3000.     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   SRP495638     noxo1a-re-4_S0_L000_R1_000.fastq.gz noxo1a-re-4_S0_L000_R2_000.fastq.gz fastq fastq 6288486900.0 20961623.0 noxo1a re 4 S0 L000 R1 000.fastq.gz 0:150 1:150 A:1666277839;C:1470224724;G:1500784713;T:1651119958;N:79666 150 150     1666277839 1470224724 1500784713 1651119958 79666 SRX23967978 SRS20767209 SRA1825819 Chinese Academy of Sciences|Institute of Hydrobiology Chinese Academy of Sciences                       B B biological fallback assumption illumina novaseq_era unknown random_priming nebnext bulk unknown unknown   China 2024-03-16 Larval Larval Trunk Surface Structure
31481 31481 SRR28362830 SRX23967977 SRS20767208 SRP495638 PRJNA1088730 Effects of noxo1a deficiency on gene expression in zebrafish larvae upon exposure to cold warm stress PRJNA1088730 Other Exposure of fish to cold warm stress was reported to elicit ROS generation and subsequent tissue damage. On the other hand ROS signaling is essential for many physiological functions of the organism. As a NADPH oxidase NOX organizer deficiency of Noxo1a is expected to decrease the content of hydrogen peroxide in fish tissue upon exposure to cold warm stress. In this study the effect on Noxo1a deficiency on gene expression in zebrafish larvae under cold warm stress was characterized by RNA sequencing.       noxo1a re#3 noxo1a re#3   strain:AB strain|dev stage:Larvae|collection date:2023 03 05|geo loc name:China: Wuhan|sex:not determined|tissue:Whole body|genotype:noxo1a mutant with indel|treatment:Exposed to 10 °C for 12 h followed by recovery at 28 °C for 6 h|replicate:replicate = biological replicate 3|BioSampleModel:Model organism or animal                 noxo1a re#3 noxo1a re#3 noxo1a re#3 One microgram total RNA from each sample was used as the beginning material for sequencing library construction. Each treatment included 4 biological replicates. The NEBNext rRNA Depletion Kit was used for rRNA depletion. post rRNA depletion Agencourt RNAClean XP Beads from Beckman Coulter were used for RNA purification. Then the NEBNext Ultra Directional RNA Library Prep Kit for Illumina was used for RNA fragmentation first and second strand cDNA synthesis double stranded cDNA end repair. Double strand cDNAs were purified using the Agencourt AMPure XP from Beckman Coulter and ligated to adaptors of NEBNext Multiplex Oligos for Illumina. Finally the Q5 Hot Start HiFi PCR Master Mix was used for PCR enrichment of the adaptor ligated DNA. The concentration and quality of the constructed sequencing libraries were measured by using the Agilent High Sensitivity DNA Kit and a Bioanalyzer 2100 from Agilent Technologies. The libraries were submitted to 51 bp single end high throughput sequencing by the Center for Advanced Technology CAT of the University of California San Francisco using Hiseq 3000.     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   SRP495638     noxo1a-re-3_S1_L001_R1_001.fastq.gz noxo1a-re-3_S1_L001_R2_001.fastq.gz noxo1a-re-3_S2_L004_R1_001.fastq.gz noxo1a-re-3_S2_L004_R2_001.fastq.gz fastq fastq fastq fastq 6993336600.0 23311122.0 noxo1a re 3 S1 L001 R1 001.fastq.gz 0:150 1:150 A:1857289544;C:1633216640;G:1660910386;T:1841856529;N:63501 150 150     1857289544 1633216640 1660910386 1841856529 63501 SRX23967977 SRS20767208 SRA1825819 Chinese Academy of Sciences|Institute of Hydrobiology Chinese Academy of Sciences                       B B biological fallback assumption illumina novaseq_era unknown random_priming nebnext bulk unknown unknown   China 2024-03-16 Larval Larval Trunk Surface Structure
31482 31482 SRR28362831 SRX23967976 SRS20767207 SRP495638 PRJNA1088730 Effects of noxo1a deficiency on gene expression in zebrafish larvae upon exposure to cold warm stress PRJNA1088730 Other Exposure of fish to cold warm stress was reported to elicit ROS generation and subsequent tissue damage. On the other hand ROS signaling is essential for many physiological functions of the organism. As a NADPH oxidase NOX organizer deficiency of Noxo1a is expected to decrease the content of hydrogen peroxide in fish tissue upon exposure to cold warm stress. In this study the effect on Noxo1a deficiency on gene expression in zebrafish larvae under cold warm stress was characterized by RNA sequencing.       noxo1a re#2 noxo1a re#2   strain:AB strain|dev stage:Larvae|collection date:2023 03 05|geo loc name:China: Wuhan|sex:not determined|tissue:Whole body|genotype:noxo1a mutant with indel|treatment:Exposed to 10 °C for 12 h followed by recovery at 28 °C for 6 h|replicate:replicate = biological replicate 2|BioSampleModel:Model organism or animal                 noxo1a re#2 noxo1a re#2 noxo1a re#2 One microgram total RNA from each sample was used as the beginning material for sequencing library construction. Each treatment included 4 biological replicates. The NEBNext rRNA Depletion Kit was used for rRNA depletion. post rRNA depletion Agencourt RNAClean XP Beads from Beckman Coulter were used for RNA purification. Then the NEBNext Ultra Directional RNA Library Prep Kit for Illumina was used for RNA fragmentation first and second strand cDNA synthesis double stranded cDNA end repair. Double strand cDNAs were purified using the Agencourt AMPure XP from Beckman Coulter and ligated to adaptors of NEBNext Multiplex Oligos for Illumina. Finally the Q5 Hot Start HiFi PCR Master Mix was used for PCR enrichment of the adaptor ligated DNA. The concentration and quality of the constructed sequencing libraries were measured by using the Agilent High Sensitivity DNA Kit and a Bioanalyzer 2100 from Agilent Technologies. The libraries were submitted to 51 bp single end high throughput sequencing by the Center for Advanced Technology CAT of the University of California San Francisco using Hiseq 3000.     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   SRP495638     noxo1a-re-2_S1_L004_R1_001.fastq.gz noxo1a-re-2_S1_L004_R2_001.fastq.gz fastq fastq 6021534600.0 20071782.0 noxo1a re 2 S1 L004 R1 001.fastq.gz 0:150 1:150 A:1597183597;C:1408878472;G:1434927510;T:1580500451;N:44570 150 150     1597183597 1408878472 1434927510 1580500451 44570 SRX23967976 SRS20767207 SRA1825819 Chinese Academy of Sciences|Institute of Hydrobiology Chinese Academy of Sciences                       B B biological fallback assumption illumina novaseq_era unknown random_priming nebnext bulk unknown unknown   China 2024-03-16 Larval Larval Trunk Surface Structure
31483 31483 SRR28362832 SRX23967975 SRS20767206 SRP495638 PRJNA1088730 Effects of noxo1a deficiency on gene expression in zebrafish larvae upon exposure to cold warm stress PRJNA1088730 Other Exposure of fish to cold warm stress was reported to elicit ROS generation and subsequent tissue damage. On the other hand ROS signaling is essential for many physiological functions of the organism. As a NADPH oxidase NOX organizer deficiency of Noxo1a is expected to decrease the content of hydrogen peroxide in fish tissue upon exposure to cold warm stress. In this study the effect on Noxo1a deficiency on gene expression in zebrafish larvae under cold warm stress was characterized by RNA sequencing.       noxo1a re#1 noxo1a re#1   strain:AB strain|dev stage:Larvae|collection date:2023 03 05|geo loc name:China: Wuhan|sex:not determined|tissue:Whole body|genotype:noxo1a mutant with indel|treatment:Exposed to 10 °C for 12 h followed by recovery at 28 °C for 6 h|replicate:replicate = biological replicate 1|BioSampleModel:Model organism or animal                 noxo1a re#1 noxo1a re#1 noxo1a re#1 One microgram total RNA from each sample was used as the beginning material for sequencing library construction. Each treatment included 4 biological replicates. The NEBNext rRNA Depletion Kit was used for rRNA depletion. post rRNA depletion Agencourt RNAClean XP Beads from Beckman Coulter were used for RNA purification. Then the NEBNext Ultra Directional RNA Library Prep Kit for Illumina was used for RNA fragmentation first and second strand cDNA synthesis double stranded cDNA end repair. Double strand cDNAs were purified using the Agencourt AMPure XP from Beckman Coulter and ligated to adaptors of NEBNext Multiplex Oligos for Illumina. Finally the Q5 Hot Start HiFi PCR Master Mix was used for PCR enrichment of the adaptor ligated DNA. The concentration and quality of the constructed sequencing libraries were measured by using the Agilent High Sensitivity DNA Kit and a Bioanalyzer 2100 from Agilent Technologies. The libraries were submitted to 51 bp single end high throughput sequencing by the Center for Advanced Technology CAT of the University of California San Francisco using Hiseq 3000.     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   SRP495638     noxo1a-re-1_S44_L004_R1_001.fastq.gz noxo1a-re-1_S44_L004_R2_001.fastq.gz fastq fastq 6459165300.0 21530551.0 noxo1a re 1 S44 L004 R1 001.fastq.gz 0:150 1:150 A:1704973328;C:1516599476;G:1546419572;T:1690833152;N:339772 150 150     1704973328 1516599476 1546419572 1690833152 339772 SRX23967975 SRS20767206 SRA1825819 Chinese Academy of Sciences|Institute of Hydrobiology Chinese Academy of Sciences                       B B biological fallback assumption illumina novaseq_era unknown random_priming nebnext bulk unknown unknown   China 2024-03-16 Larval Larval Trunk Surface Structure
31484 31484 SRR28362833 SRX23967974 SRS20767205 SRP495638 PRJNA1088730 Effects of noxo1a deficiency on gene expression in zebrafish larvae upon exposure to cold warm stress PRJNA1088730 Other Exposure of fish to cold warm stress was reported to elicit ROS generation and subsequent tissue damage. On the other hand ROS signaling is essential for many physiological functions of the organism. As a NADPH oxidase NOX organizer deficiency of Noxo1a is expected to decrease the content of hydrogen peroxide in fish tissue upon exposure to cold warm stress. In this study the effect on Noxo1a deficiency on gene expression in zebrafish larvae under cold warm stress was characterized by RNA sequencing.       WT ctrl#3 WT ctrl#3   strain:AB strain|dev stage:Larvae|collection date:2023 03 05|geo loc name:China: Wuhan|sex:not determined|tissue:Whole body|genotype:Wild type|treatment:Collected at 96 hpf|replicate:replicate = biological replicate 3|BioSampleModel:Model organism or animal                 WT ctrl#3 WT ctrl#3 WT ctrl#3 One microgram total RNA from each sample was used as the beginning material for sequencing library construction. Each treatment included 4 biological replicates. The NEBNext rRNA Depletion Kit was used for rRNA depletion. post rRNA depletion Agencourt RNAClean XP Beads from Beckman Coulter were used for RNA purification. Then the NEBNext Ultra Directional RNA Library Prep Kit for Illumina was used for RNA fragmentation first and second strand cDNA synthesis double stranded cDNA end repair. Double strand cDNAs were purified using the Agencourt AMPure XP from Beckman Coulter and ligated to adaptors of NEBNext Multiplex Oligos for Illumina. Finally the Q5 Hot Start HiFi PCR Master Mix was used for PCR enrichment of the adaptor ligated DNA. The concentration and quality of the constructed sequencing libraries were measured by using the Agilent High Sensitivity DNA Kit and a Bioanalyzer 2100 from Agilent Technologies. The libraries were submitted to 51 bp single end high throughput sequencing by the Center for Advanced Technology CAT of the University of California San Francisco using Hiseq 3000.     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   SRP495638     wt-ctrl-3_S31_L004_R1_001.fastq.gz wt-ctrl-3_S31_L004_R2_001.fastq.gz fastq fastq 7847308200.0 26157694.0 wt ctrl 3 S31 L004 R1 001.fastq.gz 0:150 1:150 A:2059319370;C:1853070672;G:1895075718;T:2039431518;N:410922 150 150     2059319370 1853070672 1895075718 2039431518 410922 SRX23967974 SRS20767205 SRA1825819 Chinese Academy of Sciences|Institute of Hydrobiology Chinese Academy of Sciences                       B B biological fallback assumption illumina novaseq_era unknown random_priming nebnext bulk unknown unknown   China 2024-03-16 Larval Larval Trunk Surface Structure
31485 31485 SRR28362834 SRX23967973 SRS20767204 SRP495638 PRJNA1088730 Effects of noxo1a deficiency on gene expression in zebrafish larvae upon exposure to cold warm stress PRJNA1088730 Other Exposure of fish to cold warm stress was reported to elicit ROS generation and subsequent tissue damage. On the other hand ROS signaling is essential for many physiological functions of the organism. As a NADPH oxidase NOX organizer deficiency of Noxo1a is expected to decrease the content of hydrogen peroxide in fish tissue upon exposure to cold warm stress. In this study the effect on Noxo1a deficiency on gene expression in zebrafish larvae under cold warm stress was characterized by RNA sequencing.       noxo1a cs#4 noxo1a cs#4   strain:AB strain|dev stage:Larvae|collection date:2023 03 05|geo loc name:China: Wuhan|sex:not determined|tissue:Whole body|genotype:noxo1a mutant with indel|treatment:Exposed to 10 °C for 12 h|replicate:replicate = biological replicate 4|BioSampleModel:Model organism or animal                 noxo1a cs#4 noxo1a cs#4 noxo1a cs#4 One microgram total RNA from each sample was used as the beginning material for sequencing library construction. Each treatment included 4 biological replicates. The NEBNext rRNA Depletion Kit was used for rRNA depletion. post rRNA depletion Agencourt RNAClean XP Beads from Beckman Coulter were used for RNA purification. Then the NEBNext Ultra Directional RNA Library Prep Kit for Illumina was used for RNA fragmentation first and second strand cDNA synthesis double stranded cDNA end repair. Double strand cDNAs were purified using the Agencourt AMPure XP from Beckman Coulter and ligated to adaptors of NEBNext Multiplex Oligos for Illumina. Finally the Q5 Hot Start HiFi PCR Master Mix was used for PCR enrichment of the adaptor ligated DNA. The concentration and quality of the constructed sequencing libraries were measured by using the Agilent High Sensitivity DNA Kit and a Bioanalyzer 2100 from Agilent Technologies. The libraries were submitted to 51 bp single end high throughput sequencing by the Center for Advanced Technology CAT of the University of California San Francisco using Hiseq 3000.     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   SRP495638     noxo1a-cs-4_S23_L004_R1_001.fastq.gz noxo1a-cs-4_S23_L004_R2_001.fastq.gz fastq fastq 6310591800.0 21035306.0 noxo1a cs 4 S23 L004 R1 001.fastq.gz 0:150 1:150 A:1649781865;C:1495677401;G:1531600458;T:1633236277;N:295799 150 150     1649781865 1495677401 1531600458 1633236277 295799 SRX23967973 SRS20767204 SRA1825819 Chinese Academy of Sciences|Institute of Hydrobiology Chinese Academy of Sciences                       B B biological fallback assumption illumina novaseq_era unknown random_priming nebnext bulk unknown unknown   China 2024-03-16 Larval Larval Trunk Surface Structure
31486 31486 SRR28362835 SRX23967972 SRS20767203 SRP495638 PRJNA1088730 Effects of noxo1a deficiency on gene expression in zebrafish larvae upon exposure to cold warm stress PRJNA1088730 Other Exposure of fish to cold warm stress was reported to elicit ROS generation and subsequent tissue damage. On the other hand ROS signaling is essential for many physiological functions of the organism. As a NADPH oxidase NOX organizer deficiency of Noxo1a is expected to decrease the content of hydrogen peroxide in fish tissue upon exposure to cold warm stress. In this study the effect on Noxo1a deficiency on gene expression in zebrafish larvae under cold warm stress was characterized by RNA sequencing.       noxo1a cs#3 noxo1a cs#3   strain:AB strain|dev stage:Larvae|collection date:2023 03 05|geo loc name:China: Wuhan|sex:not determined|tissue:Whole body|genotype:noxo1a mutant with indel|treatment:Exposed to 10 °C for 12 h|replicate:replicate = biological replicate 3|BioSampleModel:Model organism or animal                 noxo1a cs#3 noxo1a cs#3 noxo1a cs#3 One microgram total RNA from each sample was used as the beginning material for sequencing library construction. Each treatment included 4 biological replicates. The NEBNext rRNA Depletion Kit was used for rRNA depletion. post rRNA depletion Agencourt RNAClean XP Beads from Beckman Coulter were used for RNA purification. Then the NEBNext Ultra Directional RNA Library Prep Kit for Illumina was used for RNA fragmentation first and second strand cDNA synthesis double stranded cDNA end repair. Double strand cDNAs were purified using the Agencourt AMPure XP from Beckman Coulter and ligated to adaptors of NEBNext Multiplex Oligos for Illumina. Finally the Q5 Hot Start HiFi PCR Master Mix was used for PCR enrichment of the adaptor ligated DNA. The concentration and quality of the constructed sequencing libraries were measured by using the Agilent High Sensitivity DNA Kit and a Bioanalyzer 2100 from Agilent Technologies. The libraries were submitted to 51 bp single end high throughput sequencing by the Center for Advanced Technology CAT of the University of California San Francisco using Hiseq 3000.     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   SRP495638     noxo1a-cs-3_S40_L004_R1_001.fastq.gz noxo1a-cs-3_S40_L004_R2_001.fastq.gz fastq fastq 6704622300.0 22348741.0 noxo1a cs 3 S40 L004 R1 001.fastq.gz 0:150 1:150 A:1767126555;C:1576232837;G:1610607905;T:1750301837;N:353166 150 150     1767126555 1576232837 1610607905 1750301837 353166 SRX23967972 SRS20767203 SRA1825819 Chinese Academy of Sciences|Institute of Hydrobiology Chinese Academy of Sciences                       B B biological fallback assumption illumina novaseq_era unknown random_priming nebnext bulk unknown unknown   China 2024-03-16 Larval Larval Trunk Surface Structure
31487 31487 SRR28362836 SRX23967971 SRS20767202 SRP495638 PRJNA1088730 Effects of noxo1a deficiency on gene expression in zebrafish larvae upon exposure to cold warm stress PRJNA1088730 Other Exposure of fish to cold warm stress was reported to elicit ROS generation and subsequent tissue damage. On the other hand ROS signaling is essential for many physiological functions of the organism. As a NADPH oxidase NOX organizer deficiency of Noxo1a is expected to decrease the content of hydrogen peroxide in fish tissue upon exposure to cold warm stress. In this study the effect on Noxo1a deficiency on gene expression in zebrafish larvae under cold warm stress was characterized by RNA sequencing.       noxo1a cs#2 noxo1a cs#2   strain:AB strain|dev stage:Larvae|collection date:2023 03 05|geo loc name:China: Wuhan|sex:not determined|tissue:Whole body|genotype:noxo1a mutant with indel|treatment:Exposed to 10 °C for 12 h|replicate:replicate = biological replicate 2|BioSampleModel:Model organism or animal                 noxo1a cs#2 noxo1a cs#2 noxo1a cs#2 One microgram total RNA from each sample was used as the beginning material for sequencing library construction. Each treatment included 4 biological replicates. The NEBNext rRNA Depletion Kit was used for rRNA depletion. post rRNA depletion Agencourt RNAClean XP Beads from Beckman Coulter were used for RNA purification. Then the NEBNext Ultra Directional RNA Library Prep Kit for Illumina was used for RNA fragmentation first and second strand cDNA synthesis double stranded cDNA end repair. Double strand cDNAs were purified using the Agencourt AMPure XP from Beckman Coulter and ligated to adaptors of NEBNext Multiplex Oligos for Illumina. Finally the Q5 Hot Start HiFi PCR Master Mix was used for PCR enrichment of the adaptor ligated DNA. The concentration and quality of the constructed sequencing libraries were measured by using the Agilent High Sensitivity DNA Kit and a Bioanalyzer 2100 from Agilent Technologies. The libraries were submitted to 51 bp single end high throughput sequencing by the Center for Advanced Technology CAT of the University of California San Francisco using Hiseq 3000.     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   SRP495638     noxo1a-cs-2_S22_L004_R1_001.fastq.gz noxo1a-cs-2_S22_L004_R2_001.fastq.gz fastq fastq 6500565900.0 21668553.0 noxo1a cs 2 S22 L004 R1 001.fastq.gz 0:150 1:150 A:1717991417;C:1522293556;G:1558318730;T:1701666138;N:296059 150 150     1717991417 1522293556 1558318730 1701666138 296059 SRX23967971 SRS20767202 SRA1825819 Chinese Academy of Sciences|Institute of Hydrobiology Chinese Academy of Sciences                       B B biological fallback assumption illumina novaseq_era unknown random_priming nebnext bulk unknown unknown   China 2024-03-16 Larval Larval Trunk Surface Structure
31488 31488 SRR28362837 SRX23967970 SRS20767201 SRP495638 PRJNA1088730 Effects of noxo1a deficiency on gene expression in zebrafish larvae upon exposure to cold warm stress PRJNA1088730 Other Exposure of fish to cold warm stress was reported to elicit ROS generation and subsequent tissue damage. On the other hand ROS signaling is essential for many physiological functions of the organism. As a NADPH oxidase NOX organizer deficiency of Noxo1a is expected to decrease the content of hydrogen peroxide in fish tissue upon exposure to cold warm stress. In this study the effect on Noxo1a deficiency on gene expression in zebrafish larvae under cold warm stress was characterized by RNA sequencing.       noxo1a cs#1 noxo1a cs#1   strain:AB strain|dev stage:Larvae|collection date:2023 03 05|geo loc name:China: Wuhan|sex:not determined|tissue:Whole body|genotype:noxo1a mutant with indel|treatment:Exposed to 10 °C for 12 h|replicate:replicate = biological replicate 1|BioSampleModel:Model organism or animal                 noxo1a cs#1 noxo1a cs#1 noxo1a cs#1 One microgram total RNA from each sample was used as the beginning material for sequencing library construction. Each treatment included 4 biological replicates. The NEBNext rRNA Depletion Kit was used for rRNA depletion. post rRNA depletion Agencourt RNAClean XP Beads from Beckman Coulter were used for RNA purification. Then the NEBNext Ultra Directional RNA Library Prep Kit for Illumina was used for RNA fragmentation first and second strand cDNA synthesis double stranded cDNA end repair. Double strand cDNAs were purified using the Agencourt AMPure XP from Beckman Coulter and ligated to adaptors of NEBNext Multiplex Oligos for Illumina. Finally the Q5 Hot Start HiFi PCR Master Mix was used for PCR enrichment of the adaptor ligated DNA. The concentration and quality of the constructed sequencing libraries were measured by using the Agilent High Sensitivity DNA Kit and a Bioanalyzer 2100 from Agilent Technologies. The libraries were submitted to 51 bp single end high throughput sequencing by the Center for Advanced Technology CAT of the University of California San Francisco using Hiseq 3000.     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   SRP495638     noxo1a-cs-1_S39_L004_R1_001.fastq.gz noxo1a-cs-1_S39_L004_R2_001.fastq.gz fastq fastq 6662253600.0 22207512.0 noxo1a cs 1 S39 L004 R1 001.fastq.gz 0:150 1:150 A:1765032411;C:1556260041;G:1592453845;T:1748156183;N:351120 150 150     1765032411 1556260041 1592453845 1748156183 351120 SRX23967970 SRS20767201 SRA1825819 Chinese Academy of Sciences|Institute of Hydrobiology Chinese Academy of Sciences                       B B biological fallback assumption illumina novaseq_era unknown random_priming nebnext bulk unknown unknown   China 2024-03-16 Larval Larval Trunk Surface Structure
31489 31489 SRR28362838 SRX23967969 SRS20767200 SRP495638 PRJNA1088730 Effects of noxo1a deficiency on gene expression in zebrafish larvae upon exposure to cold warm stress PRJNA1088730 Other Exposure of fish to cold warm stress was reported to elicit ROS generation and subsequent tissue damage. On the other hand ROS signaling is essential for many physiological functions of the organism. As a NADPH oxidase NOX organizer deficiency of Noxo1a is expected to decrease the content of hydrogen peroxide in fish tissue upon exposure to cold warm stress. In this study the effect on Noxo1a deficiency on gene expression in zebrafish larvae under cold warm stress was characterized by RNA sequencing.       noxo1a ctrl#4 noxo1a ctrl#4   strain:AB strain|dev stage:Larvae|collection date:2023 03 05|geo loc name:China: Wuhan|sex:not determined|tissue:Whole body|genotype:noxo1a mutant with indel|treatment:Collected at 96 hpf|replicate:replicate = biological replicate 4|BioSampleModel:Model organism or animal                 noxo1a ctrl#4 noxo1a ctrl#4 noxo1a ctrl#4 One microgram total RNA from each sample was used as the beginning material for sequencing library construction. Each treatment included 4 biological replicates. The NEBNext rRNA Depletion Kit was used for rRNA depletion. post rRNA depletion Agencourt RNAClean XP Beads from Beckman Coulter were used for RNA purification. Then the NEBNext Ultra Directional RNA Library Prep Kit for Illumina was used for RNA fragmentation first and second strand cDNA synthesis double stranded cDNA end repair. Double strand cDNAs were purified using the Agencourt AMPure XP from Beckman Coulter and ligated to adaptors of NEBNext Multiplex Oligos for Illumina. Finally the Q5 Hot Start HiFi PCR Master Mix was used for PCR enrichment of the adaptor ligated DNA. The concentration and quality of the constructed sequencing libraries were measured by using the Agilent High Sensitivity DNA Kit and a Bioanalyzer 2100 from Agilent Technologies. The libraries were submitted to 51 bp single end high throughput sequencing by the Center for Advanced Technology CAT of the University of California San Francisco using Hiseq 3000.     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   SRP495638     noxo1a-ctrl-4_S21_L004_R1_001.fastq.gz noxo1a-ctrl-4_S21_L004_R2_001.fastq.gz fastq fastq 6428415000.0 21428050.0 noxo1a ctrl 4 S21 L004 R1 001.fastq.gz 0:150 1:150 A:1704089785;C:1501936031;G:1530024908;T:1692071168;N:293108 150 150     1704089785 1501936031 1530024908 1692071168 293108 SRX23967969 SRS20767200 SRA1825819 Chinese Academy of Sciences|Institute of Hydrobiology Chinese Academy of Sciences                       B B biological fallback assumption illumina novaseq_era unknown random_priming nebnext bulk unknown unknown   China 2024-03-16 Larval Larval Trunk Surface Structure
31490 31490 SRR28362839 SRX23967968 SRS20767199 SRP495638 PRJNA1088730 Effects of noxo1a deficiency on gene expression in zebrafish larvae upon exposure to cold warm stress PRJNA1088730 Other Exposure of fish to cold warm stress was reported to elicit ROS generation and subsequent tissue damage. On the other hand ROS signaling is essential for many physiological functions of the organism. As a NADPH oxidase NOX organizer deficiency of Noxo1a is expected to decrease the content of hydrogen peroxide in fish tissue upon exposure to cold warm stress. In this study the effect on Noxo1a deficiency on gene expression in zebrafish larvae under cold warm stress was characterized by RNA sequencing.       noxo1a ctrl#3 noxo1a ctrl#3   strain:AB strain|dev stage:Larvae|collection date:2023 03 05|geo loc name:China: Wuhan|sex:not determined|tissue:Whole body|genotype:noxo1a mutant with indel|treatment:Collected at 96 hpf|replicate:replicate = biological replicate 3|BioSampleModel:Model organism or animal                 noxo1a ctrl#3 noxo1a ctrl#3 noxo1a ctrl#3 One microgram total RNA from each sample was used as the beginning material for sequencing library construction. Each treatment included 4 biological replicates. The NEBNext rRNA Depletion Kit was used for rRNA depletion. post rRNA depletion Agencourt RNAClean XP Beads from Beckman Coulter were used for RNA purification. Then the NEBNext Ultra Directional RNA Library Prep Kit for Illumina was used for RNA fragmentation first and second strand cDNA synthesis double stranded cDNA end repair. Double strand cDNAs were purified using the Agencourt AMPure XP from Beckman Coulter and ligated to adaptors of NEBNext Multiplex Oligos for Illumina. Finally the Q5 Hot Start HiFi PCR Master Mix was used for PCR enrichment of the adaptor ligated DNA. The concentration and quality of the constructed sequencing libraries were measured by using the Agilent High Sensitivity DNA Kit and a Bioanalyzer 2100 from Agilent Technologies. The libraries were submitted to 51 bp single end high throughput sequencing by the Center for Advanced Technology CAT of the University of California San Francisco using Hiseq 3000.     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   SRP495638     noxo1a-ctrl-3_S34_L004_R1_001.fastq.gz noxo1a-ctrl-3_S34_L004_R2_001.fastq.gz fastq fastq 6988991100.0 23296637.0 noxo1a ctrl 3 S34 L004 R1 001.fastq.gz 0:150 1:150 A:1853131820;C:1633719581;G:1663738566;T:1838036906;N:364227 150 150     1853131820 1633719581 1663738566 1838036906 364227 SRX23967968 SRS20767199 SRA1825819 Chinese Academy of Sciences|Institute of Hydrobiology Chinese Academy of Sciences                       B B biological fallback assumption illumina novaseq_era unknown random_priming nebnext bulk unknown unknown   China 2024-03-16 Larval Larval Trunk Surface Structure
31491 31491 SRR28362840 SRX23967967 SRS20767198 SRP495638 PRJNA1088730 Effects of noxo1a deficiency on gene expression in zebrafish larvae upon exposure to cold warm stress PRJNA1088730 Other Exposure of fish to cold warm stress was reported to elicit ROS generation and subsequent tissue damage. On the other hand ROS signaling is essential for many physiological functions of the organism. As a NADPH oxidase NOX organizer deficiency of Noxo1a is expected to decrease the content of hydrogen peroxide in fish tissue upon exposure to cold warm stress. In this study the effect on Noxo1a deficiency on gene expression in zebrafish larvae under cold warm stress was characterized by RNA sequencing.       noxo1a ctrl#2 noxo1a ctrl#2   strain:AB strain|dev stage:Larvae|collection date:2023 03 05|geo loc name:China: Wuhan|sex:not determined|tissue:Whole body|genotype:noxo1a mutant with indel|treatment:Collected at 96 hpf|replicate:replicate = biological replicate 2|BioSampleModel:Model organism or animal                 noxo1a ctrl#2 noxo1a ctrl#2 noxo1a ctrl#2 One microgram total RNA from each sample was used as the beginning material for sequencing library construction. Each treatment included 4 biological replicates. The NEBNext rRNA Depletion Kit was used for rRNA depletion. post rRNA depletion Agencourt RNAClean XP Beads from Beckman Coulter were used for RNA purification. Then the NEBNext Ultra Directional RNA Library Prep Kit for Illumina was used for RNA fragmentation first and second strand cDNA synthesis double stranded cDNA end repair. Double strand cDNAs were purified using the Agencourt AMPure XP from Beckman Coulter and ligated to adaptors of NEBNext Multiplex Oligos for Illumina. Finally the Q5 Hot Start HiFi PCR Master Mix was used for PCR enrichment of the adaptor ligated DNA. The concentration and quality of the constructed sequencing libraries were measured by using the Agilent High Sensitivity DNA Kit and a Bioanalyzer 2100 from Agilent Technologies. The libraries were submitted to 51 bp single end high throughput sequencing by the Center for Advanced Technology CAT of the University of California San Francisco using Hiseq 3000.     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   SRP495638     noxo1a-ctrl-2_S33_L004_R1_001.fastq.gz noxo1a-ctrl-2_S33_L004_R2_001.fastq.gz fastq fastq 6591167700.0 21970559.0 noxo1a ctrl 2 S33 L004 R1 001.fastq.gz 0:150 1:150 A:1750729608;C:1535828938;G:1566173485;T:1738090384;N:345285 150 150     1750729608 1535828938 1566173485 1738090384 345285 SRX23967967 SRS20767198 SRA1825819 Chinese Academy of Sciences|Institute of Hydrobiology Chinese Academy of Sciences                       B B biological fallback assumption illumina novaseq_era unknown random_priming nebnext bulk unknown unknown   China 2024-03-16 Larval Larval Trunk Surface Structure
31492 31492 SRR28362841 SRX23967966 SRS20767197 SRP495638 PRJNA1088730 Effects of noxo1a deficiency on gene expression in zebrafish larvae upon exposure to cold warm stress PRJNA1088730 Other Exposure of fish to cold warm stress was reported to elicit ROS generation and subsequent tissue damage. On the other hand ROS signaling is essential for many physiological functions of the organism. As a NADPH oxidase NOX organizer deficiency of Noxo1a is expected to decrease the content of hydrogen peroxide in fish tissue upon exposure to cold warm stress. In this study the effect on Noxo1a deficiency on gene expression in zebrafish larvae under cold warm stress was characterized by RNA sequencing.       noxo1a ctrl#1 noxo1a ctrl#1   strain:AB strain|dev stage:Larvae|collection date:2023 03 05|geo loc name:China: Wuhan|sex:not determined|tissue:Whole body|genotype:noxo1a mutant with indel|treatment:Collected at 96 hpf|replicate:replicate = biological replicate 1|BioSampleModel:Model organism or animal                 noxo1a ctrl#1 noxo1a ctrl#1 noxo1a ctrl#1 One microgram total RNA from each sample was used as the beginning material for sequencing library construction. Each treatment included 4 biological replicates. The NEBNext rRNA Depletion Kit was used for rRNA depletion. post rRNA depletion Agencourt RNAClean XP Beads from Beckman Coulter were used for RNA purification. Then the NEBNext Ultra Directional RNA Library Prep Kit for Illumina was used for RNA fragmentation first and second strand cDNA synthesis double stranded cDNA end repair. Double strand cDNAs were purified using the Agencourt AMPure XP from Beckman Coulter and ligated to adaptors of NEBNext Multiplex Oligos for Illumina. Finally the Q5 Hot Start HiFi PCR Master Mix was used for PCR enrichment of the adaptor ligated DNA. The concentration and quality of the constructed sequencing libraries were measured by using the Agilent High Sensitivity DNA Kit and a Bioanalyzer 2100 from Agilent Technologies. The libraries were submitted to 51 bp single end high throughput sequencing by the Center for Advanced Technology CAT of the University of California San Francisco using Hiseq 3000.     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   SRP495638     noxo1a-ctrl-1_S32_L004_R1_001.fastq.gz noxo1a-ctrl-1_S32_L004_R2_001.fastq.gz fastq fastq 7083186300.0 23610621.0 noxo1a ctrl 1 S32 L004 R1 001.fastq.gz 0:150 1:150 A:1869161754;C:1663101510;G:1702666018;T:1847889969;N:367049 150 150     1869161754 1663101510 1702666018 1847889969 367049 SRX23967966 SRS20767197 SRA1825819 Chinese Academy of Sciences|Institute of Hydrobiology Chinese Academy of Sciences                       B B biological fallback assumption illumina novaseq_era unknown random_priming nebnext bulk unknown unknown   China 2024-03-16 Larval Larval Trunk Surface Structure
31493 31493 SRR28362842 SRX23967965 SRS20767196 SRP495638 PRJNA1088730 Effects of noxo1a deficiency on gene expression in zebrafish larvae upon exposure to cold warm stress PRJNA1088730 Other Exposure of fish to cold warm stress was reported to elicit ROS generation and subsequent tissue damage. On the other hand ROS signaling is essential for many physiological functions of the organism. As a NADPH oxidase NOX organizer deficiency of Noxo1a is expected to decrease the content of hydrogen peroxide in fish tissue upon exposure to cold warm stress. In this study the effect on Noxo1a deficiency on gene expression in zebrafish larvae under cold warm stress was characterized by RNA sequencing.       WT re#4 WT re#4   strain:AB strain|dev stage:Larvae|collection date:2023 03 05|geo loc name:China: Wuhan|sex:not determined|tissue:Whole body|genotype:Wild type|treatment:Exposed to 10 °C for 12 h followed by recovery at 28 °C for 6 h|replicate:replicate = biological replicate 4|BioSampleModel:Model organism or animal                 WT re#4 WT re#4 WT re#4 One microgram total RNA from each sample was used as the beginning material for sequencing library construction. Each treatment included 4 biological replicates. The NEBNext rRNA Depletion Kit was used for rRNA depletion. post rRNA depletion Agencourt RNAClean XP Beads from Beckman Coulter were used for RNA purification. Then the NEBNext Ultra Directional RNA Library Prep Kit for Illumina was used for RNA fragmentation first and second strand cDNA synthesis double stranded cDNA end repair. Double strand cDNAs were purified using the Agencourt AMPure XP from Beckman Coulter and ligated to adaptors of NEBNext Multiplex Oligos for Illumina. Finally the Q5 Hot Start HiFi PCR Master Mix was used for PCR enrichment of the adaptor ligated DNA. The concentration and quality of the constructed sequencing libraries were measured by using the Agilent High Sensitivity DNA Kit and a Bioanalyzer 2100 from Agilent Technologies. The libraries were submitted to 51 bp single end high throughput sequencing by the Center for Advanced Technology CAT of the University of California San Francisco using Hiseq 3000.     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   SRP495638     wt-re-4_S24_L004_R1_001.fastq.gz wt-re-4_S24_L004_R2_001.fastq.gz fastq fastq 6571058100.0 21903527.0 wt re 4 S24 L004 R1 001.fastq.gz 0:150 1:150 A:1733008779;C:1544891080;G:1572067431;T:1720784422;N:306388 150 150     1733008779 1544891080 1572067431 1720784422 306388 SRX23967965 SRS20767196 SRA1825819 Chinese Academy of Sciences|Institute of Hydrobiology Chinese Academy of Sciences                       B B biological fallback assumption illumina novaseq_era unknown random_priming nebnext bulk unknown unknown   China 2024-03-16 Larval Larval Trunk Surface Structure
31494 31494 SRR28362843 SRX23967964 SRS20767195 SRP495638 PRJNA1088730 Effects of noxo1a deficiency on gene expression in zebrafish larvae upon exposure to cold warm stress PRJNA1088730 Other Exposure of fish to cold warm stress was reported to elicit ROS generation and subsequent tissue damage. On the other hand ROS signaling is essential for many physiological functions of the organism. As a NADPH oxidase NOX organizer deficiency of Noxo1a is expected to decrease the content of hydrogen peroxide in fish tissue upon exposure to cold warm stress. In this study the effect on Noxo1a deficiency on gene expression in zebrafish larvae under cold warm stress was characterized by RNA sequencing.       WT re#3 WT re#3   strain:AB strain|dev stage:Larvae|collection date:2023 03 05|geo loc name:China: Wuhan|sex:not determined|tissue:Whole body|genotype:Wild type|treatment:Exposed to 10 °C for 12 h followed by recovery at 28 °C for 6 h|replicate:replicate = biological replicate 3|BioSampleModel:Model organism or animal                 WT re#3 WT re#3 WT re#3 One microgram total RNA from each sample was used as the beginning material for sequencing library construction. Each treatment included 4 biological replicates. The NEBNext rRNA Depletion Kit was used for rRNA depletion. post rRNA depletion Agencourt RNAClean XP Beads from Beckman Coulter were used for RNA purification. Then the NEBNext Ultra Directional RNA Library Prep Kit for Illumina was used for RNA fragmentation first and second strand cDNA synthesis double stranded cDNA end repair. Double strand cDNAs were purified using the Agencourt AMPure XP from Beckman Coulter and ligated to adaptors of NEBNext Multiplex Oligos for Illumina. Finally the Q5 Hot Start HiFi PCR Master Mix was used for PCR enrichment of the adaptor ligated DNA. The concentration and quality of the constructed sequencing libraries were measured by using the Agilent High Sensitivity DNA Kit and a Bioanalyzer 2100 from Agilent Technologies. The libraries were submitted to 51 bp single end high throughput sequencing by the Center for Advanced Technology CAT of the University of California San Francisco using Hiseq 3000.     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   SRP495638     wt-re-3_S43_L004_R1_001.fastq.gz wt-re-3_S43_L004_R2_001.fastq.gz fastq fastq 7263273300.0 24210911.0 wt re 3 S43 L004 R1 001.fastq.gz 0:150 1:150 A:1933925580;C:1690509128;G:1721840325;T:1916618378;N:379889 150 150     1933925580 1690509128 1721840325 1916618378 379889 SRX23967964 SRS20767195 SRA1825819 Chinese Academy of Sciences|Institute of Hydrobiology Chinese Academy of Sciences                       B B biological fallback assumption illumina novaseq_era unknown random_priming nebnext bulk unknown unknown   China 2024-03-16 Larval Larval Trunk Surface Structure
31495 31495 SRR28362844 SRX23967963 SRS20767194 SRP495638 PRJNA1088730 Effects of noxo1a deficiency on gene expression in zebrafish larvae upon exposure to cold warm stress PRJNA1088730 Other Exposure of fish to cold warm stress was reported to elicit ROS generation and subsequent tissue damage. On the other hand ROS signaling is essential for many physiological functions of the organism. As a NADPH oxidase NOX organizer deficiency of Noxo1a is expected to decrease the content of hydrogen peroxide in fish tissue upon exposure to cold warm stress. In this study the effect on Noxo1a deficiency on gene expression in zebrafish larvae under cold warm stress was characterized by RNA sequencing.       WT ctrl#2 WT ctrl#2   strain:AB strain|dev stage:Larvae|collection date:2023 03 05|geo loc name:China: Wuhan|sex:not determined|tissue:Whole body|genotype:Wild type|treatment:Collected at 96 hpf|replicate:replicate = biological replicate 2|BioSampleModel:Model organism or animal                 WT ctrl#2 WT ctrl#2 WT ctrl#2 One microgram total RNA from each sample was used as the beginning material for sequencing library construction. Each treatment included 4 biological replicates. The NEBNext rRNA Depletion Kit was used for rRNA depletion. post rRNA depletion Agencourt RNAClean XP Beads from Beckman Coulter were used for RNA purification. Then the NEBNext Ultra Directional RNA Library Prep Kit for Illumina was used for RNA fragmentation first and second strand cDNA synthesis double stranded cDNA end repair. Double strand cDNAs were purified using the Agencourt AMPure XP from Beckman Coulter and ligated to adaptors of NEBNext Multiplex Oligos for Illumina. Finally the Q5 Hot Start HiFi PCR Master Mix was used for PCR enrichment of the adaptor ligated DNA. The concentration and quality of the constructed sequencing libraries were measured by using the Agilent High Sensitivity DNA Kit and a Bioanalyzer 2100 from Agilent Technologies. The libraries were submitted to 51 bp single end high throughput sequencing by the Center for Advanced Technology CAT of the University of California San Francisco using Hiseq 3000.     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   SRP495638     wt-ctrl-2_S19_L004_R1_001.fastq.gz wt-ctrl-2_S19_L004_R2_001.fastq.gz fastq fastq 6989097000.0 23296990.0 wt ctrl 2 S19 L004 R1 001.fastq.gz 0:150 1:150 A:1831914872;C:1651035418;G:1692865635;T:1812968538;N:312537 150 150     1831914872 1651035418 1692865635 1812968538 312537 SRX23967963 SRS20767194 SRA1825819 Chinese Academy of Sciences|Institute of Hydrobiology Chinese Academy of Sciences                       B B biological fallback assumption illumina novaseq_era unknown random_priming nebnext bulk unknown unknown   China 2024-03-16 Larval Larval Trunk Surface Structure
31496 31496 SRR28362845 SRX23967962 SRS20767193 SRP495638 PRJNA1088730 Effects of noxo1a deficiency on gene expression in zebrafish larvae upon exposure to cold warm stress PRJNA1088730 Other Exposure of fish to cold warm stress was reported to elicit ROS generation and subsequent tissue damage. On the other hand ROS signaling is essential for many physiological functions of the organism. As a NADPH oxidase NOX organizer deficiency of Noxo1a is expected to decrease the content of hydrogen peroxide in fish tissue upon exposure to cold warm stress. In this study the effect on Noxo1a deficiency on gene expression in zebrafish larvae under cold warm stress was characterized by RNA sequencing.       WT ctrl#1 WT ctrl#1   strain:AB strain|dev stage:Larvae|collection date:2023 03 05|geo loc name:China: Wuhan|sex:not determined|tissue:Whole body|genotype:Wild type|treatment:Collected at 96 hpf|replicate:replicate = biological replicate 1|BioSampleModel:Model organism or animal                 WT ctrl#1 WT ctrl#1 WT ctrl#1 One microgram total RNA from each sample was used as the beginning material for sequencing library construction. Each treatment included 4 biological replicates. The NEBNext rRNA Depletion Kit was used for rRNA depletion. post rRNA depletion Agencourt RNAClean XP Beads from Beckman Coulter were used for RNA purification. Then the NEBNext Ultra Directional RNA Library Prep Kit for Illumina was used for RNA fragmentation first and second strand cDNA synthesis double stranded cDNA end repair. Double strand cDNAs were purified using the Agencourt AMPure XP from Beckman Coulter and ligated to adaptors of NEBNext Multiplex Oligos for Illumina. Finally the Q5 Hot Start HiFi PCR Master Mix was used for PCR enrichment of the adaptor ligated DNA. The concentration and quality of the constructed sequencing libraries were measured by using the Agilent High Sensitivity DNA Kit and a Bioanalyzer 2100 from Agilent Technologies. The libraries were submitted to 51 bp single end high throughput sequencing by the Center for Advanced Technology CAT of the University of California San Francisco using Hiseq 3000.     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   SRP495638     wt-ctrl-1_S30_L004_R1_001.fastq.gz wt-ctrl-1_S30_L004_R2_001.fastq.gz fastq fastq 7158502800.0 23861676.0 wt ctrl 1 S30 L004 R1 001.fastq.gz 0:150 1:150 A:1880251200;C:1687764492;G:1727478938;T:1862632997;N:375173 150 150     1880251200 1687764492 1727478938 1862632997 375173 SRX23967962 SRS20767193 SRA1825819 Chinese Academy of Sciences|Institute of Hydrobiology Chinese Academy of Sciences                       B B biological fallback assumption illumina novaseq_era unknown random_priming nebnext bulk unknown unknown   China 2024-03-16 Larval Larval Trunk Surface Structure
42197 42197 SRR5485641 SRX2768777 SRS2152486 SRP105410 PRJNA384462 Danio rerio Transcriptome or Gene expression PRJNA384462 Whole Genome Sequencing 5 dpf larval zebrafish Danio rerio were exposed to 0 5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.         A 3.0.2   ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:3.0.2|age:newborn|BioSampleModel:Model organism or animal                 Danio rerio Raw sequence reads A 3.0.2 A 3.0.2 Illumina HiSeq read information to generate gene expression values     WGS TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2500   SRP105410     HI.4079.001.Index_4.A_R1.fastq.gz HI.4096.008.Index_4.A_R1.fastq.gz fastq fastq 2072387100.0 20723871.0 HI.4079.001.Index 4.A R1.fastq.gz 0:100 1:0 A:539231555;C:478779687;G:466992364;T:587014266;N:369228 100 0     539231555 478779687 466992364 587014266 369228 SRX2768777 SRS2152486 SRA557480 Brandon University|Biology Brandon University 1 0.94094   0.13282   0.67566   0.46135   100   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2018-09-11 Undetermined Multi-stage Trunk Surface Structure
42198 42198 SRR5485640 SRX2768776 SRS2152485 SRP105410 PRJNA384462 Danio rerio Transcriptome or Gene expression PRJNA384462 Whole Genome Sequencing 5 dpf larval zebrafish Danio rerio were exposed to 0 5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.         B 3.5.2   ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:3.5.2|age:newborn|BioSampleModel:Model organism or animal                 Danio rerio Raw sequence reads B 3.5.2 B 3.5.2 Illumina HiSeq read information to generate gene expression values     WGS TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2500   SRP105410     HI.4079.001.Index_5.B_R1.fastq.gz HI.4096.008.Index_5.B_R1.fastq.gz fastq fastq 2236492200.0 22364922.0 HI.4079.001.Index 5.B R1.fastq.gz 0:100 1:0 A:580646206;C:518191209;G:502712894;T:634542622;N:399269 100 0     580646206 518191209 502712894 634542622 399269 SRX2768776 SRS2152485 SRA557480 Brandon University|Biology Brandon University 1 0.94188   0.13073   0.67653   0.4635   100   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2018-09-11 Undetermined Multi-stage Trunk Surface Structure
42199 42199 SRR5485639 SRX2768775 SRS2152484 SRP105410 PRJNA384462 Danio rerio Transcriptome or Gene expression PRJNA384462 Whole Genome Sequencing 5 dpf larval zebrafish Danio rerio were exposed to 0 5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.         C 3.20.2   ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:3.20.2|age:newborn|BioSampleModel:Model organism or animal                 Danio rerio Raw sequence reads C 3.20.2 C 3.20.2 Illumina HiSeq read information to generate gene expression values     WGS TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2500   SRP105410     HI.4079.001.Index_12.C_R1.fastq.gz HI.4096.008.Index_12.C_R1.fastq.gz fastq fastq 1979628000.0 19796280.0 HI.4079.001.Index 12.C R1.fastq.gz 0:100 1:0 A:519406228;C:453563284;G:442115002;T:564195493;N:347993 100 0     519406228 453563284 442115002 564195493 347993 SRX2768775 SRS2152484 SRA557480 Brandon University|Biology Brandon University 1 0.93946   0.14364   0.6759   0.46247   100   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2018-09-11 Undetermined Multi-stage Trunk Surface Structure
42200 42200 SRR5485638 SRX2768774 SRS2152483 SRP105410 PRJNA384462 Danio rerio Transcriptome or Gene expression PRJNA384462 Whole Genome Sequencing 5 dpf larval zebrafish Danio rerio were exposed to 0 5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.         D 3.0.14   ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:3.0.14|age:newborn|BioSampleModel:Model organism or animal                 Danio rerio Raw sequence reads D 3.0.14 D 3.0.14 Illumina HiSeq read information to generate gene expression values     WGS TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2500   SRP105410     HI.4079.001.Index_19.D_R1.fastq.gz HI.4096.008.Index_19.D_R1.fastq.gz fastq fastq 1856095600.0 18560956.0 HI.4079.001.Index 19.D R1.fastq.gz 0:100 1:0 A:492424946;C:416504198;G:409645413;T:537196088;N:324955 100 0     492424946 416504198 409645413 537196088 324955 SRX2768774 SRS2152483 SRA557480 Brandon University|Biology Brandon University 1 0.9288   0.15497   0.69232   0.46842   100   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2018-09-11 Undetermined Multi-stage Trunk Surface Structure
42201 42201 SRR5485637 SRX2768773 SRS2152481 SRP105410 PRJNA384462 Danio rerio Transcriptome or Gene expression PRJNA384462 Whole Genome Sequencing 5 dpf larval zebrafish Danio rerio were exposed to 0 5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.         E 3.5.14   ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:3.5.14|age:newborn|BioSampleModel:Model organism or animal                 Danio rerio Raw sequence reads E 3.5.14 E 3.5.14 Illumina HiSeq read information to generate gene expression values     WGS TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2500   SRP105410     HI.4096.008.Index_1.E_R1.fastq.gz HI.4079.001.Index_1.E_R1.fastq.gz fastq fastq 2936761500.0 29367615.0 HI.4079.001.Index 1.E R1.fastq.gz 0:100 1:0 A:762661816;C:675701333;G:661832769;T:836033713;N:531869 100 0     762661816 675701333 661832769 836033713 531869 SRX2768773 SRS2152481 SRA557480 Brandon University|Biology Brandon University 1 0.93957   0.12499   0.67714   0.4697   100   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2017-05-08 Undetermined Multi-stage Trunk Surface Structure
42202 42202 SRR5485636 SRX2768772 SRS2152480 SRP105410 PRJNA384462 Danio rerio Transcriptome or Gene expression PRJNA384462 Whole Genome Sequencing 5 dpf larval zebrafish Danio rerio were exposed to 0 5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.         F 3.20.14   ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:3.20.14|age:newborn|BioSampleModel:Model organism or animal                 Danio rerio Raw sequence reads F 3.20.14 F 3.20.14 Illumina HiSeq read information to generate gene expression values     WGS TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2500   SRP105410     HI.4079.001.Index_3.F_R1.fastq.gz HI.4096.008.Index_3.F_R1.fastq.gz fastq fastq 2169884500.0 21698845.0 HI.4079.001.Index 3.F R1.fastq.gz 0:100 1:0 A:566808272;C:496620769;G:487930959;T:618144722;N:379778 100 0     566808272 496620769 487930959 618144722 379778 SRX2768772 SRS2152480 SRA557480 Brandon University|Biology Brandon University 1 0.93678   0.13131   0.67635   0.47972   100   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2018-09-11 Undetermined Multi-stage Trunk Surface Structure
42203 42203 SRR5485635 SRX2768771 SRS2152482 SRP105410 PRJNA384462 Danio rerio Transcriptome or Gene expression PRJNA384462 Whole Genome Sequencing 5 dpf larval zebrafish Danio rerio were exposed to 0 5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.         G 4.0.2   ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:4.0.2|age:newborn|BioSampleModel:Model organism or animal                 Danio rerio Raw sequence reads G 4.0.2 G 4.0.2 Illumina HiSeq read information to generate gene expression values     WGS TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2500   SRP105410     HI.4079.001.Index_9.G_R1.fastq.gz HI.4096.008.Index_9.G_R1.fastq.gz fastq fastq 2008051800.0 20080518.0 HI.4079.001.Index 9.G R1.fastq.gz 0:100 1:0 A:518304309;C:466602325;G:455957803;T:566834696;N:352667 100 0     518304309 466602325 455957803 566834696 352667 SRX2768771 SRS2152482 SRA557480 Brandon University|Biology Brandon University 1 0.94445   0.12419   0.68201   0.46743   100   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2018-09-11 Undetermined Multi-stage Trunk Surface Structure
42204 42204 SRR5485634 SRX2768770 SRS2152479 SRP105410 PRJNA384462 Danio rerio Transcriptome or Gene expression PRJNA384462 Whole Genome Sequencing 5 dpf larval zebrafish Danio rerio were exposed to 0 5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.         H 4.5.2   ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:4.5.2|age:newborn|BioSampleModel:Model organism or animal                 Danio rerio Raw sequence reads H 4.5.2 H 4.5.2 Illumina HiSeq read information to generate gene expression values     WGS TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2500   SRP105410     HI.4079.001.Index_8.H_R1.fastq.gz HI.4096.008.Index_8.H_R1.fastq.gz fastq fastq 1908097900.0 19080979.0 HI.4079.001.Index 8.H R1.fastq.gz 0:100 1:0 A:494318032;C:441931870;G:431477592;T:540030651;N:339755 100 0     494318032 441931870 431477592 540030651 339755 SRX2768770 SRS2152479 SRA557480 Brandon University|Biology Brandon University 1 0.94216   0.1306   0.68195   0.45834   100   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2018-09-11 Undetermined Multi-stage Trunk Surface Structure
42205 42205 SRR5485633 SRX2768769 SRS2152477 SRP105410 PRJNA384462 Danio rerio Transcriptome or Gene expression PRJNA384462 Whole Genome Sequencing 5 dpf larval zebrafish Danio rerio were exposed to 0 5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.         I 4.20.2   ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:4.20.2|age:newborn|BioSampleModel:Model organism or animal                 Danio rerio Raw sequence reads I 4.20.2 I 4.20.2 Illumina HiSeq read information to generate gene expression values     WGS TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2500   SRP105410     HI.4079.001.Index_10.I_R1.fastq.gz HI.4096.008.Index_10.I_R1.fastq.gz fastq fastq 2059931100.0 20599311.0 HI.4079.001.Index 10.I R1.fastq.gz 0:100 1:0 A:536731862;C:475769707;G:462890515;T:584183211;N:355805 100 0     536731862 475769707 462890515 584183211 355805 SRX2768769 SRS2152477 SRA557480 Brandon University|Biology Brandon University 1 0.93561   0.13393   0.68225   0.46489   100   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2018-09-11 Undetermined Multi-stage Trunk Surface Structure
42206 42206 SRR5485632 SRX2768768 SRS2152478 SRP105410 PRJNA384462 Danio rerio Transcriptome or Gene expression PRJNA384462 Whole Genome Sequencing 5 dpf larval zebrafish Danio rerio were exposed to 0 5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.         J 4.0.14   ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:4.0.14|age:newborn|BioSampleModel:Model organism or animal                 Danio rerio Raw sequence reads J 4.0.14 J 4.0.14 Illumina HiSeq read information to generate gene expression values     WGS TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2500   SRP105410     HI.4079.001.Index_11.J_R1.fastq.gz HI.4096.008.Index_11.J_R1.fastq.gz fastq fastq 2199504800.0 21995048.0 HI.4079.001.Index 11.J R1.fastq.gz 0:100 1:0 A:579625731;C:499663817;G:489173373;T:630657278;N:384601 100 0     579625731 499663817 489173373 630657278 384601 SRX2768768 SRS2152478 SRA557480 Brandon University|Biology Brandon University 1 0.93523   0.13836   0.68655   0.47839   100   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2018-09-11 Undetermined Multi-stage Trunk Surface Structure
42207 42207 SRR5485631 SRX2768767 SRS2152475 SRP105410 PRJNA384462 Danio rerio Transcriptome or Gene expression PRJNA384462 Whole Genome Sequencing 5 dpf larval zebrafish Danio rerio were exposed to 0 5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.         K 4.5.14   ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:4.5.14|age:newborn|BioSampleModel:Model organism or animal                 Danio rerio Raw sequence reads K 4.5.14 K 4.5.14 Illumina HiSeq read information to generate gene expression values     WGS TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2500   SRP105410     HI.4079.001.Index_20.K_R1.fastq.gz HI.4096.008.Index_20.K_R1.fastq.gz fastq fastq 2154282200.0 21542822.0 HI.4079.001.Index 20.K R1.fastq.gz 0:100 1:0 A:563358732;C:494058898;G:482596638;T:613890813;N:377119 100 0     563358732 494058898 482596638 613890813 377119 SRX2768767 SRS2152475 SRA557480 Brandon University|Biology Brandon University 1 0.93863   0.12932   0.67801   0.46426   100   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2018-09-11 Undetermined Multi-stage Trunk Surface Structure
42208 42208 SRR5485630 SRX2768766 SRS2152476 SRP105410 PRJNA384462 Danio rerio Transcriptome or Gene expression PRJNA384462 Whole Genome Sequencing 5 dpf larval zebrafish Danio rerio were exposed to 0 5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.         L 4.20.14   ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:4.20.14|age:newborn|BioSampleModel:Model organism or animal                 Danio rerio Raw sequence reads L 4.20.14 L 4.20.14 Illumina HiSeq read information to generate gene expression values     WGS TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2500   SRP105410     HI.4096.008.Index_22.L_R1.fastq.gz HI.4079.001.Index_22.L_R1.fastq.gz fastq fastq 2702515700.0 27025157.0 HI.4079.001.Index 22.L R1.fastq.gz 0:100 1:0 A:708045960;C:615042366;G:603133757;T:775807969;N:485648 100 0     708045960 615042366 603133757 775807969 485648 SRX2768766 SRS2152476 SRA557480 Brandon University|Biology Brandon University 1 0.93316   0.14421   0.68915   0.47027   100   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2017-05-08 Undetermined Multi-stage Trunk Surface Structure
42209 42209 SRR5485629 SRX2768765 SRS2152474 SRP105410 PRJNA384462 Danio rerio Transcriptome or Gene expression PRJNA384462 Whole Genome Sequencing 5 dpf larval zebrafish Danio rerio were exposed to 0 5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.         M 5.0.2   ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:5.0.2|age:newborn|BioSampleModel:Model organism or animal                 Danio rerio Raw sequence reads M 5.0.2 M 5.0.2 Illumina HiSeq read information to generate gene expression values     WGS TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2500   SRP105410     HI.4079.001.Index_25.M_R1.fastq.gz HI.4096.008.Index_25.M_R1.fastq.gz fastq fastq 1999183400.0 19991834.0 HI.4079.001.Index 25.M R1.fastq.gz 0:100 1:0 A:526344986;C:456726468;G:447467581;T:568292150;N:352215 100 0     526344986 456726468 447467581 568292150 352215 SRX2768765 SRS2152474 SRA557480 Brandon University|Biology Brandon University 1 0.9374   0.14185   0.67665   0.47249   100   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2018-09-11 Undetermined Multi-stage Trunk Surface Structure
42210 42210 SRR5485628 SRX2768764 SRS2152473 SRP105410 PRJNA384462 Danio rerio Transcriptome or Gene expression PRJNA384462 Whole Genome Sequencing 5 dpf larval zebrafish Danio rerio were exposed to 0 5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.         N 5.5.2   ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:5.5.2|age:newborn|BioSampleModel:Model organism or animal                 Danio rerio Raw sequence reads N 5.5.2 N 5.5.2 Illumina HiSeq read information to generate gene expression values     WGS TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2500   SRP105410     HI.4079.001.Index_21.N_R1.fastq.gz HI.4096.008.Index_21.N_R1.fastq.gz fastq fastq 2097386100.0 20973861.0 HI.4079.001.Index 21.N R1.fastq.gz 0:100 1:0 A:551586521;C:479609380;G:467572413;T:598246436;N:371350 100 0     551586521 479609380 467572413 598246436 371350 SRX2768764 SRS2152473 SRA557480 Brandon University|Biology Brandon University 1 0.93984   0.13949   0.68219   0.46921   100   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2018-09-11 Undetermined Multi-stage Trunk Surface Structure
42211 42211 SRR5485627 SRX2768763 SRS2152472 SRP105410 PRJNA384462 Danio rerio Transcriptome or Gene expression PRJNA384462 Whole Genome Sequencing 5 dpf larval zebrafish Danio rerio were exposed to 0 5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.         O 5.20.2   ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:5.20.2|age:newborn|BioSampleModel:Model organism or animal                 Danio rerio Raw sequence reads O 5.20.2 O 5.20.2 Illumina HiSeq read information to generate gene expression values     WGS TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2500   SRP105410     HI.4079.001.Index_23.O_R1.fastq.gz HI.4096.008.Index_23.O_R1.fastq.gz fastq fastq 2003835800.0 20038358.0 HI.4079.001.Index 23.O R1.fastq.gz 0:100 1:0 A:529075084;C:456810826;G:444441300;T:573155538;N:353052 100 0     529075084 456810826 444441300 573155538 353052 SRX2768763 SRS2152472 SRA557480 Brandon University|Biology Brandon University 1 0.93635   0.15287   0.67712   0.45807   100   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2018-09-11 Undetermined Multi-stage Trunk Surface Structure
42212 42212 SRR5485626 SRX2768762 SRS2152471 SRP105410 PRJNA384462 Danio rerio Transcriptome or Gene expression PRJNA384462 Whole Genome Sequencing 5 dpf larval zebrafish Danio rerio were exposed to 0 5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.         P 5.0.14   ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:5.0.14|age:newborn|BioSampleModel:Model organism or animal                 Danio rerio Raw sequence reads P 5.0.14 P 5.0.14 Illumina HiSeq read information to generate gene expression values     WGS TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2500   SRP105410     HI.4079.001.Index_27.P_R1.fastq.gz HI.4096.008.Index_27.P_R1.fastq.gz fastq fastq 1799355500.0 17993555.0 HI.4079.001.Index 27.P R1.fastq.gz 0:100 1:0 A:485156399;C:399414298;G:389730888;T:524733869;N:320046 100 0     485156399 399414298 389730888 524733869 320046 SRX2768762 SRS2152471 SRA557480 Brandon University|Biology Brandon University 1 0.92813   0.15749   0.67943   0.47424   100   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2018-09-11 Undetermined Multi-stage Trunk Surface Structure
42213 42213 SRR5485625 SRX2768761 SRS2152470 SRP105410 PRJNA384462 Danio rerio Transcriptome or Gene expression PRJNA384462 Whole Genome Sequencing 5 dpf larval zebrafish Danio rerio were exposed to 0 5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.         Q 5.5.14   ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:5.5.14|age:newborn|BioSampleModel:Model organism or animal                 Danio rerio Raw sequence reads Q 5.5.14 Q 5.5.14 Illumina HiSeq read information to generate gene expression values     WGS TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2500   SRP105410     HI.4079.001.Index_2.Q_R1.fastq.gz HI.4096.008.Index_2.Q_R1.fastq.gz fastq fastq 2260494100.0 22604941.0 HI.4079.001.Index 2.Q R1.fastq.gz 0:100 1:0 A:602519260;C:506296484;G:495685951;T:655587703;N:404702 100 0     602519260 506296484 495685951 655587703 404702 SRX2768761 SRS2152470 SRA557480 Brandon University|Biology Brandon University 1 0.92524   0.14979   0.6859   0.47957   100   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2018-09-11 Undetermined Multi-stage Trunk Surface Structure
42214 42214 SRR5485624 SRX2768760 SRS2152469 SRP105410 PRJNA384462 Danio rerio Transcriptome or Gene expression PRJNA384462 Whole Genome Sequencing 5 dpf larval zebrafish Danio rerio were exposed to 0 5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.         R 5.20.14   ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:5.20.14|age:newborn|BioSampleModel:Model organism or animal                 Danio rerio Raw sequence reads R 5.20.14 R 5.20.14 Illumina HiSeq read information to generate gene expression values     WGS TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2500   SRP105410     HI.4079.001.Index_13.R_R1.fastq.gz HI.4096.008.Index_13.R_R1.fastq.gz fastq fastq 1975297900.0 19752979.0 HI.4079.001.Index 13.R R1.fastq.gz 0:100 1:0 A:527732232;C:440160233;G:430962427;T:576091914;N:351094 100 0     527732232 440160233 430962427 576091914 351094 SRX2768760 SRS2152469 SRA557480 Brandon University|Biology Brandon University 1 0.92785   0.15864   0.6814   0.47773   100   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2018-09-11 Undetermined Multi-stage Trunk Surface Structure
42215 42215 SRR5485623 SRX2768759 SRS2152468 SRP105410 PRJNA384462 Danio rerio Transcriptome or Gene expression PRJNA384462 Whole Genome Sequencing 5 dpf larval zebrafish Danio rerio were exposed to 0 5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.         S 6.0.2   ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:S 6.0.2|age:newborn|BioSampleModel:Model organism or animal                 Danio rerio Raw sequence reads S 6.0.2 S 6.0.2 Illumina HiSeq read information to generate gene expression values     WGS TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2500   SRP105410     HI.4079.001.Index_6.S_R1.fastq.gz HI.4096.008.Index_6.S_R1.fastq.gz fastq fastq 2690628500.0 26906285.0 HI.4079.001.Index 6.S R1.fastq.gz 0:100 1:0 A:713021693;C:609779787;G:594591832;T:772745072;N:490116 100 0     713021693 609779787 594591832 772745072 490116 SRX2768759 SRS2152468 SRA557480 Brandon University|Biology Brandon University 1 0.93405   0.15472   0.68505   0.45796   100   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2018-09-11 Undetermined Multi-stage Trunk Surface Structure
42216 42216 SRR5485622 SRX2768758 SRS2152466 SRP105410 PRJNA384462 Danio rerio Transcriptome or Gene expression PRJNA384462 Whole Genome Sequencing 5 dpf larval zebrafish Danio rerio were exposed to 0 5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.         T 6.5.2   ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:6.5.2|age:newborn|BioSampleModel:Model organism or animal                 Danio rerio Raw sequence reads T 6.5.2 T 6.5.2 Illumina HiSeq read information to generate gene expression values     WGS TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2500   SRP105410     HI.4079.001.Index_15.T_R1.fastq.gz HI.4096.008.Index_15.T_R1.fastq.gz fastq fastq 1949043500.0 19490435.0 HI.4079.001.Index 15.T R1.fastq.gz 0:100 1:0 A:515794596;C:441198348;G:430323928;T:561379111;N:347517 100 0     515794596 441198348 430323928 561379111 347517 SRX2768758 SRS2152466 SRA557480 Brandon University|Biology Brandon University 1 0.93579   0.16207   0.68473   0.44993   100   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2018-09-11 Undetermined Multi-stage Trunk Surface Structure
42217 42217 SRR5485621 SRX2768757 SRS2152467 SRP105410 PRJNA384462 Danio rerio Transcriptome or Gene expression PRJNA384462 Whole Genome Sequencing 5 dpf larval zebrafish Danio rerio were exposed to 0 5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.         U 6.20.2   ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:6.20.2|age:newborn|BioSampleModel:Model organism or animal                 Danio rerio Raw sequence reads U 6.20.2 U 6.20.2 Illumina HiSeq read information to generate gene expression values     WGS TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2500   SRP105410     HI.4079.001.Index_7.U_R1.fastq.gz HI.4096.008.Index_7.U_R1.fastq.gz fastq fastq 1754851900.0 17548519.0 HI.4079.001.Index 7.U R1.fastq.gz 0:100 1:0 A:464191451;C:397313933;G:387262108;T:505777499;N:306909 100 0     464191451 397313933 387262108 505777499 306909 SRX2768757 SRS2152467 SRA557480 Brandon University|Biology Brandon University 1 0.93016   0.16163   0.68329   0.47088   100   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2018-09-11 Undetermined Multi-stage Trunk Surface Structure
42218 42218 SRR5485620 SRX2768756 SRS2152463 SRP105410 PRJNA384462 Danio rerio Transcriptome or Gene expression PRJNA384462 Whole Genome Sequencing 5 dpf larval zebrafish Danio rerio were exposed to 0 5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.         V 6.0.14   ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:6.0.14|age:newborn|BioSampleModel:Model organism or animal                 Danio rerio Raw sequence reads V 6.0.14 V 6.0.14 Illumina HiSeq read information to generate gene expression values     WGS TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2500   SRP105410     HI.4079.001.Index_18.V_R1.fastq.gz HI.4096.008.Index_18.V_R1.fastq.gz fastq fastq 2027423200.0 20274232.0 HI.4079.001.Index 18.V R1.fastq.gz 0:100 1:0 A:542440452;C:449399743;G:440389586;T:594839784;N:353635 100 0     542440452 449399743 440389586 594839784 353635 SRX2768756 SRS2152463 SRA557480 Brandon University|Biology Brandon University 1 0.92441   0.16974   0.6842   0.48209   100   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2018-09-11 Undetermined Multi-stage Trunk Surface Structure
42219 42219 SRR5485619 SRX2768755 SRS2152464 SRP105410 PRJNA384462 Danio rerio Transcriptome or Gene expression PRJNA384462 Whole Genome Sequencing 5 dpf larval zebrafish Danio rerio were exposed to 0 5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.         W 6.5.14   ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:6.5.14|age:newborn|BioSampleModel:Model organism or animal                 Danio rerio Raw sequence reads W 6.5.14 W 6.5.14 Illumina HiSeq read information to generate gene expression values     WGS TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2500   SRP105410     HI.4079.001.Index_14.W_R1.fastq.gz HI.4096.008.Index_14.W_R1.fastq.gz fastq fastq 2139528300.0 21395283.0 HI.4079.001.Index 14.W R1.fastq.gz 0:100 1:0 A:569259910;C:478055273;G:469309420;T:622525486;N:378211 100 0     569259910 478055273 469309420 622525486 378211 SRX2768755 SRS2152464 SRA557480 Brandon University|Biology Brandon University 1 0.92551   0.15358   0.68136   0.47093   100   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2018-09-11 Undetermined Multi-stage Trunk Surface Structure
42220 42220 SRR5485618 SRX2768754 SRS2152465 SRP105410 PRJNA384462 Danio rerio Transcriptome or Gene expression PRJNA384462 Whole Genome Sequencing 5 dpf larval zebrafish Danio rerio were exposed to 0 5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.         X 6.20.14   ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:6.20.14|age:newborn|BioSampleModel:Model organism or animal                 Danio rerio Raw sequence reads X 6.20.14 X 6.20.14 Illumina HiSeq read information to generate gene expression values     WGS TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2500   SRP105410     HI.4079.001.Index_16.X_R1.fastq.gz HI.4096.008.Index_16.X_R1.fastq.gz fastq fastq 1768110400.0 17681104.0 HI.4079.001.Index 16.X R1.fastq.gz 0:100 1:0 A:472810124;C:392555880;G:382616900;T:519817796;N:309700 100 0     472810124 392555880 382616900 519817796 309700 SRX2768754 SRS2152465 SRA557480 Brandon University|Biology Brandon University 1 0.92486   0.16073   0.69041   0.48403   100   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2018-09-11 Undetermined Multi-stage Trunk Surface Structure
53587 53587 SRR11886668 SRX8434202 SRS6745285 SRP265421 PRJNA559885 A comparative epigenomic and single cell transcriptomic analysis of teleost regeneration PRJNA559885 Other The ability to regenerate body parts lost to amputation is widely but non uniformly distributed in animals. Species such as bony fishes display extensive regenerative capacities while others such as mammals regenerate poorly. Even though regeneration has been the subject of extensive phylogenetic developmental cellular and molecular studies the mechanisms underlying the broad disparity of regenerative capacities in animals remain elusive. Here we report on a comparative epigenomic and transcriptomic approach which identified an evolutionarily conserved regeneration response program in vertebrates. By defining the cis regulomes and single cell transcriptomes of early stages of regeneration in the distantly related African killifish Nothobranchius furzeri and the zebrafish Danio rerio we uncovered species specific and evolutionarily conserved genomic responses to amputation.       zebrafish fin regeneration zebrafish fin 1dpa   strain:AB|isolate:12|breed:N/A|cultivar:N/A|ecotype:N/A|age:6 mpf|dev stage:Adult|sex:not collected|tissue:caudal fin|BioSampleModel:Model organism or animal                 zebrafish RNAseq 1dpa R3 L34024 L34024 Three biological replicates 6 fish per replicate were prepared for each fin regeneration time point. Ten different African killifish time points were studied including 0dpa 3hpa 6hpa 14hpa 1dpa 2dpa 3dpa 4dpa 7dpa and 18dpa. Samples from 0dpa and 1dpa were collected for zebrafish. All the freshly dissected samples used for RNA seq were quickly rinsed in cold PBS and placed in a 1.5 ml Eppendorf tube followed by flash freezing in liquid nitrogen. Samples were then homogenized with a sterile pestle in 1 ml Trizol reagent Ambion and stored at 80 C until RNA extraction.     RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2500   SRP265421     ws_3_1_GCCAAT.fastq.gz fastq 1907555958.0 37403058.0 ws 3 1 GCCAAT.fastq.gz 0:51 1:0 A:417030128;C:470533688;G:468961155;T:550856047;N:174940 51 0     417030128 470533688 468961155 550856047 174940 SRX8434202 SRS6745285 SRA1081627 Stowers Institute for Medical Research|Sanchez lab Stowers Institute for Medical Research 1 0.96213   0.05602   0.72967   0.45848   51   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   United States 2020-05-31 Adult Adult Fin Surface Structure
53588 53588 SRR11886669 SRX8434201 SRS6745285 SRP265421 PRJNA559885 A comparative epigenomic and single cell transcriptomic analysis of teleost regeneration PRJNA559885 Other The ability to regenerate body parts lost to amputation is widely but non uniformly distributed in animals. Species such as bony fishes display extensive regenerative capacities while others such as mammals regenerate poorly. Even though regeneration has been the subject of extensive phylogenetic developmental cellular and molecular studies the mechanisms underlying the broad disparity of regenerative capacities in animals remain elusive. Here we report on a comparative epigenomic and transcriptomic approach which identified an evolutionarily conserved regeneration response program in vertebrates. By defining the cis regulomes and single cell transcriptomes of early stages of regeneration in the distantly related African killifish Nothobranchius furzeri and the zebrafish Danio rerio we uncovered species specific and evolutionarily conserved genomic responses to amputation.       zebrafish fin regeneration zebrafish fin 1dpa   strain:AB|isolate:12|breed:N/A|cultivar:N/A|ecotype:N/A|age:6 mpf|dev stage:Adult|sex:not collected|tissue:caudal fin|BioSampleModel:Model organism or animal                 zebrafish RNAseq 1dpa R2 L34023 L34023 Three biological replicates 6 fish per replicate were prepared for each fin regeneration time point. Ten different African killifish time points were studied including 0dpa 3hpa 6hpa 14hpa 1dpa 2dpa 3dpa 4dpa 7dpa and 18dpa. Samples from 0dpa and 1dpa were collected for zebrafish. All the freshly dissected samples used for RNA seq were quickly rinsed in cold PBS and placed in a 1.5 ml Eppendorf tube followed by flash freezing in liquid nitrogen. Samples were then homogenized with a sterile pestle in 1 ml Trizol reagent Ambion and stored at 80 C until RNA extraction.     RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2500   SRP265421     ws_3_1_ACAGTG.fastq.gz fastq 1731933225.0 33959475.0 ws 3 1 ACAGTG.fastq.gz 0:51 1:0 A:381487795;C:424246634;G:426026749;T:500012138;N:159909 51 0     381487795 424246634 426026749 500012138 159909 SRX8434201 SRS6745285 SRA1081627 Stowers Institute for Medical Research|Sanchez lab Stowers Institute for Medical Research 1 0.96269   0.05578   0.73261   0.45837   51   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   United States 2020-05-31 Adult Adult Fin Surface Structure
53589 53589 SRR11886671 SRX8434200 SRS6745285 SRP265421 PRJNA559885 A comparative epigenomic and single cell transcriptomic analysis of teleost regeneration PRJNA559885 Other The ability to regenerate body parts lost to amputation is widely but non uniformly distributed in animals. Species such as bony fishes display extensive regenerative capacities while others such as mammals regenerate poorly. Even though regeneration has been the subject of extensive phylogenetic developmental cellular and molecular studies the mechanisms underlying the broad disparity of regenerative capacities in animals remain elusive. Here we report on a comparative epigenomic and transcriptomic approach which identified an evolutionarily conserved regeneration response program in vertebrates. By defining the cis regulomes and single cell transcriptomes of early stages of regeneration in the distantly related African killifish Nothobranchius furzeri and the zebrafish Danio rerio we uncovered species specific and evolutionarily conserved genomic responses to amputation.       zebrafish fin regeneration zebrafish fin 1dpa   strain:AB|isolate:12|breed:N/A|cultivar:N/A|ecotype:N/A|age:6 mpf|dev stage:Adult|sex:not collected|tissue:caudal fin|BioSampleModel:Model organism or animal                 zebrafish RNAseq 1dpa R1 L34022 L34022 Three biological replicates 6 fish per replicate were prepared for each fin regeneration time point. Ten different African killifish time points were studied including 0dpa 3hpa 6hpa 14hpa 1dpa 2dpa 3dpa 4dpa 7dpa and 18dpa. Samples from 0dpa and 1dpa were collected for zebrafish. All the freshly dissected samples used for RNA seq were quickly rinsed in cold PBS and placed in a 1.5 ml Eppendorf tube followed by flash freezing in liquid nitrogen. Samples were then homogenized with a sterile pestle in 1 ml Trizol reagent Ambion and stored at 80 C until RNA extraction.     RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2500   SRP265421     ws_3_1_TGACCA.fastq.gz fastq 1814021907.0 35569057.0 ws 3 1 TGACCA.fastq.gz 0:51 1:0 A:404693395;C:438897306;G:444600496;T:525663505;N:167205 51 0     404693395 438897306 444600496 525663505 167205 SRX8434200 SRS6745285 SRA1081627 Stowers Institute for Medical Research|Sanchez lab Stowers Institute for Medical Research 1 0.95686   0.06383   0.72677   0.44564   51   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   United States 2020-05-31 Adult Adult Fin Surface Structure
53590 53590 SRR11886672 SRX8434199 SRS6745284 SRP265421 PRJNA559885 A comparative epigenomic and single cell transcriptomic analysis of teleost regeneration PRJNA559885 Other The ability to regenerate body parts lost to amputation is widely but non uniformly distributed in animals. Species such as bony fishes display extensive regenerative capacities while others such as mammals regenerate poorly. Even though regeneration has been the subject of extensive phylogenetic developmental cellular and molecular studies the mechanisms underlying the broad disparity of regenerative capacities in animals remain elusive. Here we report on a comparative epigenomic and transcriptomic approach which identified an evolutionarily conserved regeneration response program in vertebrates. By defining the cis regulomes and single cell transcriptomes of early stages of regeneration in the distantly related African killifish Nothobranchius furzeri and the zebrafish Danio rerio we uncovered species specific and evolutionarily conserved genomic responses to amputation.       zebrafish fin regeneration zebrafish fin 0dpa   strain:AB|isolate:11|breed:N/A|cultivar:N/A|ecotype:N/A|age:6 mpf|dev stage:Adult|sex:not collected|tissue:caudal fin|BioSampleModel:Model organism or animal                 zebrafish RNAseq 0dpa R3 L34021 L34021 Three biological replicates 6 fish per replicate were prepared for each fin regeneration time point. Ten different African killifish time points were studied including 0dpa 3hpa 6hpa 14hpa 1dpa 2dpa 3dpa 4dpa 7dpa and 18dpa. Samples from 0dpa and 1dpa were collected for zebrafish. All the freshly dissected samples used for RNA seq were quickly rinsed in cold PBS and placed in a 1.5 ml Eppendorf tube followed by flash freezing in liquid nitrogen. Samples were then homogenized with a sterile pestle in 1 ml Trizol reagent Ambion and stored at 80 C until RNA extraction.     RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2500   SRP265421     ws_3_1_TTAGGC.fastq.gz fastq 1894657395.0 37150145.0 ws 3 1 TTAGGC.fastq.gz 0:51 1:0 A:424630121;C:461337738;G:460024108;T:548490887;N:174541 51 0     424630121 461337738 460024108 548490887 174541 SRX8434199 SRS6745284 SRA1081627 Stowers Institute for Medical Research|Sanchez lab Stowers Institute for Medical Research 1 0.9524   0.08535   0.70999   0.44299   51   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   United States 2020-05-31 Adult Adult Fin Surface Structure
53591 53591 SRR11886673 SRX8434198 SRS6745284 SRP265421 PRJNA559885 A comparative epigenomic and single cell transcriptomic analysis of teleost regeneration PRJNA559885 Other The ability to regenerate body parts lost to amputation is widely but non uniformly distributed in animals. Species such as bony fishes display extensive regenerative capacities while others such as mammals regenerate poorly. Even though regeneration has been the subject of extensive phylogenetic developmental cellular and molecular studies the mechanisms underlying the broad disparity of regenerative capacities in animals remain elusive. Here we report on a comparative epigenomic and transcriptomic approach which identified an evolutionarily conserved regeneration response program in vertebrates. By defining the cis regulomes and single cell transcriptomes of early stages of regeneration in the distantly related African killifish Nothobranchius furzeri and the zebrafish Danio rerio we uncovered species specific and evolutionarily conserved genomic responses to amputation.       zebrafish fin regeneration zebrafish fin 0dpa   strain:AB|isolate:11|breed:N/A|cultivar:N/A|ecotype:N/A|age:6 mpf|dev stage:Adult|sex:not collected|tissue:caudal fin|BioSampleModel:Model organism or animal                 zebrafish RNAseq 0dpa R2 L34020 L34020 Three biological replicates 6 fish per replicate were prepared for each fin regeneration time point. Ten different African killifish time points were studied including 0dpa 3hpa 6hpa 14hpa 1dpa 2dpa 3dpa 4dpa 7dpa and 18dpa. Samples from 0dpa and 1dpa were collected for zebrafish. All the freshly dissected samples used for RNA seq were quickly rinsed in cold PBS and placed in a 1.5 ml Eppendorf tube followed by flash freezing in liquid nitrogen. Samples were then homogenized with a sterile pestle in 1 ml Trizol reagent Ambion and stored at 80 C until RNA extraction.     RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2500   SRP265421     ws_3_1_CGATGT.fastq.gz fastq 1826016036.0 35804236.0 ws 3 1 CGATGT.fastq.gz 0:51 1:0 A:408512993;C:445830968;G:443573205;T:527930321;N:168549 51 0     408512993 445830968 443573205 527930321 168549 SRX8434198 SRS6745284 SRA1081627 Stowers Institute for Medical Research|Sanchez lab Stowers Institute for Medical Research 1 0.95224   0.08373   0.70934   0.45345   51   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   United States 2020-05-31 Adult Adult Fin Surface Structure
53592 53592 SRR11886674 SRX8434197 SRS6745284 SRP265421 PRJNA559885 A comparative epigenomic and single cell transcriptomic analysis of teleost regeneration PRJNA559885 Other The ability to regenerate body parts lost to amputation is widely but non uniformly distributed in animals. Species such as bony fishes display extensive regenerative capacities while others such as mammals regenerate poorly. Even though regeneration has been the subject of extensive phylogenetic developmental cellular and molecular studies the mechanisms underlying the broad disparity of regenerative capacities in animals remain elusive. Here we report on a comparative epigenomic and transcriptomic approach which identified an evolutionarily conserved regeneration response program in vertebrates. By defining the cis regulomes and single cell transcriptomes of early stages of regeneration in the distantly related African killifish Nothobranchius furzeri and the zebrafish Danio rerio we uncovered species specific and evolutionarily conserved genomic responses to amputation.       zebrafish fin regeneration zebrafish fin 0dpa   strain:AB|isolate:11|breed:N/A|cultivar:N/A|ecotype:N/A|age:6 mpf|dev stage:Adult|sex:not collected|tissue:caudal fin|BioSampleModel:Model organism or animal                 zebrafish RNAseq 0dpa R1 L34019 L34019 Three biological replicates 6 fish per replicate were prepared for each fin regeneration time point. Ten different African killifish time points were studied including 0dpa 3hpa 6hpa 14hpa 1dpa 2dpa 3dpa 4dpa 7dpa and 18dpa. Samples from 0dpa and 1dpa were collected for zebrafish. All the freshly dissected samples used for RNA seq were quickly rinsed in cold PBS and placed in a 1.5 ml Eppendorf tube followed by flash freezing in liquid nitrogen. Samples were then homogenized with a sterile pestle in 1 ml Trizol reagent Ambion and stored at 80 C until RNA extraction.     RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2500   SRP265421     ws_3_1_ATCACG.fastq.gz fastq 1889698206.0 37052906.0 ws 3 1 ATCACG.fastq.gz 0:51 1:0 A:425019592;C:459513661;G:459679307;T:545311781;N:173865 51 0     425019592 459513661 459679307 545311781 173865 SRX8434197 SRS6745284 SRA1081627 Stowers Institute for Medical Research|Sanchez lab Stowers Institute for Medical Research 1 0.95224   0.08995   0.71106   0.45283   51   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   United States 2020-05-31 Adult Adult Fin Surface Structure
53593 53593 SRR11886700 SRX8434172 SRS6745285 SRP265421 PRJNA559885 A comparative epigenomic and single cell transcriptomic analysis of teleost regeneration PRJNA559885 Other The ability to regenerate body parts lost to amputation is widely but non uniformly distributed in animals. Species such as bony fishes display extensive regenerative capacities while others such as mammals regenerate poorly. Even though regeneration has been the subject of extensive phylogenetic developmental cellular and molecular studies the mechanisms underlying the broad disparity of regenerative capacities in animals remain elusive. Here we report on a comparative epigenomic and transcriptomic approach which identified an evolutionarily conserved regeneration response program in vertebrates. By defining the cis regulomes and single cell transcriptomes of early stages of regeneration in the distantly related African killifish Nothobranchius furzeri and the zebrafish Danio rerio we uncovered species specific and evolutionarily conserved genomic responses to amputation.       zebrafish fin regeneration zebrafish fin 1dpa   strain:AB|isolate:12|breed:N/A|cultivar:N/A|ecotype:N/A|age:6 mpf|dev stage:Adult|sex:not collected|tissue:caudal fin|BioSampleModel:Model organism or animal                 zebrafish blastema single cell L41598 L41598 The African killifish and zebrafish single cell RNA seq were done with the 10x Chromium platform. About 20 fish were used for cell dissociation in each experiment. Hoechst stained cells 100 000 cells from the dissected blastema tissues at 1dpa were collected on ice using a BD Influx sorter. The viability of cells 94.5% was determined before loading cells into 10x Chromium platform.     RNA-Seq TRANSCRIPTOMIC SINGLE CELL RANDOM PAIRED ILLUMINA Illumina HiSeq 2500   SRP265421   loader:fastq load.py L41598_S1_L001_I1_001.fastq.gz L41598_S1_L001_R1_001.fastq.gz L41598_S1_L001_R2_001.fastq.gz L41598_S1_L002_I1_001.fastq.gz L41598_S1_L002_R1_001.fastq.gz L41598_S1_L002_R2_001.fastq.gz L41598_S1_L003_I1_001.fastq.gz L41598_S1_L003_R1_001.fastq.gz L41598_S1_L003_R2_001.fastq.gz L41598_S1_L004_I1_001.fastq.gz L41598_S1_L004_R1_001.fastq.gz L41598_S1_L004_R2_001.fastq.gz fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq 52222012142.0 411196946.0 L41598 S1 L001 I1 001.fastq.gz 0:8 1:28 2:91 A:10978857897;C:7760934381;G:8557391299;T:10029401940;N:92336569 8 28 91   10978857897 7760934381 8557391299 10029401940 92336569 SRX8434172 SRS6745285 SRA1081627 Stowers Institute for Medical Research|Sanchez lab Stowers Institute for Medical Research 1 0.92629   0.12539   0.78589   0.5225   91   B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_droplet 10x   United States 2020-08-11 Adult Adult Fin Surface Structure
55982 55982 SRR10895887 SRX7564592 SRS6001802 SRP241982 PRJNA599026 Project of basal ray finned fishes PRJNA599026 Other The project is to study the oldest fish lineages in the ray finned fishes. Although they belong to fish their body structure and behavior remain highly similar to that of the tetrapods. Through comparative genome analysis with living vertebrates we provides insights into the molecular basis of terrestrial adaptation of basal ray finned fishes.   pubmed:33545088;pubmed:12470943     Zebrafish 007   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:Adult|sex:not determined|tissue:Skin|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio : adult CL100101924 L01 9 CL100101924 L01 9       RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED BGISEQ BGISEQ-500   SRP241982     CL100101924_L01_550_1.fq.gz CL100101924_L01_550_2.fq.gz fastq fastq 8780226200.0 87802262.0 CL100101924 L01 550 1.fq.gz 0:100 1:100 A:2363664067;C:1983383192;G:2025795704;T:2396528723;N:10854514 100 100     2363664067 1983383192 2025795704 2396528723 10854514 SRX7564592 SRS6001802 SRA1026516 BGI|BGI-Research BGI 1 0.92686   0.10085   0.70903   0.51488   100   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2020-01-15 Adult Adult Skin Surface Structure
55983 55983 SRR10895888 SRX7564591 SRS6001802 SRP241982 PRJNA599026 Project of basal ray finned fishes PRJNA599026 Other The project is to study the oldest fish lineages in the ray finned fishes. Although they belong to fish their body structure and behavior remain highly similar to that of the tetrapods. Through comparative genome analysis with living vertebrates we provides insights into the molecular basis of terrestrial adaptation of basal ray finned fishes.   pubmed:33545088;pubmed:12470943     Zebrafish 007   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:Adult|sex:not determined|tissue:Skin|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio : adult CL100101924 L01 8 CL100101924 L01 8       RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED BGISEQ BGISEQ-500   SRP241982     CL100101924_L01_549_2.fq.gz CL100101924_L01_549_1.fq.gz fastq fastq 9805051200.0 98050512.0 CL100101924 L01 549 1.fq.gz 0:100 1:100 A:2663706429;C:2193838939;G:2241619945;T:2693859046;N:12026841 100 100     2663706429 2193838939 2241619945 2693859046 12026841 SRX7564591 SRS6001802 SRA1026516 BGI|BGI-Research BGI 1 0.92652   0.0983   0.71043   0.53401   100   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2020-01-15 Adult Adult Skin Surface Structure
55984 55984 SRR10895889 SRX7564590 SRS6001802 SRP241982 PRJNA599026 Project of basal ray finned fishes PRJNA599026 Other The project is to study the oldest fish lineages in the ray finned fishes. Although they belong to fish their body structure and behavior remain highly similar to that of the tetrapods. Through comparative genome analysis with living vertebrates we provides insights into the molecular basis of terrestrial adaptation of basal ray finned fishes.   pubmed:33545088;pubmed:12470943     Zebrafish 007   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:Adult|sex:not determined|tissue:Skin|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio : adult CL100101924 L01 7 CL100101924 L01 7       RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED BGISEQ BGISEQ-500   SRP241982     CL100101924_L01_547_1.fq.gz CL100101924_L01_547_2.fq.gz fastq fastq 9137587600.0 91375876.0 CL100101924 L01 547 1.fq.gz 0:100 1:100 A:2471506783;C:2052808667;G:2096159921;T:2505897469;N:11214760 100 100     2471506783 2052808667 2096159921 2505897469 11214760 SRX7564590 SRS6001802 SRA1026516 BGI|BGI-Research BGI 1 0.93126   0.09864   0.70613   0.51947   100   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2020-01-15 Adult Adult Skin Surface Structure
55985 55985 SRR10895890 SRX7564589 SRS6001802 SRP241982 PRJNA599026 Project of basal ray finned fishes PRJNA599026 Other The project is to study the oldest fish lineages in the ray finned fishes. Although they belong to fish their body structure and behavior remain highly similar to that of the tetrapods. Through comparative genome analysis with living vertebrates we provides insights into the molecular basis of terrestrial adaptation of basal ray finned fishes.   pubmed:33545088;pubmed:12470943     Zebrafish 007   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:Adult|sex:not determined|tissue:Skin|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio : adult CL100101924 L01 6 CL100101924 L01 6       RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED BGISEQ BGISEQ-500   SRP241982     CL100101924_L01_551_1.fq.gz CL100101924_L01_551_2.fq.gz fastq fastq 7665129600.0 76651296.0 CL100101924 L01 551 1.fq.gz 0:100 1:100 A:2062939973;C:1731950056;G:1768675635;T:2092110510;N:9453426 100 100     2062939973 1731950056 1768675635 2092110510 9453426 SRX7564589 SRS6001802 SRA1026516 BGI|BGI-Research BGI 1 0.93022   0.10662   0.70512   0.50773   100   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2020-01-15 Adult Adult Skin Surface Structure
55986 55986 SRR10895892 SRX7564587 SRS6001802 SRP241982 PRJNA599026 Project of basal ray finned fishes PRJNA599026 Other The project is to study the oldest fish lineages in the ray finned fishes. Although they belong to fish their body structure and behavior remain highly similar to that of the tetrapods. Through comparative genome analysis with living vertebrates we provides insights into the molecular basis of terrestrial adaptation of basal ray finned fishes.   pubmed:33545088;pubmed:12470943     Zebrafish 007   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:Adult|sex:not determined|tissue:Skin|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio : adult CL100101924 L01 5 CL100101924 L01 5       RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED BGISEQ BGISEQ-500   SRP241982     CL100101924_L01_548_1.fq.gz CL100101924_L01_548_2.fq.gz fastq fastq 6527814200.0 65278142.0 CL100101924 L01 548 1.fq.gz 0:100 1:100 A:1748761735;C:1483522306;G:1516468410;T:1771028617;N:8033132 100 100     1748761735 1483522306 1516468410 1771028617 8033132 SRX7564587 SRS6001802 SRA1026516 BGI|BGI-Research BGI 1 0.93149   0.09371   0.70542   0.51664   100   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2020-01-15 Adult Adult Skin Surface Structure
56002 56002 SRR10895909 SRX7564570 SRS6001798 SRP241982 PRJNA599026 Project of basal ray finned fishes PRJNA599026 Other The project is to study the oldest fish lineages in the ray finned fishes. Although they belong to fish their body structure and behavior remain highly similar to that of the tetrapods. Through comparative genome analysis with living vertebrates we provides insights into the molecular basis of terrestrial adaptation of basal ray finned fishes.   pubmed:33545088;pubmed:12470943     Zebrafish 003   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:Adult|sex:not determined|tissue:Jaw|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio : adult CL100103858 L02 6 CL100103858 L02 6       RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED BGISEQ BGISEQ-500   SRP241982     CL100103858_L02_524_1.fq.gz CL100103858_L02_524_2.fq.gz fastq fastq 8863838800.0 88638388.0 CL100103858 L02 524 1.fq.gz 0:100 1:100 A:2346347928;C:2037236505;G:2089998345;T:2378150886;N:12105136 100 100     2346347928 2037236505 2089998345 2378150886 12105136 SRX7564570 SRS6001798 SRA1026516 BGI|BGI-Research BGI 1 0.93198   0.08128   0.74519   0.48951   100   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2020-01-15 Adult Adult Jaw Surface Structure
56003 56003 SRR10895910 SRX7564569 SRS6001798 SRP241982 PRJNA599026 Project of basal ray finned fishes PRJNA599026 Other The project is to study the oldest fish lineages in the ray finned fishes. Although they belong to fish their body structure and behavior remain highly similar to that of the tetrapods. Through comparative genome analysis with living vertebrates we provides insights into the molecular basis of terrestrial adaptation of basal ray finned fishes.   pubmed:33545088;pubmed:12470943     Zebrafish 003   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:Adult|sex:not determined|tissue:Jaw|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio : adult CL100103858 L02 5 CL100103858 L02 5       RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED BGISEQ BGISEQ-500   SRP241982     CL100103858_L02_521_2.fq.gz CL100103858_L02_521_1.fq.gz fastq fastq 10301853000.0 103018530.0 CL100103858 L02 521 1.fq.gz 0:100 1:100 A:2719789797;C:2379371302;G:2435354849;T:2753122052;N:14215000 100 100     2719789797 2379371302 2435354849 2753122052 14215000 SRX7564569 SRS6001798 SRA1026516 BGI|BGI-Research BGI 1 0.93582   0.08016   0.73466   0.4997   100   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2020-01-15 Adult Adult Jaw Surface Structure
56004 56004 SRR10895911 SRX7564568 SRS6001798 SRP241982 PRJNA599026 Project of basal ray finned fishes PRJNA599026 Other The project is to study the oldest fish lineages in the ray finned fishes. Although they belong to fish their body structure and behavior remain highly similar to that of the tetrapods. Through comparative genome analysis with living vertebrates we provides insights into the molecular basis of terrestrial adaptation of basal ray finned fishes.   pubmed:33545088;pubmed:12470943     Zebrafish 003   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:Adult|sex:not determined|tissue:Jaw|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio : adult CL100103858 L02 4 CL100103858 L02 4       RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED BGISEQ BGISEQ-500   SRP241982     CL100103858_L02_522_1.fq.gz CL100103858_L02_522_2.fq.gz fastq fastq 8856151600.0 88561516.0 CL100103858 L02 522 1.fq.gz 0:100 1:100 A:2327973616;C:2055012813;G:2104952956;T:2356113813;N:12098402 100 100     2327973616 2055012813 2104952956 2356113813 12098402 SRX7564568 SRS6001798 SRA1026516 BGI|BGI-Research BGI 1 0.93888   0.07312   0.74337   0.50608   100   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2020-01-15 Adult Adult Jaw Surface Structure
56005 56005 SRR10895912 SRX7564567 SRS6001798 SRP241982 PRJNA599026 Project of basal ray finned fishes PRJNA599026 Other The project is to study the oldest fish lineages in the ray finned fishes. Although they belong to fish their body structure and behavior remain highly similar to that of the tetrapods. Through comparative genome analysis with living vertebrates we provides insights into the molecular basis of terrestrial adaptation of basal ray finned fishes.   pubmed:33545088;pubmed:12470943     Zebrafish 003   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:Adult|sex:not determined|tissue:Jaw|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio : adult CL100103858 L02 3 CL100103858 L02 3       RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED BGISEQ BGISEQ-500   SRP241982     CL100103858_L02_525_1.fq.gz CL100103858_L02_525_2.fq.gz fastq fastq 8393966200.0 83939662.0 CL100103858 L02 525 1.fq.gz 0:100 1:100 A:2205916604;C:1944354784;G:1992482736;T:2239434609;N:11777467 100 100     2205916604 1944354784 1992482736 2239434609 11777467 SRX7564567 SRS6001798 SRA1026516 BGI|BGI-Research BGI 1 0.93522   0.07124   0.73939   0.50385   100   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2020-01-15 Adult Adult Jaw Surface Structure
56006 56006 SRR10895914 SRX7564565 SRS6001798 SRP241982 PRJNA599026 Project of basal ray finned fishes PRJNA599026 Other The project is to study the oldest fish lineages in the ray finned fishes. Although they belong to fish their body structure and behavior remain highly similar to that of the tetrapods. Through comparative genome analysis with living vertebrates we provides insights into the molecular basis of terrestrial adaptation of basal ray finned fishes.   pubmed:33545088;pubmed:12470943     Zebrafish 003   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:Adult|sex:not determined|tissue:Jaw|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio : adult CL100103858 L02 2 CL100103858 L02 2       RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED BGISEQ BGISEQ-500   SRP241982     CL100103858_L02_523_2.fq.gz CL100103858_L02_523_1.fq.gz fastq fastq 9645085400.0 96450854.0 CL100103858 L02 523 1.fq.gz 0:100 1:100 A:2543300716;C:2229112849;G:2282624833;T:2576502560;N:13544442 100 100     2543300716 2229112849 2282624833 2576502560 13544442 SRX7564565 SRS6001798 SRA1026516 BGI|BGI-Research BGI 1 0.93673   0.0738   0.74337   0.49427   100   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2020-01-15 Adult Adult Jaw Surface Structure
58983 58983 SRR11610427 SRX8176695 SRS6536450 SRP258542 PRJNA626778 Transcriptome sequencing for larvae and adult zebrafish liver post difenoconazole exposure PRJNA626778 Metagenomics RNA seq was performed on zebrafish larvae post embryos exposed to 0.400 mg/L difenoconazole for 120 h and on zebrafish liver post 21 d exposure in triplicate using Illumina HiSeq X Ten         T06   cultivar:WT type AB strain|age:10 days|dev stage:larvae|sex:male|tissue:larvae whole body|treatment:D larvae3|BioSampleModel:Model organism or animal                 NS 3 D larvae3 D larvae3 D larvae3     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA HiSeq X Ten   SRP258542     T06_2.fq.gz T06_1.fq.gz fastq fastq 8705370600.0 29017902.0 T06 1.fq.gz 0:150 1:150 A:2317335170;C:2020864131;G:2032474454;T:2333792505;N:904340 150 150     2317335170 2020864131 2032474454 2333792505 904340 SRX8176695 SRS6536450 SRA1069066 Zhejiang Academy of Agricultural Sciences|Institute of Quality and Standard for Agroproducts Zhejiang Academy of Agricultural Sciences 2 0.94348 0.94914 0.10329 0.1021 0.65163 0.6524 0.47004 0.46491 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2020-04-26 Larval Larval Trunk Surface Structure
58984 58984 SRR11610428 SRX8176694 SRS6536449 SRP258542 PRJNA626778 Transcriptome sequencing for larvae and adult zebrafish liver post difenoconazole exposure PRJNA626778 Metagenomics RNA seq was performed on zebrafish larvae post embryos exposed to 0.400 mg/L difenoconazole for 120 h and on zebrafish liver post 21 d exposure in triplicate using Illumina HiSeq X Ten         T05   cultivar:WT type AB strain|age:9 days|dev stage:larvae|sex:male|tissue:larvae whole body|treatment:D larvae2|BioSampleModel:Model organism or animal                 NS 2 D larvae2 D larvae2 D larvae2     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA HiSeq X Ten   SRP258542     T05_2.fq.gz T05_1.fq.gz fastq fastq 8775682200.0 29252274.0 T05 1.fq.gz 0:150 1:150 A:2343850546;C:2028804671;G:2042371366;T:2359745584;N:910033 150 150     2343850546 2028804671 2042371366 2359745584 910033 SRX8176694 SRS6536449 SRA1069066 Zhejiang Academy of Agricultural Sciences|Institute of Quality and Standard for Agroproducts Zhejiang Academy of Agricultural Sciences 2 0.94324 0.9478 0.10742 0.10626 0.65374 0.65423 0.46936 0.47023 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2020-04-26 Larval Larval Trunk Surface Structure
58985 58985 SRR11610429 SRX8176693 SRS6536448 SRP258542 PRJNA626778 Transcriptome sequencing for larvae and adult zebrafish liver post difenoconazole exposure PRJNA626778 Metagenomics RNA seq was performed on zebrafish larvae post embryos exposed to 0.400 mg/L difenoconazole for 120 h and on zebrafish liver post 21 d exposure in triplicate using Illumina HiSeq X Ten         T04   cultivar:WT type AB strain|age:8 days|dev stage:larvae|sex:male|tissue:larvae whole body|treatment:D larvae1|BioSampleModel:Model organism or animal                 NS 1 D larvae1 D larvae1 D larvae1     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA HiSeq X Ten   SRP258542     T04_1.fq.gz T04_2.fq.gz fastq fastq 9470209800.0 31567366.0 T04 1.fq.gz 0:150 1:150 A:2512151104;C:2206180833;G:2224120159;T:2526778146;N:979558 150 150     2512151104 2206180833 2224120159 2526778146 979558 SRX8176693 SRS6536448 SRA1069066 Zhejiang Academy of Agricultural Sciences|Institute of Quality and Standard for Agroproducts Zhejiang Academy of Agricultural Sciences 2 0.94469 0.94918 0.09968 0.09817 0.65224 0.6538 0.45967 0.46068 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2020-04-26 Larval Larval Trunk Surface Structure
58986 58986 SRR11610430 SRX8176692 SRS6536447 SRP258542 PRJNA626778 Transcriptome sequencing for larvae and adult zebrafish liver post difenoconazole exposure PRJNA626778 Metagenomics RNA seq was performed on zebrafish larvae post embryos exposed to 0.400 mg/L difenoconazole for 120 h and on zebrafish liver post 21 d exposure in triplicate using Illumina HiSeq X Ten         T03   cultivar:WT type AB strain|age:7 days|dev stage:larvae|sex:male|tissue:larvae whole body|treatment:ck larvae3|BioSampleModel:Model organism or animal                 LS 3 ck larvae3 ck larvae3 ck larvae3     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA HiSeq X Ten   SRP258542     T03_1.fq.gz T03_2.fq.gz fastq fastq 8454791400.0 28182638.0 T03 1.fq.gz 0:150 1:150 A:2264436569;C:1947544159;G:1962858262;T:2279085384;N:867026 150 150     2264436569 1947544159 1962858262 2279085384 867026 SRX8176692 SRS6536447 SRA1069066 Zhejiang Academy of Agricultural Sciences|Institute of Quality and Standard for Agroproducts Zhejiang Academy of Agricultural Sciences 2 0.94312 0.94697 0.11012 0.10792 0.65042 0.65017 0.47003 0.47097 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2020-04-26 Larval Larval Trunk Surface Structure
58989 58989 SRR11610433 SRX8176689 SRS6536445 SRP258542 PRJNA626778 Transcriptome sequencing for larvae and adult zebrafish liver post difenoconazole exposure PRJNA626778 Metagenomics RNA seq was performed on zebrafish larvae post embryos exposed to 0.400 mg/L difenoconazole for 120 h and on zebrafish liver post 21 d exposure in triplicate using Illumina HiSeq X Ten         T02   cultivar:WT type AB strain|age:6 days|dev stage:larvae|sex:male|tissue:larvae whole body|treatment:ck larvae2|BioSampleModel:Model organism or animal                 LS 2 ck larvae2 ck larvae2 ck larvae2     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA HiSeq X Ten   SRP258542     T02_1.fq.gz T02_2.fq.gz fastq fastq 9808202700.0 32694009.0 T02 1.fq.gz 0:150 1:150 A:2611961476;C:2273571725;G:2295489444;T:2626158782;N:1021273 150 150     2611961476 2273571725 2295489444 2626158782 1021273 SRX8176689 SRS6536445 SRA1069066 Zhejiang Academy of Agricultural Sciences|Institute of Quality and Standard for Agroproducts Zhejiang Academy of Agricultural Sciences 2 0.94301 0.94782 0.10296 0.10114 0.65111 0.6507 0.47143 0.46806 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2020-04-26 Larval Larval Trunk Surface Structure
58990 58990 SRR11610434 SRX8176688 SRS6536444 SRP258542 PRJNA626778 Transcriptome sequencing for larvae and adult zebrafish liver post difenoconazole exposure PRJNA626778 Metagenomics RNA seq was performed on zebrafish larvae post embryos exposed to 0.400 mg/L difenoconazole for 120 h and on zebrafish liver post 21 d exposure in triplicate using Illumina HiSeq X Ten         T01   cultivar:WT type AB strain|age:5 days|dev stage:larvae|sex:male|tissue:larvae whole body|treatment:ck larvae1|BioSampleModel:Model organism or animal                 LS 1 ck larvae1 ck larvae1 ck larvae1     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA HiSeq X Ten   SRP258542     T01_1.fq.gz T01_2.fq.gz fastq fastq 8337627600.0 27792092.0 T01 1.fq.gz 0:150 1:150 A:2205115835;C:1947292476;G:1965213034;T:2219138382;N:867873 150 150     2205115835 1947292476 1965213034 2219138382 867873 SRX8176688 SRS6536444 SRA1069066 Zhejiang Academy of Agricultural Sciences|Institute of Quality and Standard for Agroproducts Zhejiang Academy of Agricultural Sciences 2 0.94524 0.94926 0.09868 0.09692 0.65251 0.65399 0.47004 0.46218 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2020-04-26 Larval Larval Trunk Surface Structure
66804 66804 SRR16647484 SRX12848204 SRS10791664 SRP343938 PRJNA776643 RNAseq study for assessed the microcystin LR and geosmin differential gene expression modulation in zebrafish larvae 30 dph PRJNA776643 Other Microcystin LR and Geosmin effects over whole body zebrafish Danio rerio larvae transcriptome       Cyanotoxins exposition Cyanotoxins   strain:Wild|dev stage:31 dph|sex:Not collected|tissue:whole body|BioSampleModel:Model organism or animal                 Geosmin Group Geosmin5 Geosmin5 TruSeq stranded mRNA library     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   SRP343938     Geos_9_2.fastq.gz Geos_9_1.fastq.gz fastq fastq 6334215404.0 31357502.0 Geos 9 1.fastq.gz 0:101 1:101 A:1660680129;C:1502146962;G:1509550327;T:1661764270;N:73716 101 101     1660680129 1502146962 1509550327 1661764270 73716 SRX12848204 SRS10791664 SRA1320158 University of Chile|INTA University of Chile 2 0.9606 0.96446 0.06247 0.06142 0.68024 0.67868 0.46945 0.48301 101 101 B B biological fallback assumption illumina novaseq_era unknown random_priming trueseq bulk unknown unknown   Chile 2021-10-31 Undetermined Larval Trunk Surface Structure
66805 66805 SRR16647485 SRX12848203 SRS10791664 SRP343938 PRJNA776643 RNAseq study for assessed the microcystin LR and geosmin differential gene expression modulation in zebrafish larvae 30 dph PRJNA776643 Other Microcystin LR and Geosmin effects over whole body zebrafish Danio rerio larvae transcriptome       Cyanotoxins exposition Cyanotoxins   strain:Wild|dev stage:31 dph|sex:Not collected|tissue:whole body|BioSampleModel:Model organism or animal                 Geosmin Group Geosmin4 Geosmin4 TruSeq stranded mRNA library     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   SRP343938     Geos_8_2.fastq.gz Geos_8_1.fastq.gz fastq fastq 4083342938.0 20214569.0 Geos 8 1.fastq.gz 0:101 1:101 A:1059060815;C:981147486;G:980661533;T:1062425066;N:48038 101 101     1059060815 981147486 980661533 1062425066 48038 SRX12848203 SRS10791664 SRA1320158 University of Chile|INTA University of Chile 2 0.95947 0.96443 0.05387 0.05331 0.66395 0.66419 0.49093 0.48488 101 101 B B biological fallback assumption illumina novaseq_era unknown random_priming trueseq bulk unknown unknown   Chile 2021-10-31 Undetermined Larval Trunk Surface Structure
66806 66806 SRR16647486 SRX12848202 SRS10791664 SRP343938 PRJNA776643 RNAseq study for assessed the microcystin LR and geosmin differential gene expression modulation in zebrafish larvae 30 dph PRJNA776643 Other Microcystin LR and Geosmin effects over whole body zebrafish Danio rerio larvae transcriptome       Cyanotoxins exposition Cyanotoxins   strain:Wild|dev stage:31 dph|sex:Not collected|tissue:whole body|BioSampleModel:Model organism or animal                 Geosmin Group Geosmin3 Geosmin3 TruSeq stranded mRNA library     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   SRP343938     Geos_7_1.fastq.gz Geos_7_2.fastq.gz fastq fastq 6351796272.0 31444536.0 Geos 7 1.fastq.gz 0:101 1:101 A:1666018762;C:1507166887;G:1508718223;T:1669818164;N:74236 101 101     1666018762 1507166887 1508718223 1669818164 74236 SRX12848202 SRS10791664 SRA1320158 University of Chile|INTA University of Chile 2 0.95901 0.96323 0.05991 0.05856 0.66703 0.6663 0.47986 0.48189 101 101 B B biological fallback assumption illumina novaseq_era unknown random_priming trueseq bulk unknown unknown   Chile 2021-10-31 Undetermined Larval Trunk Surface Structure
66807 66807 SRR16647487 SRX12848201 SRS10791664 SRP343938 PRJNA776643 RNAseq study for assessed the microcystin LR and geosmin differential gene expression modulation in zebrafish larvae 30 dph PRJNA776643 Other Microcystin LR and Geosmin effects over whole body zebrafish Danio rerio larvae transcriptome       Cyanotoxins exposition Cyanotoxins   strain:Wild|dev stage:31 dph|sex:Not collected|tissue:whole body|BioSampleModel:Model organism or animal                 Geosmin Group Geosmin2 Geosmin2 TruSeq stranded mRNA library     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   SRP343938     Geos_5_2.fastq.gz Geos_5_1.fastq.gz fastq fastq 5034600934.0 24923767.0 Geos 5 1.fastq.gz 0:101 1:101 A:1324246402;C:1190124296;G:1192268426;T:1327901769;N:60041 101 101     1324246402 1190124296 1192268426 1327901769 60041 SRX12848201 SRS10791664 SRA1320158 University of Chile|INTA University of Chile 2 0.95626 0.96096 0.06801 0.06708 0.67292 0.67109 0.47788 0.48168 101 101 B B biological fallback assumption illumina novaseq_era unknown random_priming trueseq bulk unknown unknown   Chile 2021-10-31 Undetermined Larval Trunk Surface Structure
66808 66808 SRR16647488 SRX12848200 SRS10791664 SRP343938 PRJNA776643 RNAseq study for assessed the microcystin LR and geosmin differential gene expression modulation in zebrafish larvae 30 dph PRJNA776643 Other Microcystin LR and Geosmin effects over whole body zebrafish Danio rerio larvae transcriptome       Cyanotoxins exposition Cyanotoxins   strain:Wild|dev stage:31 dph|sex:Not collected|tissue:whole body|BioSampleModel:Model organism or animal                 Geosmin Group Geosmin1 Geosmin1 TruSeq stranded mRNA library     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   SRP343938     Geos_2_1.fastq.gz Geos_2_2.fastq.gz fastq fastq 5540468928.0 27428064.0 Geos 2 1.fastq.gz 0:101 1:101 A:1453397068;C:1314496546;G:1318965254;T:1453545221;N:64839 101 101     1453397068 1314496546 1318965254 1453545221 64839 SRX12848200 SRS10791664 SRA1320158 University of Chile|INTA University of Chile 2 0.96164 0.96533 0.0572 0.056 0.68712 0.68682 0.47672 0.48134 101 101 B B biological fallback assumption illumina novaseq_era unknown random_priming trueseq bulk unknown unknown   Chile 2021-10-31 Undetermined Larval Trunk Surface Structure
66809 66809 SRR16647489 SRX12848199 SRS10791664 SRP343938 PRJNA776643 RNAseq study for assessed the microcystin LR and geosmin differential gene expression modulation in zebrafish larvae 30 dph PRJNA776643 Other Microcystin LR and Geosmin effects over whole body zebrafish Danio rerio larvae transcriptome       Cyanotoxins exposition Cyanotoxins   strain:Wild|dev stage:31 dph|sex:Not collected|tissue:whole body|BioSampleModel:Model organism or animal                 Control Group Control5 Control5 TruSeq stranded mRNA library     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   SRP343938     Control_10_2.fastq.gz Control_10_1.fastq.gz fastq fastq 4443325118.0 21996659.0 Control 10 1.fastq.gz 0:101 1:101 A:1166167313;C:1050165932;G:1062683912;T:1164256629;N:51332 101 101     1166167313 1050165932 1062683912 1164256629 51332 SRX12848199 SRS10791664 SRA1320158 University of Chile|INTA University of Chile 2 0.96096 0.96463 0.06551 0.06521 0.68091 0.67884 0.46365 0.47531 101 101 B B biological fallback assumption illumina novaseq_era unknown random_priming trueseq bulk unknown unknown   Chile 2021-10-31 Undetermined Larval Trunk Surface Structure
66810 66810 SRR16647490 SRX12848198 SRS10791664 SRP343938 PRJNA776643 RNAseq study for assessed the microcystin LR and geosmin differential gene expression modulation in zebrafish larvae 30 dph PRJNA776643 Other Microcystin LR and Geosmin effects over whole body zebrafish Danio rerio larvae transcriptome       Cyanotoxins exposition Cyanotoxins   strain:Wild|dev stage:31 dph|sex:Not collected|tissue:whole body|BioSampleModel:Model organism or animal                 Control Group Control4 Control4 TruSeq stranded mRNA library     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   SRP343938     Control_9_1.fastq.gz Control_9_2.fastq.gz fastq fastq 4929324190.0 24402595.0 Control 9 1.fastq.gz 0:101 1:101 A:1284447529;C:1179260179;G:1182075889;T:1283482794;N:57799 101 101     1284447529 1179260179 1182075889 1283482794 57799 SRX12848198 SRS10791664 SRA1320158 University of Chile|INTA University of Chile 2 0.96315 0.96562 0.0579 0.05684 0.6872 0.6854 0.4698 0.47885 101 101 B B biological fallback assumption illumina novaseq_era unknown random_priming trueseq bulk unknown unknown   Chile 2021-10-31 Undetermined Larval Trunk Surface Structure
66811 66811 SRR16647491 SRX12848197 SRS10791664 SRP343938 PRJNA776643 RNAseq study for assessed the microcystin LR and geosmin differential gene expression modulation in zebrafish larvae 30 dph PRJNA776643 Other Microcystin LR and Geosmin effects over whole body zebrafish Danio rerio larvae transcriptome       Cyanotoxins exposition Cyanotoxins   strain:Wild|dev stage:31 dph|sex:Not collected|tissue:whole body|BioSampleModel:Model organism or animal                 Control group Control3 Control3 TruSeq stranded mRNA library     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   SRP343938     Control_7_1.fastq.gz Control_7_2.fastq.gz fastq fastq 5451223308.0 26986254.0 Control 7 1.fastq.gz 0:101 1:101 A:1430742224;C:1290445675;G:1297973588;T:1431995526;N:66295 101 101     1430742224 1290445675 1297973588 1431995526 66295 SRX12848197 SRS10791664 SRA1320158 University of Chile|INTA University of Chile 2 0.95748 0.96139 0.06511 0.06325 0.6786 0.67683 0.48371 0.47809 101 101 B B biological fallback assumption illumina novaseq_era unknown random_priming trueseq bulk unknown unknown   Chile 2021-10-31 Undetermined Larval Trunk Surface Structure
66812 66812 SRR16647492 SRX12848196 SRS10791664 SRP343938 PRJNA776643 RNAseq study for assessed the microcystin LR and geosmin differential gene expression modulation in zebrafish larvae 30 dph PRJNA776643 Other Microcystin LR and Geosmin effects over whole body zebrafish Danio rerio larvae transcriptome       Cyanotoxins exposition Cyanotoxins   strain:Wild|dev stage:31 dph|sex:Not collected|tissue:whole body|BioSampleModel:Model organism or animal                 MCLR Group Microcystin5 Microcystin5 TruSeq stranded mRNA library     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   SRP343938     MCLR_9_2.fastq.gz MCLR_9_1.fastq.gz fastq fastq 6319760688.0 31285944.0 MCLR 9 1.fastq.gz 0:101 1:101 A:1651386984;C:1506636394;G:1503844710;T:1657818616;N:73984 101 101     1651386984 1506636394 1503844710 1657818616 73984 SRX12848196 SRS10791664 SRA1320158 University of Chile|INTA University of Chile 2 0.96138 0.9653 0.06138 0.06096 0.68527 0.68375 0.47357 0.47623 101 101 B B biological fallback assumption illumina novaseq_era unknown random_priming trueseq bulk unknown unknown   Chile 2021-10-31 Undetermined Larval Trunk Surface Structure
66813 66813 SRR16647493 SRX12848195 SRS10791664 SRP343938 PRJNA776643 RNAseq study for assessed the microcystin LR and geosmin differential gene expression modulation in zebrafish larvae 30 dph PRJNA776643 Other Microcystin LR and Geosmin effects over whole body zebrafish Danio rerio larvae transcriptome       Cyanotoxins exposition Cyanotoxins   strain:Wild|dev stage:31 dph|sex:Not collected|tissue:whole body|BioSampleModel:Model organism or animal                 MCLR Group Microcystin4 Microcystin4 TruSeq stranded mRNA library     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   SRP343938     MCLR_6_1.fastq.gz MCLR_6_2.fastq.gz fastq fastq 5958169780.0 29495890.0 MCLR 6 1.fastq.gz 0:101 1:101 A:1554274821;C:1422499065;G:1422743047;T:1558582611;N:70236 101 101     1554274821 1422499065 1422743047 1558582611 70236 SRX12848195 SRS10791664 SRA1320158 University of Chile|INTA University of Chile 2 0.96155 0.96352 0.05329 0.05208 0.67838 0.67671 0.46412 0.46602 101 101 B B biological fallback assumption illumina novaseq_era unknown random_priming trueseq bulk unknown unknown   Chile 2021-10-31 Undetermined Larval Trunk Surface Structure
66814 66814 SRR16647494 SRX12848194 SRS10791664 SRP343938 PRJNA776643 RNAseq study for assessed the microcystin LR and geosmin differential gene expression modulation in zebrafish larvae 30 dph PRJNA776643 Other Microcystin LR and Geosmin effects over whole body zebrafish Danio rerio larvae transcriptome       Cyanotoxins exposition Cyanotoxins   strain:Wild|dev stage:31 dph|sex:Not collected|tissue:whole body|BioSampleModel:Model organism or animal                 MCLR Group Microcystin3 Microcystin3 TruSeq stranded mRNA library     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   SRP343938     MCLR_4_1.fastq.gz MCLR_4_2.fastq.gz fastq fastq 4299813410.0 21286205.0 MCLR 4 1.fastq.gz 0:101 1:101 A:1130530424;C:1017015892;G:1018283950;T:1133933238;N:49906 101 101     1130530424 1017015892 1018283950 1133933238 49906 SRX12848194 SRS10791664 SRA1320158 University of Chile|INTA University of Chile 2 0.95994 0.96417 0.06438 0.06329 0.68164 0.68024 0.46908 0.45721 101 101 B B biological fallback assumption illumina novaseq_era unknown random_priming trueseq bulk unknown unknown   Chile 2021-10-31 Undetermined Larval Trunk Surface Structure
66815 66815 SRR16647495 SRX12848193 SRS10791664 SRP343938 PRJNA776643 RNAseq study for assessed the microcystin LR and geosmin differential gene expression modulation in zebrafish larvae 30 dph PRJNA776643 Other Microcystin LR and Geosmin effects over whole body zebrafish Danio rerio larvae transcriptome       Cyanotoxins exposition Cyanotoxins   strain:Wild|dev stage:31 dph|sex:Not collected|tissue:whole body|BioSampleModel:Model organism or animal                 MCLR Group Microcystin2 Microcystin2 TruSeq stranded mRNA library     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   SRP343938     MCLR_2_1.fastq.gz MCLR_2_2.fastq.gz fastq fastq 4423131582.0 21896691.0 MCLR 2 1.fastq.gz 0:101 1:101 A:1149883296;C:1057886123;G:1061611354;T:1153698579;N:52230 101 101     1149883296 1057886123 1061611354 1153698579 52230 SRX12848193 SRS10791664 SRA1320158 University of Chile|INTA University of Chile 2 0.95613 0.95907 0.05023 0.04906 0.66797 0.66728 0.46443 0.47031 101 101 B B biological fallback assumption illumina novaseq_era unknown random_priming trueseq bulk unknown unknown   Chile 2021-10-31 Undetermined Larval Trunk Surface Structure
66816 66816 SRR16647496 SRX12848192 SRS10791664 SRP343938 PRJNA776643 RNAseq study for assessed the microcystin LR and geosmin differential gene expression modulation in zebrafish larvae 30 dph PRJNA776643 Other Microcystin LR and Geosmin effects over whole body zebrafish Danio rerio larvae transcriptome       Cyanotoxins exposition Cyanotoxins   strain:Wild|dev stage:31 dph|sex:Not collected|tissue:whole body|BioSampleModel:Model organism or animal                 MCLR Group Microcystin1 Microcystin1 TruSeq stranded mRNA library     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   SRP343938     MCLR_1_1.fastq.gz MCLR_1_2.fastq.gz fastq fastq 4515806556.0 22355478.0 MCLR 1 1.fastq.gz 0:101 1:101 A:1182700971;C:1072987233;G:1076179047;T:1183885831;N:53474 101 101     1182700971 1072987233 1076179047 1183885831 53474 SRX12848192 SRS10791664 SRA1320158 University of Chile|INTA University of Chile 2 0.96333 0.96773 0.05947 0.05827 0.68674 0.68592 0.48455 0.48382 101 101 B B biological fallback assumption illumina novaseq_era unknown random_priming trueseq bulk unknown unknown   Chile 2021-10-31 Undetermined Larval Trunk Surface Structure
66817 66817 SRR16647497 SRX12848191 SRS10791664 SRP343938 PRJNA776643 RNAseq study for assessed the microcystin LR and geosmin differential gene expression modulation in zebrafish larvae 30 dph PRJNA776643 Other Microcystin LR and Geosmin effects over whole body zebrafish Danio rerio larvae transcriptome       Cyanotoxins exposition Cyanotoxins   strain:Wild|dev stage:31 dph|sex:Not collected|tissue:whole body|BioSampleModel:Model organism or animal                 Control group Control2 Control2 TruSeq stranded mRNA library     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   SRP343938     Control_4_2.fastq.gz Control_4_1.fastq.gz fastq fastq 5751744364.0 28473982.0 Control 4 1.fastq.gz 0:101 1:101 A:1506277501;C:1366270345;G:1370493240;T:1508634723;N:68555 101 101     1506277501 1366270345 1370493240 1508634723 68555 SRX12848191 SRS10791664 SRA1320158 University of Chile|INTA University of Chile 2 0.95986 0.96351 0.06011 0.05885 0.66849 0.66665 0.48168 0.48854 101 101 B B biological fallback assumption illumina novaseq_era unknown random_priming trueseq bulk unknown unknown   Chile 2021-10-31 Undetermined Larval Trunk Surface Structure
66818 66818 SRR16647498 SRX12848190 SRS10791664 SRP343938 PRJNA776643 RNAseq study for assessed the microcystin LR and geosmin differential gene expression modulation in zebrafish larvae 30 dph PRJNA776643 Other Microcystin LR and Geosmin effects over whole body zebrafish Danio rerio larvae transcriptome       Cyanotoxins exposition Cyanotoxins   strain:Wild|dev stage:31 dph|sex:Not collected|tissue:whole body|BioSampleModel:Model organism or animal                 Control group Control1 Control1 TruSeq stranded mRNA library     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   SRP343938     Control_1_1.fastq.gz Control_1_2.fastq.gz fastq fastq 5858177356.0 29000878.0 Control 1 1.fastq.gz 0:101 1:101 A:1526389428;C:1399991038;G:1403067225;T:1528661140;N:68525 101 101     1526389428 1399991038 1403067225 1528661140 68525 SRX12848190 SRS10791664 SRA1320158 University of Chile|INTA University of Chile 2 0.96083 0.96528 0.05769 0.05658 0.67393 0.67294 0.4684 0.46759 101 101 B B biological fallback assumption illumina novaseq_era unknown random_priming trueseq bulk unknown unknown   Chile 2021-10-31 Undetermined Larval Trunk Surface Structure

Advanced export

JSON shape: default, array, newline-delimited

CSV options: 

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");;