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run_metadata

53 rows where experiment.platform = "BGISEQ" and tissue_curation = "Liver"

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devstage_curation_coarse 3

devstage_curation 3

experiment.library_selection 2

tissue_curation_coarse 1

tissue_curation 1

  • Liver · 53 ✖

technology 1

experiment.platform 1

  • BGISEQ · 53 ✖

experiment.library_strategy 1

experiment.library_source 1

experiment.library_layout 1

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
56012 56012 SRR10895920 SRX7564559 SRS6001795 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 001   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:Liver|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio : adult CL100103858 L01 5 CL100103858 L01 5       RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED BGISEQ BGISEQ-500   SRP241982     CL100103858_L01_506_2.fq.gz CL100103858_L01_506_1.fq.gz fastq fastq 8894951400.0 88949514.0 CL100103858 L01 506 1.fq.gz 0:100 1:100 A:2342120919;C:2080816976;G:2120799988;T:2335970174;N:15243343 100 100     2342120919 2080816976 2120799988 2335970174 15243343 SRX7564559 SRS6001795 SRA1026516 BGI|BGI-Research BGI 1 0.9583   0.02358   0.88609   0.21491   100   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2020-01-15 Adult Adult Liver Liver and Biliary System
56013 56013 SRR10895921 SRX7564558 SRS6001795 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 001   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:Liver|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio : adult CL100103858 L01 4 CL100103858 L01 4       RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED BGISEQ BGISEQ-500   SRP241982     CL100103858_L01_502_1.fq.gz CL100103858_L01_502_2.fq.gz fastq fastq 9016276200.0 90162762.0 CL100103858 L01 502 1.fq.gz 0:100 1:100 A:2351547777;C:2123700654;G:2170958690;T:2354500550;N:15568529 100 100     2351547777 2123700654 2170958690 2354500550 15568529 SRX7564558 SRS6001795 SRA1026516 BGI|BGI-Research BGI 1 0.951   0.0278   0.84476   0.28629   100   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2020-01-15 Adult Adult Liver Liver and Biliary System
56014 56014 SRR10895922 SRX7564557 SRS6001795 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 001   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:Liver|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio : adult CL100103858 L01 3 CL100103858 L01 3       RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED BGISEQ BGISEQ-500   SRP241982     CL100103858_L01_504_2.fq.gz CL100103858_L01_504_1.fq.gz fastq fastq 8533635000.0 85336350.0 CL100103858 L01 504 1.fq.gz 0:100 1:100 A:2252394702;C:1967888849;G:2019361190;T:2279066552;N:14923707 100 100     2252394702 1967888849 2019361190 2279066552 14923707 SRX7564557 SRS6001795 SRA1026516 BGI|BGI-Research BGI 1 0.94212   0.04536   0.80099   0.49769   100   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2020-01-15 Adult Adult Liver Liver and Biliary System
56015 56015 SRR10895923 SRX7564556 SRS6001795 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 001   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:Liver|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio : adult CL100103858 L01 2 CL100103858 L01 2       RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED BGISEQ BGISEQ-500   SRP241982     CL100103858_L01_503_1.fq.gz CL100103858_L01_503_2.fq.gz fastq fastq 9344789800.0 93447898.0 CL100103858 L01 503 1.fq.gz 0:100 1:100 A:2456933695;C:2188901617;G:2230043511;T:2452921108;N:15989869 100 100     2456933695 2188901617 2230043511 2452921108 15989869 SRX7564556 SRS6001795 SRA1026516 BGI|BGI-Research BGI 1 0.95239   0.01872   0.88026   0.24265   100   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2020-01-15 Adult Adult Liver Liver and Biliary System
56016 56016 SRR10895925 SRX7564554 SRS6001795 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 001   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:Liver|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio : adult CL100103858 L01 CL100103858 L01       RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED BGISEQ BGISEQ-500   SRP241982     CL100103858_L01_501_1.fq.gz CL100103858_L01_501_2.fq.gz fastq fastq 8939441800.0 89394418.0 CL100103858 L01 501 1.fq.gz 0:100 1:100 A:2371368780;C:2076807210;G:2121148823;T:2354885910;N:15231077 100 100     2371368780 2076807210 2121148823 2354885910 15231077 SRX7564554 SRS6001795 SRA1026516 BGI|BGI-Research BGI 1 0.94776   0.01842   0.88822   0.16376   100   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2020-01-15 Adult Adult Liver Liver and Biliary System
63064 63064 SRR13587396 SRX9982091 SRS8153596 SRP303929 PRJNA698005 Danio rerio Raw sequence reads PRJNA698005 Whole Genome Sequencing Danio rerio Raw RNA sequence reads       Model organism or animal sample from Danio rerio The liver of Danio rerio   isolate:river|age:adult|sex:not collected|tissue:liver|BioSampleModel:Model organism or animal                 9ZL 9ZL 9ZL The liver experiment repeat 3 of Gobiocypris rarus     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED BGISEQ BGISEQ-500   SRP303929     9ZL_1.fq.gz 9ZL_2.fq.gz fastq fastq 8277847200.0 55185648.0 9ZL 1.fq.gz 0:150 1:150 A:2225896552;C:1891447719;G:1890393643;T:2270109286;N:0 150 150     2225896552 1891447719 1890393643 2270109286 0 SRX9982091 SRS8153596 SRA1189625 Center for Ecological and Environmental Sciences|Northwestern Polytechnical University Center for Ecological and Environmental Sciences 1 0.92352   0.05455   0.78634   0.53539   150   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2021-01-30 Adult Adult Liver Liver and Biliary System
63065 63065 SRR13587397 SRX9982090 SRS8153596 SRP303929 PRJNA698005 Danio rerio Raw sequence reads PRJNA698005 Whole Genome Sequencing Danio rerio Raw RNA sequence reads       Model organism or animal sample from Danio rerio The liver of Danio rerio   isolate:river|age:adult|sex:not collected|tissue:liver|BioSampleModel:Model organism or animal                 24ZL 24ZL 24ZL The liver control repeat 3 of Gobiocypris rarus     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED BGISEQ BGISEQ-500   SRP303929     24ZL_1.fq.gz 24ZL_2.fq.gz fastq fastq 8242802100.0 54952014.0 24ZL 1.fq.gz 0:150 1:150 A:2188471818;C:1925051043;G:1912682001;T:2215800017;N:797221 150 150     2188471818 1925051043 1912682001 2215800017 797221 SRX9982090 SRS8153596 SRA1189625 Center for Ecological and Environmental Sciences|Northwestern Polytechnical University Center for Ecological and Environmental Sciences 1 0.96458   0.02693   0.88657   0.1634   150   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2021-01-30 Adult Adult Liver Liver and Biliary System
63066 63066 SRR13587398 SRX9982089 SRS8153596 SRP303929 PRJNA698005 Danio rerio Raw sequence reads PRJNA698005 Whole Genome Sequencing Danio rerio Raw RNA sequence reads       Model organism or animal sample from Danio rerio The liver of Danio rerio   isolate:river|age:adult|sex:not collected|tissue:liver|BioSampleModel:Model organism or animal                 8ZL 8ZL 8ZL The liver experiment repeat 2 of Gobiocypris rarus     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED BGISEQ BGISEQ-500   SRP303929     8ZL_1.fq.gz 8ZL_2.fq.gz fastq fastq 8320145700.0 55467638.0 8ZL 1.fq.gz 0:150 1:150 A:2269869967;C:1877995864;G:1875902564;T:2295652508;N:724797 150 150     2269869967 1877995864 1875902564 2295652508 724797 SRX9982089 SRS8153596 SRA1189625 Center for Ecological and Environmental Sciences|Northwestern Polytechnical University Center for Ecological and Environmental Sciences 1 0.92304   0.06156   0.76934   0.50603   150   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2021-01-30 Adult Adult Liver Liver and Biliary System
63067 63067 SRR13587399 SRX9982088 SRS8153596 SRP303929 PRJNA698005 Danio rerio Raw sequence reads PRJNA698005 Whole Genome Sequencing Danio rerio Raw RNA sequence reads       Model organism or animal sample from Danio rerio The liver of Danio rerio   isolate:river|age:adult|sex:not collected|tissue:liver|BioSampleModel:Model organism or animal                 19Z L 19Z L 19Z L The liver control repeat 2 of Gobiocypris rarus     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED BGISEQ BGISEQ-500   SRP303929     19Z_L_1.fq.gz 19Z_L_2.fq.gz fastq fastq 8201244900.0 54674966.0 19Z L 1.fq.gz 0:150 1:150 A:2200752559;C:1868893233;G:1888687787;T:2242402488;N:508833 150 150     2200752559 1868893233 1888687787 2242402488 508833 SRX9982088 SRS8153596 SRA1189625 Center for Ecological and Environmental Sciences|Northwestern Polytechnical University Center for Ecological and Environmental Sciences 1 0.92245   0.05108   0.81537   0.53503   150   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2021-01-30 Adult Adult Liver Liver and Biliary System
63068 63068 SRR13587400 SRX9982087 SRS8153596 SRP303929 PRJNA698005 Danio rerio Raw sequence reads PRJNA698005 Whole Genome Sequencing Danio rerio Raw RNA sequence reads       Model organism or animal sample from Danio rerio The liver of Danio rerio   isolate:river|age:adult|sex:not collected|tissue:liver|BioSampleModel:Model organism or animal                 10ZL 10ZL 10ZL The liver experiment repeat 1 of Gobiocypris rarus     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED BGISEQ BGISEQ-500   SRP303929     10ZL_1.fq.gz 10ZL_2.fq.gz fastq fastq 8354384700.0 55695898.0 10ZL 1.fq.gz 0:150 1:150 A:2242193475;C:1918649445;G:1915390096;T:2278151684;N:0 150 150     2242193475 1918649445 1915390096 2278151684 0 SRX9982087 SRS8153596 SRA1189625 Center for Ecological and Environmental Sciences|Northwestern Polytechnical University Center for Ecological and Environmental Sciences 1 0.93588   0.03779   0.82467   0.32152   150   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2021-01-30 Adult Adult Liver Liver and Biliary System
63069 63069 SRR13587401 SRX9982086 SRS8153596 SRP303929 PRJNA698005 Danio rerio Raw sequence reads PRJNA698005 Whole Genome Sequencing Danio rerio Raw RNA sequence reads       Model organism or animal sample from Danio rerio The liver of Danio rerio   isolate:river|age:adult|sex:not collected|tissue:liver|BioSampleModel:Model organism or animal                 10Z L 10Z L 10Z L The liver control repeat 1 of Gobiocypris rarus     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED BGISEQ BGISEQ-500   SRP303929     10Z_L_1.fq.gz 10Z_L_2.fq.gz fastq fastq 8165319000.0 54435460.0 10Z L 1.fq.gz 0:150 1:150 A:2167746213;C:1898899329;G:1895642875;T:2202563231;N:467352 150 150     2167746213 1898899329 1895642875 2202563231 467352 SRX9982086 SRS8153596 SRA1189625 Center for Ecological and Environmental Sciences|Northwestern Polytechnical University Center for Ecological and Environmental Sciences 1 0.92701   0.02566   0.85064   0.19733   150   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2021-01-30 Adult Adult Liver Liver and Biliary System
65384 65384 SRR15090129 SRX11400004 SRS9443139 SRP327684 PRJNA745176 5 aminolevulinic acid alleviates alpha cypermethrin toxicity in the liver intestine axis in zebrafish PRJNA745176 Other Transcriptome sequencing of liver tissue shows that ALA rescues the differential gene expression on the oxidation reduction heme metabolism and complement activation pathways associated with alpha CP toxicity.         a CP 2   isolate:Zebrafish Wildtype Lines|age:3 month|sex:not collected|tissue:liver|treatment:α cypermethrin α CP single treatment|replicate:biological replicate 2|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio:liver with cypermethrin CP single treatment CP2 CP2 Transcriptome sequencing of liver tissue isolated from Danio rerio with cypermethrin CP single treatment     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED BGISEQ MGISEQ-2000RS   SRP327684     CP2.1.fq.gz CP2.2.fq.gz fastq fastq 6816619800.0 45444132.0 CP2.1.fq.gz 0:150 1:150 A:1891684962;C:1501309861;G:1520270555;T:1903228215;N:126207 150 150     1891684962 1501309861 1520270555 1903228215 126207 SRX11400004 SRS9443139 SRA1257080 China Agricultural University|Department of Applied Chemistry, College of Scienc China Agricultural University 1 0.90339   0.05682   0.74272   0.4834   150   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2021-07-09 Adult Adult Liver Liver and Biliary System
65385 65385 SRR15090130 SRX11400003 SRS9443138 SRP327684 PRJNA745176 5 aminolevulinic acid alleviates alpha cypermethrin toxicity in the liver intestine axis in zebrafish PRJNA745176 Other Transcriptome sequencing of liver tissue shows that ALA rescues the differential gene expression on the oxidation reduction heme metabolism and complement activation pathways associated with alpha CP toxicity.         a CP 1   isolate:Zebrafish Wildtype Lines|age:3 month|sex:not collected|tissue:liver|treatment:α cypermethrin α CP single treatment|replicate:biological replicate 1|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio:liver with cypermethrin CP single treatment CP1 CP1 Transcriptome sequencing of liver tissue isolated from Danio rerio with cypermethrin CP single treatment     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED BGISEQ MGISEQ-2000RS   SRP327684     CP1.1.fq.gz CP1.2.fq.gz fastq fastq 6801338100.0 45342254.0 CP1.1.fq.gz 0:150 1:150 A:1867686743;C:1516132586;G:1535971522;T:1881429395;N:117854 150 150     1867686743 1516132586 1535971522 1881429395 117854 SRX11400003 SRS9443138 SRA1257080 China Agricultural University|Department of Applied Chemistry, College of Scienc China Agricultural University 1 0.90967   0.04288   0.7433   0.51144   150   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2021-07-09 Adult Adult Liver Liver and Biliary System
65386 65386 SRR15090131 SRX11400002 SRS9443137 SRP327684 PRJNA745176 5 aminolevulinic acid alleviates alpha cypermethrin toxicity in the liver intestine axis in zebrafish PRJNA745176 Other Transcriptome sequencing of liver tissue shows that ALA rescues the differential gene expression on the oxidation reduction heme metabolism and complement activation pathways associated with alpha CP toxicity.         a CP+ALA 2   isolate:Zebrafish Wildtype Lines|age:3 month|sex:not collected|tissue:liver|treatment:α cypermethrin α CP + 5 aminolevulinic acid ALA co treatment|replicate:biological replicate 2|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio:liver with cypermethrin CP + 5 aminolevulinic acid ALA co treatment CP.ALA2 CP.ALA2 Transcriptome sequencing of liver tissue isolated from Danio rerio with cypermethrin CP + 5 aminolevulinic acid ALA co treatment     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED BGISEQ MGISEQ-2000RS   SRP327684     CP.ALA2.1.fq.gz CP.ALA2.2.fq.gz fastq fastq 6826417800.0 45509452.0 CP.ALA2.1.fq.gz 0:150 1:150 A:1880324963;C:1518162498;G:1528544942;T:1899329442;N:55955 150 150     1880324963 1518162498 1528544942 1899329442 55955 SRX11400002 SRS9443137 SRA1257080 China Agricultural University|Department of Applied Chemistry, College of Scienc China Agricultural University 1 0.90511   0.03383   0.75225   0.50503   150   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2021-07-09 Adult Adult Liver Liver and Biliary System
65387 65387 SRR15090132 SRX11400001 SRS9443136 SRP327684 PRJNA745176 5 aminolevulinic acid alleviates alpha cypermethrin toxicity in the liver intestine axis in zebrafish PRJNA745176 Other Transcriptome sequencing of liver tissue shows that ALA rescues the differential gene expression on the oxidation reduction heme metabolism and complement activation pathways associated with alpha CP toxicity.         a CP+ALA 1   isolate:Zebrafish Wildtype Lines|age:3 month|sex:not collected|tissue:liver|treatment:α cypermethrin α CP + 5 aminolevulinic acid ALA co treatment|replicate:biological replicate 1|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio:liver with cypermethrin CP + 5 aminolevulinic acid ALA co treatment CP.ALA1 CP.ALA1 Transcriptome sequencing of liver tissue isolated from Danio rerio with cypermethrin CP + 5 aminolevulinic acid ALA co treatment     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED BGISEQ MGISEQ-2000RS   SRP327684     CP.ALA1.1.fq.gz CP.ALA1.2.fq.gz fastq fastq 6787614000.0 45250760.0 CP.ALA1.1.fq.gz 0:150 1:150 A:1883241447;C:1496341973;G:1511662052;T:1896312396;N:56132 150 150     1883241447 1496341973 1511662052 1896312396 56132 SRX11400001 SRS9443136 SRA1257080 China Agricultural University|Department of Applied Chemistry, College of Scienc China Agricultural University 1 0.89741   0.03801   0.74943   0.50457   150   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2021-07-09 Adult Adult Liver Liver and Biliary System
65388 65388 SRR15090133 SRX11400000 SRS9443135 SRP327684 PRJNA745176 5 aminolevulinic acid alleviates alpha cypermethrin toxicity in the liver intestine axis in zebrafish PRJNA745176 Other Transcriptome sequencing of liver tissue shows that ALA rescues the differential gene expression on the oxidation reduction heme metabolism and complement activation pathways associated with alpha CP toxicity.         Control 2   isolate:Zebrafish Wildtype Lines|age:3 month|sex:not collected|tissue:liver|treatment:Control treatment|replicate:biological replicate 2|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio:liver with Control treatment CK 2 CK 2 Transcriptome sequencing of liver tissue isolated from Danio rerio with untreatment     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED BGISEQ MGISEQ-2000RS   SRP327684     CK2.1.fq.gz CK2.2.fq.gz fastq fastq 4937307600.0 32915384.0 CK2.1.fq.gz 0:150 1:150 A:1353639761;C:1104257332;G:1111219864;T:1368151010;N:39633 150 150     1353639761 1104257332 1111219864 1368151010 39633 SRX11400000 SRS9443135 SRA1257080 China Agricultural University|Department of Applied Chemistry, College of Scienc China Agricultural University 1 0.90129   0.03238   0.75406   0.49273   150   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2021-07-09 Adult Adult Liver Liver and Biliary System
65389 65389 SRR15090134 SRX11399999 SRS9443134 SRP327684 PRJNA745176 5 aminolevulinic acid alleviates alpha cypermethrin toxicity in the liver intestine axis in zebrafish PRJNA745176 Other Transcriptome sequencing of liver tissue shows that ALA rescues the differential gene expression on the oxidation reduction heme metabolism and complement activation pathways associated with alpha CP toxicity.         Control 1   isolate:Zebrafish Wildtype Lines|age:3 month|sex:not collected|tissue:liver|treatment:Control treatment|replicate:biological replicate 1|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio:liver with Control treatment CK 1 CK 1 Transcriptome sequencing of liver tissue isolated from Danio rerio with untreatment     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED BGISEQ MGISEQ-2000RS   SRP327684     CK1.1.fq.gz CK1.2.fq.gz fastq fastq 5002504200.0 33350028.0 CK1.1.fq.gz 0:150 1:150 A:1371483028;C:1118930644;G:1125887754;T:1386162333;N:40441 150 150     1371483028 1118930644 1125887754 1386162333 40441 SRX11399999 SRS9443134 SRA1257080 China Agricultural University|Department of Applied Chemistry, College of Scienc China Agricultural University 1 0.90179   0.03287   0.75349   0.49689   150   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2021-07-09 Adult Adult Liver Liver and Biliary System
65887 65887 SRR15667963 SRX11964789 SRS9973857 SRP334698 PRJNA758884 Metabolic and transcriptional adaptations improve physical performance of zebrafish GSE183023 Transcriptome Analysis Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2 and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately the effects of training and overfeeding on blood glucose muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain including 6 control fish 6 overfed fish 6 trained fish 6 trained and overfed fish   pubmed:34679716   liver train overfeed 6 GSM5549117   source name:liver|tissue:liver|training:trained|feed:overfeed|gender:male|strain:ABTL liver train overfeed 6 trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. liver Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total. Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols Zebrafish of the ABTL strain were reared and maintained at 28 °C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank. tissue:liver|training:trained|feed:overfeed|gender:male|strain:ABTL GSM5549117 GSM5549117: liver train overfeed 6; Danio rerio; RNA Seq GSM5549117   1 Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols GEO Accession:GSM5549117 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED BGISEQ BGISEQ-500   SRP334698     L24B_1.fq.gz L24B_2.fq.gz fastq fastq 4893222400.0 48932224.0 GSM5549117 r1 0:100 1:100 A:1299363606;C:1127714226;G:1149448002;T:1316696566;N:0 100 100     1299363606 1127714226 1149448002 1316696566 0 SRX11964789 SRS9973857 SRA1285419 GEO ZMF, University Heidelberg 1 0.94811   0.06102   0.81306   0.58353   100   B   usable mapping rate bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Germany 2021-08-30 Juvenile Juvenile Liver Liver and Biliary System
65888 65888 SRR15667962 SRX11964788 SRS9973856 SRP334698 PRJNA758884 Metabolic and transcriptional adaptations improve physical performance of zebrafish GSE183023 Transcriptome Analysis Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2 and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately the effects of training and overfeeding on blood glucose muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain including 6 control fish 6 overfed fish 6 trained fish 6 trained and overfed fish   pubmed:34679716   liver train overfeed 5 GSM5549116   source name:liver|tissue:liver|training:trained|feed:overfeed|gender:male|strain:ABTL liver train overfeed 5 trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. liver Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total. Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols Zebrafish of the ABTL strain were reared and maintained at 28 °C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank. tissue:liver|training:trained|feed:overfeed|gender:male|strain:ABTL GSM5549116 GSM5549116: liver train overfeed 5; Danio rerio; RNA Seq GSM5549116   1 Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols GEO Accession:GSM5549116 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED BGISEQ BGISEQ-500   SRP334698     L23B_1.fq.gz L23B_2.fq.gz fastq fastq 4864315800.0 48643158.0 GSM5549116 r1 0:100 1:100 A:1269157216;C:1139579077;G:1173873653;T:1281705854;N:0 100 100     1269157216 1139579077 1173873653 1281705854 0 SRX11964788 SRS9973856 SRA1285419 GEO ZMF, University Heidelberg 1 0.94747   0.0487   0.81779   0.56304   100   B   usable mapping rate bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Germany 2021-08-30 Juvenile Juvenile Liver Liver and Biliary System
65889 65889 SRR15667961 SRX11964787 SRS9973855 SRP334698 PRJNA758884 Metabolic and transcriptional adaptations improve physical performance of zebrafish GSE183023 Transcriptome Analysis Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2 and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately the effects of training and overfeeding on blood glucose muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain including 6 control fish 6 overfed fish 6 trained fish 6 trained and overfed fish   pubmed:34679716   liver train overfeed 4 GSM5549115   source name:liver|tissue:liver|training:trained|feed:overfeed|gender:male|strain:ABTL liver train overfeed 4 trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. liver Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total. Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols Zebrafish of the ABTL strain were reared and maintained at 28 °C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank. tissue:liver|training:trained|feed:overfeed|gender:male|strain:ABTL GSM5549115 GSM5549115: liver train overfeed 4; Danio rerio; RNA Seq GSM5549115   1 Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols GEO Accession:GSM5549115 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED BGISEQ BGISEQ-500   SRP334698     L22B_1.fq.gz L22B_2.fq.gz fastq fastq 4861767400.0 48617674.0 GSM5549115 r1 0:100 1:100 A:1272156595;C:1138672054;G:1163686667;T:1287252084;N:0 100 100     1272156595 1138672054 1163686667 1287252084 0 SRX11964787 SRS9973855 SRA1285419 GEO ZMF, University Heidelberg 1 0.95316   0.0514   0.82008   0.50642   100   B   usable mapping rate bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Germany 2021-08-30 Juvenile Juvenile Liver Liver and Biliary System
65890 65890 SRR15667960 SRX11964786 SRS9973854 SRP334698 PRJNA758884 Metabolic and transcriptional adaptations improve physical performance of zebrafish GSE183023 Transcriptome Analysis Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2 and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately the effects of training and overfeeding on blood glucose muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain including 6 control fish 6 overfed fish 6 trained fish 6 trained and overfed fish   pubmed:34679716   liver train overfeed 3 GSM5549114   source name:liver|tissue:liver|training:trained|feed:overfeed|gender:female|strain:ABTL liver train overfeed 3 trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. liver Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total. Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols Zebrafish of the ABTL strain were reared and maintained at 28 °C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank. tissue:liver|training:trained|feed:overfeed|gender:female|strain:ABTL GSM5549114 GSM5549114: liver train overfeed 3; Danio rerio; RNA Seq GSM5549114   1 Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols GEO Accession:GSM5549114 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED BGISEQ BGISEQ-500   SRP334698     L21B_1.fq.gz L21B_2.fq.gz fastq fastq 4830571800.0 48305718.0 GSM5549114 r1 0:100 1:100 A:1279428022;C:1123545637;G:1144703564;T:1282894577;N:0 100 100     1279428022 1123545637 1144703564 1282894577 0 SRX11964786 SRS9973854 SRA1285419 GEO ZMF, University Heidelberg 1 0.95734   0.02001   0.8868   0.12725   100   B   usable mapping rate bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Germany 2021-08-30 Juvenile Juvenile Liver Liver and Biliary System
65891 65891 SRR15667959 SRX11964785 SRS9973853 SRP334698 PRJNA758884 Metabolic and transcriptional adaptations improve physical performance of zebrafish GSE183023 Transcriptome Analysis Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2 and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately the effects of training and overfeeding on blood glucose muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain including 6 control fish 6 overfed fish 6 trained fish 6 trained and overfed fish   pubmed:34679716   liver train overfeed 2 GSM5549113   source name:liver|tissue:liver|training:trained|feed:overfeed|gender:female|strain:ABTL liver train overfeed 2 trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. liver Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total. Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols Zebrafish of the ABTL strain were reared and maintained at 28 °C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank. tissue:liver|training:trained|feed:overfeed|gender:female|strain:ABTL GSM5549113 GSM5549113: liver train overfeed 2; Danio rerio; RNA Seq GSM5549113   1 Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols GEO Accession:GSM5549113 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED BGISEQ BGISEQ-500   SRP334698     L20B_1.fq.gz L20B_2.fq.gz fastq fastq 4798900200.0 47989002.0 GSM5549113 r1 0:100 1:100 A:1264903507;C:1122454994;G:1142785530;T:1268756169;N:0 100 100     1264903507 1122454994 1142785530 1268756169 0 SRX11964785 SRS9973853 SRA1285419 GEO ZMF, University Heidelberg 1 0.95953   0.02579   0.87251   0.20039   100   B   usable mapping rate bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Germany 2021-08-30 Juvenile Juvenile Liver Liver and Biliary System
65892 65892 SRR15667958 SRX11964784 SRS9973852 SRP334698 PRJNA758884 Metabolic and transcriptional adaptations improve physical performance of zebrafish GSE183023 Transcriptome Analysis Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2 and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately the effects of training and overfeeding on blood glucose muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain including 6 control fish 6 overfed fish 6 trained fish 6 trained and overfed fish   pubmed:34679716   liver train overfeed 1 GSM5549112   source name:liver|tissue:liver|training:trained|feed:overfeed|gender:female|strain:ABTL liver train overfeed 1 trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. liver Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total. Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols Zebrafish of the ABTL strain were reared and maintained at 28 °C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank. tissue:liver|training:trained|feed:overfeed|gender:female|strain:ABTL GSM5549112 GSM5549112: liver train overfeed 1; Danio rerio; RNA Seq GSM5549112   1 Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols GEO Accession:GSM5549112 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED BGISEQ BGISEQ-500   SRP334698     L19B_1.fq.gz L19B_2.fq.gz fastq fastq 4834397800.0 48343978.0 GSM5549112 r1 0:100 1:100 A:1279393804;C:1125815329;G:1148443590;T:1280745077;N:0 100 100     1279393804 1125815329 1148443590 1280745077 0 SRX11964784 SRS9973852 SRA1285419 GEO ZMF, University Heidelberg 1 0.95933   0.02008   0.89483   0.14592   100   B   usable mapping rate bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Germany 2021-08-30 Juvenile Juvenile Liver Liver and Biliary System
65893 65893 SRR15667957 SRX11964783 SRS9973851 SRP334698 PRJNA758884 Metabolic and transcriptional adaptations improve physical performance of zebrafish GSE183023 Transcriptome Analysis Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2 and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately the effects of training and overfeeding on blood glucose muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain including 6 control fish 6 overfed fish 6 trained fish 6 trained and overfed fish   pubmed:34679716   liver train ctrl 6 GSM5549111   source name:liver|tissue:liver|training:trained|feed:ctrl|gender:male|strain:ABTL liver train ctrl 6 trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. liver Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total. Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols Zebrafish of the ABTL strain were reared and maintained at 28 °C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank. tissue:liver|training:trained|feed:ctrl|gender:male|strain:ABTL GSM5549111 GSM5549111: liver train ctrl 6; Danio rerio; RNA Seq GSM5549111   1 Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols GEO Accession:GSM5549111 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED BGISEQ BGISEQ-500   SRP334698     L18B_1.fq.gz L18B_2.fq.gz fastq fastq 4821948400.0 48219484.0 GSM5549111 r1 0:100 1:100 A:1291565962;C:1101325255;G:1121237816;T:1307819367;N:0 100 100     1291565962 1101325255 1121237816 1307819367 0 SRX11964783 SRS9973851 SRA1285419 GEO ZMF, University Heidelberg 1 0.94729   0.06306   0.81207   0.58228   100   B   usable mapping rate bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Germany 2021-08-30 Juvenile Juvenile Liver Liver and Biliary System
65894 65894 SRR15667956 SRX11964782 SRS9973850 SRP334698 PRJNA758884 Metabolic and transcriptional adaptations improve physical performance of zebrafish GSE183023 Transcriptome Analysis Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2 and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately the effects of training and overfeeding on blood glucose muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain including 6 control fish 6 overfed fish 6 trained fish 6 trained and overfed fish   pubmed:34679716   liver train ctrl 5 GSM5549110   source name:liver|tissue:liver|training:trained|feed:ctrl|gender:male|strain:ABTL liver train ctrl 5 trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. liver Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total. Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols Zebrafish of the ABTL strain were reared and maintained at 28 °C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank. tissue:liver|training:trained|feed:ctrl|gender:male|strain:ABTL GSM5549110 GSM5549110: liver train ctrl 5; Danio rerio; RNA Seq GSM5549110   1 Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols GEO Accession:GSM5549110 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED BGISEQ BGISEQ-500   SRP334698     L17B_1.fq.gz L17B_2.fq.gz fastq fastq 4803628200.0 48036282.0 GSM5549110 r1 0:100 1:100 A:1284799467;C:1098135007;G:1120469212;T:1300224514;N:0 100 100     1284799467 1098135007 1120469212 1300224514 0 SRX11964782 SRS9973850 SRA1285419 GEO ZMF, University Heidelberg 1 0.9496   0.0625   0.81456   0.59107   100   B   usable mapping rate bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Germany 2021-08-30 Juvenile Juvenile Liver Liver and Biliary System
65895 65895 SRR15667955 SRX11964781 SRS9973849 SRP334698 PRJNA758884 Metabolic and transcriptional adaptations improve physical performance of zebrafish GSE183023 Transcriptome Analysis Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2 and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately the effects of training and overfeeding on blood glucose muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain including 6 control fish 6 overfed fish 6 trained fish 6 trained and overfed fish   pubmed:34679716   liver train ctrl 4 GSM5549109   source name:liver|tissue:liver|training:trained|feed:ctrl|gender:male|strain:ABTL liver train ctrl 4 trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. liver Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total. Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols Zebrafish of the ABTL strain were reared and maintained at 28 °C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank. tissue:liver|training:trained|feed:ctrl|gender:male|strain:ABTL GSM5549109 GSM5549109: liver train ctrl 4; Danio rerio; RNA Seq GSM5549109   1 Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols GEO Accession:GSM5549109 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED BGISEQ BGISEQ-500   SRP334698     L16B_1.fq.gz L16B_2.fq.gz fastq fastq 4810847400.0 48108474.0 GSM5549109 r1 0:100 1:100 A:1282522728;C:1105003262;G:1127602301;T:1295719109;N:0 100 100     1282522728 1105003262 1127602301 1295719109 0 SRX11964781 SRS9973849 SRA1285419 GEO ZMF, University Heidelberg 1 0.94654   0.05935   0.81525   0.55406   100   B   usable mapping rate bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Germany 2021-08-30 Juvenile Juvenile Liver Liver and Biliary System
65896 65896 SRR15667954 SRX11964780 SRS9973848 SRP334698 PRJNA758884 Metabolic and transcriptional adaptations improve physical performance of zebrafish GSE183023 Transcriptome Analysis Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2 and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately the effects of training and overfeeding on blood glucose muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain including 6 control fish 6 overfed fish 6 trained fish 6 trained and overfed fish   pubmed:34679716   liver train ctrl 3 GSM5549108   source name:liver|tissue:liver|training:trained|feed:ctrl|gender:female|strain:ABTL liver train ctrl 3 trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. liver Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total. Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols Zebrafish of the ABTL strain were reared and maintained at 28 °C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank. tissue:liver|training:trained|feed:ctrl|gender:female|strain:ABTL GSM5549108 GSM5549108: liver train ctrl 3; Danio rerio; RNA Seq GSM5549108   1 Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols GEO Accession:GSM5549108 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED BGISEQ BGISEQ-500   SRP334698     L15B_1.fq.gz L15B_2.fq.gz fastq fastq 4985037400.0 49850374.0 GSM5549108 r1 0:100 1:100 A:1350433123;C:1126555415;G:1149552334;T:1358496528;N:0 100 100     1350433123 1126555415 1149552334 1358496528 0 SRX11964780 SRS9973848 SRA1285419 GEO ZMF, University Heidelberg 1 0.94223   0.05241   0.81753   0.38734   100   B   usable mapping rate bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Germany 2021-08-30 Juvenile Juvenile Liver Liver and Biliary System
65897 65897 SRR15667953 SRX11964779 SRS9973847 SRP334698 PRJNA758884 Metabolic and transcriptional adaptations improve physical performance of zebrafish GSE183023 Transcriptome Analysis Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2 and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately the effects of training and overfeeding on blood glucose muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain including 6 control fish 6 overfed fish 6 trained fish 6 trained and overfed fish   pubmed:34679716   liver train ctrl 2 GSM5549107   source name:liver|tissue:liver|training:trained|feed:ctrl|gender:female|strain:ABTL liver train ctrl 2 trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. liver Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total. Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols Zebrafish of the ABTL strain were reared and maintained at 28 °C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank. tissue:liver|training:trained|feed:ctrl|gender:female|strain:ABTL GSM5549107 GSM5549107: liver train ctrl 2; Danio rerio; RNA Seq GSM5549107   1 Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols GEO Accession:GSM5549107 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED BGISEQ BGISEQ-500   SRP334698     L14B_1.fq.gz L14B_2.fq.gz fastq fastq 4804454800.0 48044548.0 GSM5549107 r1 0:100 1:100 A:1265573746;C:1124189778;G:1148662079;T:1266029197;N:0 100 100     1265573746 1124189778 1148662079 1266029197 0 SRX11964779 SRS9973847 SRA1285419 GEO ZMF, University Heidelberg 1 0.95891   0.02268   0.88392   0.17772   100   B   usable mapping rate bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Germany 2021-08-30 Juvenile Juvenile Liver Liver and Biliary System
65898 65898 SRR15667952 SRX11964778 SRS9973846 SRP334698 PRJNA758884 Metabolic and transcriptional adaptations improve physical performance of zebrafish GSE183023 Transcriptome Analysis Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2 and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately the effects of training and overfeeding on blood glucose muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain including 6 control fish 6 overfed fish 6 trained fish 6 trained and overfed fish   pubmed:34679716   liver train ctrl 1 GSM5549106   source name:liver|tissue:liver|training:trained|feed:ctrl|gender:female|strain:ABTL liver train ctrl 1 trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. liver Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total. Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols Zebrafish of the ABTL strain were reared and maintained at 28 °C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank. tissue:liver|training:trained|feed:ctrl|gender:female|strain:ABTL GSM5549106 GSM5549106: liver train ctrl 1; Danio rerio; RNA Seq GSM5549106   1 Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols GEO Accession:GSM5549106 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED BGISEQ BGISEQ-500   SRP334698     L13B_1.fq.gz L13B_2.fq.gz fastq fastq 4822830200.0 48228302.0 GSM5549106 r1 0:100 1:100 A:1276481281;C:1123835516;G:1144873235;T:1277640168;N:0 100 100     1276481281 1123835516 1144873235 1277640168 0 SRX11964778 SRS9973846 SRA1285419 GEO ZMF, University Heidelberg 1 0.96141   0.0197   0.89388   0.1349   100   B   usable mapping rate bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Germany 2021-08-30 Juvenile Juvenile Liver Liver and Biliary System
65899 65899 SRR15667951 SRX11964777 SRS9973845 SRP334698 PRJNA758884 Metabolic and transcriptional adaptations improve physical performance of zebrafish GSE183023 Transcriptome Analysis Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2 and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately the effects of training and overfeeding on blood glucose muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain including 6 control fish 6 overfed fish 6 trained fish 6 trained and overfed fish   pubmed:34679716   liver ctrl overfeed 6 GSM5549105   source name:liver|tissue:liver|training:ctrl|feed:overfeed|gender:female|strain:ABTL liver ctrl overfeed 6 trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. liver Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total. Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols Zebrafish of the ABTL strain were reared and maintained at 28 °C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank. tissue:liver|training:ctrl|feed:overfeed|gender:female|strain:ABTL GSM5549105 GSM5549105: liver ctrl overfeed 6; Danio rerio; RNA Seq GSM5549105   1 Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols GEO Accession:GSM5549105 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED BGISEQ BGISEQ-500   SRP334698     L9B_1.fq.gz L9B_2.fq.gz fastq fastq 4818164600.0 48181646.0 GSM5549105 r1 0:100 1:100 A:1279585168;C:1117941633;G:1137085086;T:1283552713;N:0 100 100     1279585168 1117941633 1137085086 1283552713 0 SRX11964777 SRS9973845 SRA1285419 GEO ZMF, University Heidelberg 1 0.95794   0.0217   0.8772   0.13327   100   B   usable mapping rate bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Germany 2021-08-30 Juvenile Juvenile Liver Liver and Biliary System
65900 65900 SRR15667950 SRX11964776 SRS9973844 SRP334698 PRJNA758884 Metabolic and transcriptional adaptations improve physical performance of zebrafish GSE183023 Transcriptome Analysis Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2 and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately the effects of training and overfeeding on blood glucose muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain including 6 control fish 6 overfed fish 6 trained fish 6 trained and overfed fish   pubmed:34679716   liver ctrl overfeed 5 GSM5549104   source name:liver|tissue:liver|training:ctrl|feed:overfeed|gender:female|strain:ABTL liver ctrl overfeed 5 trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. liver Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total. Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols Zebrafish of the ABTL strain were reared and maintained at 28 °C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank. tissue:liver|training:ctrl|feed:overfeed|gender:female|strain:ABTL GSM5549104 GSM5549104: liver ctrl overfeed 5; Danio rerio; RNA Seq GSM5549104   1 Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols GEO Accession:GSM5549104 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED BGISEQ BGISEQ-500   SRP334698     L8B_1.fq.gz L8B_2.fq.gz fastq fastq 4815366200.0 48153662.0 GSM5549104 r1 0:100 1:100 A:1274920749;C:1122213902;G:1140211257;T:1278020292;N:0 100 100     1274920749 1122213902 1140211257 1278020292 0 SRX11964776 SRS9973844 SRA1285419 GEO ZMF, University Heidelberg 1 0.95864   0.02123   0.88805   0.13863   100   B   usable mapping rate bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Germany 2021-08-30 Juvenile Juvenile Liver Liver and Biliary System
65901 65901 SRR15667949 SRX11964775 SRS9973843 SRP334698 PRJNA758884 Metabolic and transcriptional adaptations improve physical performance of zebrafish GSE183023 Transcriptome Analysis Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2 and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately the effects of training and overfeeding on blood glucose muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain including 6 control fish 6 overfed fish 6 trained fish 6 trained and overfed fish   pubmed:34679716   liver ctrl overfeed 4 GSM5549103   source name:liver|tissue:liver|training:ctrl|feed:overfeed|gender:female|strain:ABTL liver ctrl overfeed 4 trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. liver Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total. Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols Zebrafish of the ABTL strain were reared and maintained at 28 °C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank. tissue:liver|training:ctrl|feed:overfeed|gender:female|strain:ABTL GSM5549103 GSM5549103: liver ctrl overfeed 4; Danio rerio; RNA Seq GSM5549103   1 Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols GEO Accession:GSM5549103 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED BGISEQ BGISEQ-500   SRP334698     L7B_1.fq.gz L7B_2.fq.gz fastq fastq 4806451200.0 48064512.0 GSM5549103 r1 0:100 1:100 A:1272428504;C:1119437887;G:1139899400;T:1274685409;N:0 100 100     1272428504 1119437887 1139899400 1274685409 0 SRX11964775 SRS9973843 SRA1285419 GEO ZMF, University Heidelberg 1 0.9605   0.02337   0.87625   0.17173   100   B   usable mapping rate bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Germany 2021-08-30 Juvenile Juvenile Liver Liver and Biliary System
65902 65902 SRR15667948 SRX11964774 SRS9973842 SRP334698 PRJNA758884 Metabolic and transcriptional adaptations improve physical performance of zebrafish GSE183023 Transcriptome Analysis Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2 and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately the effects of training and overfeeding on blood glucose muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain including 6 control fish 6 overfed fish 6 trained fish 6 trained and overfed fish   pubmed:34679716   liver ctrl overfeed 3 GSM5549102   source name:liver|tissue:liver|training:ctrl|feed:overfeed|gender:male|strain:ABTL liver ctrl overfeed 3 trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. liver Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total. Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols Zebrafish of the ABTL strain were reared and maintained at 28 °C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank. tissue:liver|training:ctrl|feed:overfeed|gender:male|strain:ABTL GSM5549102 GSM5549102: liver ctrl overfeed 3; Danio rerio; RNA Seq GSM5549102   1 Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols GEO Accession:GSM5549102 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED BGISEQ BGISEQ-500   SRP334698     L12B_1.fq.gz L12B_2.fq.gz fastq fastq 4808986200.0 48089862.0 GSM5549102 r1 0:100 1:100 A:1282711930;C:1106482446;G:1126540026;T:1293251798;N:0 100 100     1282711930 1106482446 1126540026 1293251798 0 SRX11964774 SRS9973842 SRA1285419 GEO ZMF, University Heidelberg 1 0.95163   0.05783   0.80872   0.56282   100   B   usable mapping rate bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Germany 2021-08-30 Juvenile Juvenile Liver Liver and Biliary System
65903 65903 SRR15667947 SRX11964773 SRS9973841 SRP334698 PRJNA758884 Metabolic and transcriptional adaptations improve physical performance of zebrafish GSE183023 Transcriptome Analysis Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2 and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately the effects of training and overfeeding on blood glucose muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain including 6 control fish 6 overfed fish 6 trained fish 6 trained and overfed fish   pubmed:34679716   liver ctrl overfeed 2 GSM5549101   source name:liver|tissue:liver|training:ctrl|feed:overfeed|gender:male|strain:ABTL liver ctrl overfeed 2 trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. liver Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total. Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols Zebrafish of the ABTL strain were reared and maintained at 28 °C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank. tissue:liver|training:ctrl|feed:overfeed|gender:male|strain:ABTL GSM5549101 GSM5549101: liver ctrl overfeed 2; Danio rerio; RNA Seq GSM5549101   1 Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols GEO Accession:GSM5549101 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED BGISEQ BGISEQ-500   SRP334698     L11B_1.fq.gz L11B_2.fq.gz fastq fastq 4813626000.0 48136260.0 GSM5549101 r1 0:100 1:100 A:1280868095;C:1108012462;G:1126540954;T:1298204489;N:0 100 100     1280868095 1108012462 1126540954 1298204489 0 SRX11964773 SRS9973841 SRA1285419 GEO ZMF, University Heidelberg 1 0.94831   0.05349   0.81513   0.57243   100   B   usable mapping rate bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Germany 2021-08-30 Juvenile Juvenile Liver Liver and Biliary System
65904 65904 SRR15667946 SRX11964772 SRS9973840 SRP334698 PRJNA758884 Metabolic and transcriptional adaptations improve physical performance of zebrafish GSE183023 Transcriptome Analysis Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2 and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately the effects of training and overfeeding on blood glucose muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain including 6 control fish 6 overfed fish 6 trained fish 6 trained and overfed fish   pubmed:34679716   liver ctrl overfeed 1 GSM5549100   source name:liver|tissue:liver|training:ctrl|feed:overfeed|gender:male|strain:ABTL liver ctrl overfeed 1 trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. liver Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total. Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols Zebrafish of the ABTL strain were reared and maintained at 28 °C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank. tissue:liver|training:ctrl|feed:overfeed|gender:male|strain:ABTL GSM5549100 GSM5549100: liver ctrl overfeed 1; Danio rerio; RNA Seq GSM5549100   1 Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols GEO Accession:GSM5549100 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED BGISEQ BGISEQ-500   SRP334698     L10B_1.fq.gz L10B_2.fq.gz fastq fastq 4810219200.0 48102192.0 GSM5549100 r1 0:100 1:100 A:1291986049;C:1097301072;G:1114733041;T:1306199038;N:0 100 100     1291986049 1097301072 1114733041 1306199038 0 SRX11964772 SRS9973840 SRA1285419 GEO ZMF, University Heidelberg 1 0.9477   0.06719   0.80762   0.56967   100   B   usable mapping rate bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Germany 2021-08-30 Juvenile Juvenile Liver Liver and Biliary System
65905 65905 SRR15667945 SRX11964771 SRS9973839 SRP334698 PRJNA758884 Metabolic and transcriptional adaptations improve physical performance of zebrafish GSE183023 Transcriptome Analysis Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2 and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately the effects of training and overfeeding on blood glucose muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain including 6 control fish 6 overfed fish 6 trained fish 6 trained and overfed fish   pubmed:34679716   liver ctrl ctrl 6 GSM5549099   source name:liver|tissue:liver|training:ctrl|feed:ctrl|gender:male|strain:ABTL liver ctrl ctrl 6 trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. liver Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total. Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols Zebrafish of the ABTL strain were reared and maintained at 28 °C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank. tissue:liver|training:ctrl|feed:ctrl|gender:male|strain:ABTL GSM5549099 GSM5549099: liver ctrl ctrl 6; Danio rerio; RNA Seq GSM5549099   1 Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols GEO Accession:GSM5549099 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED BGISEQ BGISEQ-500   SRP334698     L6B_1.fq.gz L6B_2.fq.gz fastq fastq 4800718000.0 48007180.0 GSM5549099 r1 0:100 1:100 A:1258342638;C:1122320482;G:1144931913;T:1275122967;N:0 100 100     1258342638 1122320482 1144931913 1275122967 0 SRX11964771 SRS9973839 SRA1285419 GEO ZMF, University Heidelberg 1 0.953   0.05324   0.81257   0.58562   100   B   usable mapping rate bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Germany 2021-08-30 Juvenile Juvenile Liver Liver and Biliary System
65906 65906 SRR15667944 SRX11964770 SRS9973838 SRP334698 PRJNA758884 Metabolic and transcriptional adaptations improve physical performance of zebrafish GSE183023 Transcriptome Analysis Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2 and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately the effects of training and overfeeding on blood glucose muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain including 6 control fish 6 overfed fish 6 trained fish 6 trained and overfed fish   pubmed:34679716   liver ctrl ctrl 5 GSM5549098   source name:liver|tissue:liver|training:ctrl|feed:ctrl|gender:male|strain:ABTL liver ctrl ctrl 5 trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. liver Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total. Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols Zebrafish of the ABTL strain were reared and maintained at 28 °C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank. tissue:liver|training:ctrl|feed:ctrl|gender:male|strain:ABTL GSM5549098 GSM5549098: liver ctrl ctrl 5; Danio rerio; RNA Seq GSM5549098   1 Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols GEO Accession:GSM5549098 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED BGISEQ BGISEQ-500   SRP334698     L5B_1.fq.gz L5B_2.fq.gz fastq fastq 4806088800.0 48060888.0 GSM5549098 r1 0:100 1:100 A:1271888694;C:1114093824;G:1133421540;T:1286684742;N:0 100 100     1271888694 1114093824 1133421540 1286684742 0 SRX11964770 SRS9973838 SRA1285419 GEO ZMF, University Heidelberg 1 0.95001   0.05792   0.807   0.56126   100   B   usable mapping rate bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Germany 2021-08-30 Juvenile Juvenile Liver Liver and Biliary System
65907 65907 SRR15667943 SRX11964769 SRS9973837 SRP334698 PRJNA758884 Metabolic and transcriptional adaptations improve physical performance of zebrafish GSE183023 Transcriptome Analysis Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2 and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately the effects of training and overfeeding on blood glucose muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain including 6 control fish 6 overfed fish 6 trained fish 6 trained and overfed fish   pubmed:34679716   liver ctrl ctrl 4 GSM5549097   source name:liver|tissue:liver|training:ctrl|feed:ctrl|gender:male|strain:ABTL liver ctrl ctrl 4 trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. liver Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total. Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols Zebrafish of the ABTL strain were reared and maintained at 28 °C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank. tissue:liver|training:ctrl|feed:ctrl|gender:male|strain:ABTL GSM5549097 GSM5549097: liver ctrl ctrl 4; Danio rerio; RNA Seq GSM5549097   1 Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols GEO Accession:GSM5549097 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED BGISEQ BGISEQ-500   SRP334698     L4B_1.fq.gz L4B_2.fq.gz fastq fastq 4793658200.0 47936582.0 GSM5549097 r1 0:100 1:100 A:1278328591;C:1101882376;G:1120230481;T:1293216752;N:0 100 100     1278328591 1101882376 1120230481 1293216752 0 SRX11964769 SRS9973837 SRA1285419 GEO ZMF, University Heidelberg 1 0.94635   0.06821   0.77814   0.57203   100   B   usable mapping rate bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Germany 2021-08-30 Juvenile Juvenile Liver Liver and Biliary System
65908 65908 SRR15667942 SRX11964768 SRS9973836 SRP334698 PRJNA758884 Metabolic and transcriptional adaptations improve physical performance of zebrafish GSE183023 Transcriptome Analysis Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2 and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately the effects of training and overfeeding on blood glucose muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain including 6 control fish 6 overfed fish 6 trained fish 6 trained and overfed fish   pubmed:34679716   liver ctrl ctrl 3 GSM5549096   source name:liver|tissue:liver|training:ctrl|feed:ctrl|gender:female|strain:ABTL liver ctrl ctrl 3 trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. liver Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total. Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols Zebrafish of the ABTL strain were reared and maintained at 28 °C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank. tissue:liver|training:ctrl|feed:ctrl|gender:female|strain:ABTL GSM5549096 GSM5549096: liver ctrl ctrl 3; Danio rerio; RNA Seq GSM5549096   1 Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols GEO Accession:GSM5549096 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED BGISEQ BGISEQ-500   SRP334698     L3B_1.fq.gz L3B_2.fq.gz fastq fastq 4826663000.0 48266630.0 GSM5549096 r1 0:100 1:100 A:1279595092;C:1123953174;G:1141367365;T:1281747369;N:0 100 100     1279595092 1123953174 1141367365 1281747369 0 SRX11964768 SRS9973836 SRA1285419 GEO ZMF, University Heidelberg 1 0.9594   0.02127   0.88463   0.12493   100   B   usable mapping rate bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Germany 2021-08-30 Juvenile Juvenile Liver Liver and Biliary System
65909 65909 SRR15667941 SRX11964767 SRS9973835 SRP334698 PRJNA758884 Metabolic and transcriptional adaptations improve physical performance of zebrafish GSE183023 Transcriptome Analysis Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2 and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately the effects of training and overfeeding on blood glucose muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain including 6 control fish 6 overfed fish 6 trained fish 6 trained and overfed fish   pubmed:34679716   liver ctrl ctrl 2 GSM5549095   source name:liver|tissue:liver|training:ctrl|feed:ctrl|gender:female|strain:ABTL liver ctrl ctrl 2 trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. liver Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total. Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols Zebrafish of the ABTL strain were reared and maintained at 28 °C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank. tissue:liver|training:ctrl|feed:ctrl|gender:female|strain:ABTL GSM5549095 GSM5549095: liver ctrl ctrl 2; Danio rerio; RNA Seq GSM5549095   1 Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols GEO Accession:GSM5549095 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED BGISEQ BGISEQ-500   SRP334698     L2B_1.fq.gz L2B_2.fq.gz fastq fastq 4825604600.0 48256046.0 GSM5549095 r1 0:100 1:100 A:1280321186;C:1120511740;G:1138899889;T:1285871785;N:0 100 100     1280321186 1120511740 1138899889 1285871785 0 SRX11964767 SRS9973835 SRA1285419 GEO ZMF, University Heidelberg 1 0.95896   0.0192   0.88899   0.11515   100   B   usable mapping rate bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Germany 2021-08-30 Juvenile Juvenile Liver Liver and Biliary System
65910 65910 SRR15667940 SRX11964766 SRS9973834 SRP334698 PRJNA758884 Metabolic and transcriptional adaptations improve physical performance of zebrafish GSE183023 Transcriptome Analysis Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2 and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately the effects of training and overfeeding on blood glucose muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain including 6 control fish 6 overfed fish 6 trained fish 6 trained and overfed fish   pubmed:34679716   liver ctrl ctrl 1 GSM5549094   source name:liver|tissue:liver|training:ctrl|feed:ctrl|gender:female|strain:ABTL liver ctrl ctrl 1 trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. liver Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total. Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols Zebrafish of the ABTL strain were reared and maintained at 28 °C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank. tissue:liver|training:ctrl|feed:ctrl|gender:female|strain:ABTL GSM5549094 GSM5549094: liver ctrl ctrl 1; Danio rerio; RNA Seq GSM5549094   1 Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols GEO Accession:GSM5549094 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED BGISEQ BGISEQ-500   SRP334698     L1B_1.fq.gz L1B_2.fq.gz fastq fastq 4829756800.0 48297568.0 GSM5549094 r1 0:100 1:100 A:1282017434;C:1119791375;G:1138880812;T:1289067179;N:0 100 100     1282017434 1119791375 1138880812 1289067179 0 SRX11964766 SRS9973834 SRA1285419 GEO ZMF, University Heidelberg 1 0.95838   0.03146   0.8479   0.28451   100   B   usable mapping rate bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Germany 2021-08-30 Juvenile Juvenile Liver Liver and Biliary System
70080 70080 SRR19445938 SRX15499122 SRS13214006 SRP377632 PRJNA843695 Loss of Glo2 alters the glucose metabolism in zebrafish GSE205085 Transcriptome Analysis Glyoxalase 2 is the second enzyme of the glyoxalase system catalyzing the detoxification of methylglyoxal to D lactate via SD Lactoylglutathione. Recent studies have suggested Glo2 as a regulator of glycolysis but the physiological functions of Glo2 in vivo and organ specific functions of the enzyme have not yet been evaluated. Therefore a CRISPR/Cas9 knockout of glo2 in zebrafish was created and analyzed. Consistent with its function in methylglyoxal detoxification SD Lactoylglutathione but not methylglyoxal accumulated in glo2 / larvae with no change in longevity. Adult glo2 / livers developed an impaired insulin signaling indicated by a reduced hepatic P70 S6 kinase activation and reduced hepatic hexose concentration. In contrast glo2 / skeletal muscle remained functionally intact compensating for the dysfunctional liver through increased glucose uptake thereby maintaining euglycemia and preventing damage of the retina and kidney. In conclusion the data identified Glo2 to fulfill similar but unique functions compared to Glo1 and established Glo2 as a novel target in diabetes research regulating hepatic insulin signaling. Overall design: A CRISPR based knockout of Glyoxalase 2 was created in zebrafish. The development of the fish was analyzed as well as organ specific glucose metabolism in skeletal muscle and liver. Imaging studies of Retina kidney liver and skeletal muscle were conducted. RNA sequencing was performed on adult liver tissue of glo2+/+ and glo2 / fish by BGI in collaboration with the NGS Core facility in Mannheim University of Heidelberg.   pubmed:36535130   Glo2 / 6 GSM6205029   source name:Tgfli1:EGFP|tissue:whole liver|trained:no|genotype:KO Glo2 / 6 trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Assembly: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. Tgfli1:EGFP   Total RNA was extracted using TRIzol method RNA libraries were prepared for sequencing using standard BGISeq 500 protocols   tissue:whole liver|trained:no|genotype:KO GSM6205029 GSM6205029: Glo2 / 6; Danio rerio; RNA Seq GSM6205029 r1 GSM6205029 1 Total RNA was extracted using TRIzol method RNA libraries were prepared for sequencing using standard BGISeq 500 protocols   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED BGISEQ BGISEQ-500   SRP377632     12.1_1.fq.gz 12.1_2.fq.gz fastq fastq 4163038200.0 41630382.0 GSM6205029 r1 0:100 1:100 A:1080428167;C:982538284;G:1004098821;T:1095972928;N:0 100 100     1080428167 982538284 1004098821 1095972928 0 SRX15499122 SRS13214006 SRA1428824 ZMF, University Heidelberg ZMF, University Heidelberg 1 0.95934   0.04773   0.80028   0.52892   100   B   usable mapping rate bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Germany 2022-05-30 Undetermined Larval Liver Liver and Biliary System
70081 70081 SRR19445939 SRX15499121 SRS13214005 SRP377632 PRJNA843695 Loss of Glo2 alters the glucose metabolism in zebrafish GSE205085 Transcriptome Analysis Glyoxalase 2 is the second enzyme of the glyoxalase system catalyzing the detoxification of methylglyoxal to D lactate via SD Lactoylglutathione. Recent studies have suggested Glo2 as a regulator of glycolysis but the physiological functions of Glo2 in vivo and organ specific functions of the enzyme have not yet been evaluated. Therefore a CRISPR/Cas9 knockout of glo2 in zebrafish was created and analyzed. Consistent with its function in methylglyoxal detoxification SD Lactoylglutathione but not methylglyoxal accumulated in glo2 / larvae with no change in longevity. Adult glo2 / livers developed an impaired insulin signaling indicated by a reduced hepatic P70 S6 kinase activation and reduced hepatic hexose concentration. In contrast glo2 / skeletal muscle remained functionally intact compensating for the dysfunctional liver through increased glucose uptake thereby maintaining euglycemia and preventing damage of the retina and kidney. In conclusion the data identified Glo2 to fulfill similar but unique functions compared to Glo1 and established Glo2 as a novel target in diabetes research regulating hepatic insulin signaling. Overall design: A CRISPR based knockout of Glyoxalase 2 was created in zebrafish. The development of the fish was analyzed as well as organ specific glucose metabolism in skeletal muscle and liver. Imaging studies of Retina kidney liver and skeletal muscle were conducted. RNA sequencing was performed on adult liver tissue of glo2+/+ and glo2 / fish by BGI in collaboration with the NGS Core facility in Mannheim University of Heidelberg.   pubmed:36535130   Glo2 +/+ 6 GSM6205028   source name:Tgfli1:EGFP|tissue:whole liver|trained:no|genotype:WT Glo2 +/+ 6 trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Assembly: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. Tgfli1:EGFP   Total RNA was extracted using TRIzol method RNA libraries were prepared for sequencing using standard BGISeq 500 protocols   tissue:whole liver|trained:no|genotype:WT GSM6205028 GSM6205028: Glo2 +/+ 6; Danio rerio; RNA Seq GSM6205028 r1 GSM6205028 1 Total RNA was extracted using TRIzol method RNA libraries were prepared for sequencing using standard BGISeq 500 protocols   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED BGISEQ BGISEQ-500   SRP377632     11.1_1.fq.gz 11.1_2.fq.gz fastq fastq 4170292600.0 41702926.0 GSM6205028 r1 0:100 1:100 A:1081431596;C:983791100;G:1012532071;T:1092537833;N:0 100 100     1081431596 983791100 1012532071 1092537833 0 SRX15499121 SRS13214005 SRA1428824 ZMF, University Heidelberg ZMF, University Heidelberg 1 0.95587   0.0499   0.80805   0.50421   100   B   usable mapping rate bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Germany 2022-05-30 Undetermined Larval Liver Liver and Biliary System
70082 70082 SRR19445940 SRX15499120 SRS13214004 SRP377632 PRJNA843695 Loss of Glo2 alters the glucose metabolism in zebrafish GSE205085 Transcriptome Analysis Glyoxalase 2 is the second enzyme of the glyoxalase system catalyzing the detoxification of methylglyoxal to D lactate via SD Lactoylglutathione. Recent studies have suggested Glo2 as a regulator of glycolysis but the physiological functions of Glo2 in vivo and organ specific functions of the enzyme have not yet been evaluated. Therefore a CRISPR/Cas9 knockout of glo2 in zebrafish was created and analyzed. Consistent with its function in methylglyoxal detoxification SD Lactoylglutathione but not methylglyoxal accumulated in glo2 / larvae with no change in longevity. Adult glo2 / livers developed an impaired insulin signaling indicated by a reduced hepatic P70 S6 kinase activation and reduced hepatic hexose concentration. In contrast glo2 / skeletal muscle remained functionally intact compensating for the dysfunctional liver through increased glucose uptake thereby maintaining euglycemia and preventing damage of the retina and kidney. In conclusion the data identified Glo2 to fulfill similar but unique functions compared to Glo1 and established Glo2 as a novel target in diabetes research regulating hepatic insulin signaling. Overall design: A CRISPR based knockout of Glyoxalase 2 was created in zebrafish. The development of the fish was analyzed as well as organ specific glucose metabolism in skeletal muscle and liver. Imaging studies of Retina kidney liver and skeletal muscle were conducted. RNA sequencing was performed on adult liver tissue of glo2+/+ and glo2 / fish by BGI in collaboration with the NGS Core facility in Mannheim University of Heidelberg.   pubmed:36535130   Glo2 / 5 GSM6205027   source name:Tgfli1:EGFP|tissue:whole liver|trained:no|genotype:KO Glo2 / 5 trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Assembly: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. Tgfli1:EGFP   Total RNA was extracted using TRIzol method RNA libraries were prepared for sequencing using standard BGISeq 500 protocols   tissue:whole liver|trained:no|genotype:KO GSM6205027 GSM6205027: Glo2 / 5; Danio rerio; RNA Seq GSM6205027 r1 GSM6205027 1 Total RNA was extracted using TRIzol method RNA libraries were prepared for sequencing using standard BGISeq 500 protocols   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED BGISEQ BGISEQ-500   SRP377632     10.1_1.fq.gz 10.1_2.fq.gz fastq fastq 4165964600.0 41659646.0 GSM6205027 r1 0:100 1:100 A:1087548367;C:975174787;G:1002623835;T:1100617611;N:0 100 100     1087548367 975174787 1002623835 1100617611 0 SRX15499120 SRS13214004 SRA1428824 ZMF, University Heidelberg ZMF, University Heidelberg 1 0.95351   0.05573   0.80229   0.5231   100   B   usable mapping rate bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Germany 2022-05-30 Undetermined Larval Liver Liver and Biliary System
70083 70083 SRR19445941 SRX15499119 SRS13214003 SRP377632 PRJNA843695 Loss of Glo2 alters the glucose metabolism in zebrafish GSE205085 Transcriptome Analysis Glyoxalase 2 is the second enzyme of the glyoxalase system catalyzing the detoxification of methylglyoxal to D lactate via SD Lactoylglutathione. Recent studies have suggested Glo2 as a regulator of glycolysis but the physiological functions of Glo2 in vivo and organ specific functions of the enzyme have not yet been evaluated. Therefore a CRISPR/Cas9 knockout of glo2 in zebrafish was created and analyzed. Consistent with its function in methylglyoxal detoxification SD Lactoylglutathione but not methylglyoxal accumulated in glo2 / larvae with no change in longevity. Adult glo2 / livers developed an impaired insulin signaling indicated by a reduced hepatic P70 S6 kinase activation and reduced hepatic hexose concentration. In contrast glo2 / skeletal muscle remained functionally intact compensating for the dysfunctional liver through increased glucose uptake thereby maintaining euglycemia and preventing damage of the retina and kidney. In conclusion the data identified Glo2 to fulfill similar but unique functions compared to Glo1 and established Glo2 as a novel target in diabetes research regulating hepatic insulin signaling. Overall design: A CRISPR based knockout of Glyoxalase 2 was created in zebrafish. The development of the fish was analyzed as well as organ specific glucose metabolism in skeletal muscle and liver. Imaging studies of Retina kidney liver and skeletal muscle were conducted. RNA sequencing was performed on adult liver tissue of glo2+/+ and glo2 / fish by BGI in collaboration with the NGS Core facility in Mannheim University of Heidelberg.   pubmed:36535130   Glo2 +/+ 5 GSM6205026   source name:Tgfli1:EGFP|tissue:whole liver|trained:no|genotype:WT Glo2 +/+ 5 trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Assembly: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. Tgfli1:EGFP   Total RNA was extracted using TRIzol method RNA libraries were prepared for sequencing using standard BGISeq 500 protocols   tissue:whole liver|trained:no|genotype:WT GSM6205026 GSM6205026: Glo2 +/+ 5; Danio rerio; RNA Seq GSM6205026 r1 GSM6205026 1 Total RNA was extracted using TRIzol method RNA libraries were prepared for sequencing using standard BGISeq 500 protocols   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED BGISEQ BGISEQ-500   SRP377632     9.1_1.fq.gz 9.1_2.fq.gz fastq fastq 4161803400.0 41618034.0 GSM6205026 r1 0:100 1:100 A:1084378904;C:978685192;G:1004569873;T:1094169431;N:0 100 100     1084378904 978685192 1004569873 1094169431 0 SRX15499119 SRS13214003 SRA1428824 ZMF, University Heidelberg ZMF, University Heidelberg 1 0.95218   0.04867   0.80732   0.52859   100   B   usable mapping rate bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Germany 2022-05-30 Undetermined Larval Liver Liver and Biliary System
70084 70084 SRR19445942 SRX15499118 SRS13214002 SRP377632 PRJNA843695 Loss of Glo2 alters the glucose metabolism in zebrafish GSE205085 Transcriptome Analysis Glyoxalase 2 is the second enzyme of the glyoxalase system catalyzing the detoxification of methylglyoxal to D lactate via SD Lactoylglutathione. Recent studies have suggested Glo2 as a regulator of glycolysis but the physiological functions of Glo2 in vivo and organ specific functions of the enzyme have not yet been evaluated. Therefore a CRISPR/Cas9 knockout of glo2 in zebrafish was created and analyzed. Consistent with its function in methylglyoxal detoxification SD Lactoylglutathione but not methylglyoxal accumulated in glo2 / larvae with no change in longevity. Adult glo2 / livers developed an impaired insulin signaling indicated by a reduced hepatic P70 S6 kinase activation and reduced hepatic hexose concentration. In contrast glo2 / skeletal muscle remained functionally intact compensating for the dysfunctional liver through increased glucose uptake thereby maintaining euglycemia and preventing damage of the retina and kidney. In conclusion the data identified Glo2 to fulfill similar but unique functions compared to Glo1 and established Glo2 as a novel target in diabetes research regulating hepatic insulin signaling. Overall design: A CRISPR based knockout of Glyoxalase 2 was created in zebrafish. The development of the fish was analyzed as well as organ specific glucose metabolism in skeletal muscle and liver. Imaging studies of Retina kidney liver and skeletal muscle were conducted. RNA sequencing was performed on adult liver tissue of glo2+/+ and glo2 / fish by BGI in collaboration with the NGS Core facility in Mannheim University of Heidelberg.   pubmed:36535130   Glo2 / 4 GSM6205025   source name:Tgfli1:EGFP|tissue:whole liver|trained:no|genotype:KO Glo2 / 4 trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Assembly: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. Tgfli1:EGFP   Total RNA was extracted using TRIzol method RNA libraries were prepared for sequencing using standard BGISeq 500 protocols   tissue:whole liver|trained:no|genotype:KO GSM6205025 GSM6205025: Glo2 / 4; Danio rerio; RNA Seq GSM6205025 r1 GSM6205025 1 Total RNA was extracted using TRIzol method RNA libraries were prepared for sequencing using standard BGISeq 500 protocols   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED BGISEQ BGISEQ-500   SRP377632     8.1_1.fq.gz 8.1_2.fq.gz fastq fastq 4152089400.0 41520894.0 GSM6205025 r1 0:100 1:100 A:1071439906;C:981252736;G:1021757559;T:1077639199;N:0 100 100     1071439906 981252736 1021757559 1077639199 0 SRX15499118 SRS13214002 SRA1428824 ZMF, University Heidelberg ZMF, University Heidelberg 1 0.94509   0.04233   0.82031   0.5193   100   B   usable mapping rate bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Germany 2022-05-30 Undetermined Larval Liver Liver and Biliary System
70085 70085 SRR19445943 SRX15499117 SRS13214001 SRP377632 PRJNA843695 Loss of Glo2 alters the glucose metabolism in zebrafish GSE205085 Transcriptome Analysis Glyoxalase 2 is the second enzyme of the glyoxalase system catalyzing the detoxification of methylglyoxal to D lactate via SD Lactoylglutathione. Recent studies have suggested Glo2 as a regulator of glycolysis but the physiological functions of Glo2 in vivo and organ specific functions of the enzyme have not yet been evaluated. Therefore a CRISPR/Cas9 knockout of glo2 in zebrafish was created and analyzed. Consistent with its function in methylglyoxal detoxification SD Lactoylglutathione but not methylglyoxal accumulated in glo2 / larvae with no change in longevity. Adult glo2 / livers developed an impaired insulin signaling indicated by a reduced hepatic P70 S6 kinase activation and reduced hepatic hexose concentration. In contrast glo2 / skeletal muscle remained functionally intact compensating for the dysfunctional liver through increased glucose uptake thereby maintaining euglycemia and preventing damage of the retina and kidney. In conclusion the data identified Glo2 to fulfill similar but unique functions compared to Glo1 and established Glo2 as a novel target in diabetes research regulating hepatic insulin signaling. Overall design: A CRISPR based knockout of Glyoxalase 2 was created in zebrafish. The development of the fish was analyzed as well as organ specific glucose metabolism in skeletal muscle and liver. Imaging studies of Retina kidney liver and skeletal muscle were conducted. RNA sequencing was performed on adult liver tissue of glo2+/+ and glo2 / fish by BGI in collaboration with the NGS Core facility in Mannheim University of Heidelberg.   pubmed:36535130   Glo2 +/+ 4 GSM6205024   source name:Tgfli1:EGFP|tissue:whole liver|trained:no|genotype:WT Glo2 +/+ 4 trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Assembly: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. Tgfli1:EGFP   Total RNA was extracted using TRIzol method RNA libraries were prepared for sequencing using standard BGISeq 500 protocols   tissue:whole liver|trained:no|genotype:WT GSM6205024 GSM6205024: Glo2 +/+ 4; Danio rerio; RNA Seq GSM6205024 r1 GSM6205024 1 Total RNA was extracted using TRIzol method RNA libraries were prepared for sequencing using standard BGISeq 500 protocols   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED BGISEQ BGISEQ-500   SRP377632     7.1_1.fq.gz 7.1_2.fq.gz fastq fastq 4164307200.0 41643072.0 GSM6205024 r1 0:100 1:100 A:1089101337;C:971144234;G:1001055993;T:1103005636;N:0 100 100     1089101337 971144234 1001055993 1103005636 0 SRX15499117 SRS13214001 SRA1428824 ZMF, University Heidelberg ZMF, University Heidelberg 1 0.95715   0.05232   0.8062   0.52299   100   B   usable mapping rate bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Germany 2022-05-30 Undetermined Larval Liver Liver and Biliary System
70086 70086 SRR19445944 SRX15499116 SRS13214000 SRP377632 PRJNA843695 Loss of Glo2 alters the glucose metabolism in zebrafish GSE205085 Transcriptome Analysis Glyoxalase 2 is the second enzyme of the glyoxalase system catalyzing the detoxification of methylglyoxal to D lactate via SD Lactoylglutathione. Recent studies have suggested Glo2 as a regulator of glycolysis but the physiological functions of Glo2 in vivo and organ specific functions of the enzyme have not yet been evaluated. Therefore a CRISPR/Cas9 knockout of glo2 in zebrafish was created and analyzed. Consistent with its function in methylglyoxal detoxification SD Lactoylglutathione but not methylglyoxal accumulated in glo2 / larvae with no change in longevity. Adult glo2 / livers developed an impaired insulin signaling indicated by a reduced hepatic P70 S6 kinase activation and reduced hepatic hexose concentration. In contrast glo2 / skeletal muscle remained functionally intact compensating for the dysfunctional liver through increased glucose uptake thereby maintaining euglycemia and preventing damage of the retina and kidney. In conclusion the data identified Glo2 to fulfill similar but unique functions compared to Glo1 and established Glo2 as a novel target in diabetes research regulating hepatic insulin signaling. Overall design: A CRISPR based knockout of Glyoxalase 2 was created in zebrafish. The development of the fish was analyzed as well as organ specific glucose metabolism in skeletal muscle and liver. Imaging studies of Retina kidney liver and skeletal muscle were conducted. RNA sequencing was performed on adult liver tissue of glo2+/+ and glo2 / fish by BGI in collaboration with the NGS Core facility in Mannheim University of Heidelberg.   pubmed:36535130   Glo2 / 3 GSM6205023   source name:Tgfli1:EGFP|tissue:whole liver|trained:no|genotype:KO Glo2 / 3 trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Assembly: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. Tgfli1:EGFP   Total RNA was extracted using TRIzol method RNA libraries were prepared for sequencing using standard BGISeq 500 protocols   tissue:whole liver|trained:no|genotype:KO GSM6205023 GSM6205023: Glo2 / 3; Danio rerio; RNA Seq GSM6205023 r1 GSM6205023 1 Total RNA was extracted using TRIzol method RNA libraries were prepared for sequencing using standard BGISeq 500 protocols   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED BGISEQ BGISEQ-500   SRP377632     6.1_1.fq.gz 6.1_2.fq.gz fastq fastq 4160202200.0 41602022.0 GSM6205023 r1 0:100 1:100 A:1078397784;C:984320163;G:1006828922;T:1090655331;N:0 100 100     1078397784 984320163 1006828922 1090655331 0 SRX15499116 SRS13214000 SRA1428824 ZMF, University Heidelberg ZMF, University Heidelberg 1 0.95752   0.04539   0.8072   0.5241   100   B   usable mapping rate bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Germany 2022-05-30 Undetermined Larval Liver Liver and Biliary System
70087 70087 SRR19445945 SRX15499115 SRS13213999 SRP377632 PRJNA843695 Loss of Glo2 alters the glucose metabolism in zebrafish GSE205085 Transcriptome Analysis Glyoxalase 2 is the second enzyme of the glyoxalase system catalyzing the detoxification of methylglyoxal to D lactate via SD Lactoylglutathione. Recent studies have suggested Glo2 as a regulator of glycolysis but the physiological functions of Glo2 in vivo and organ specific functions of the enzyme have not yet been evaluated. Therefore a CRISPR/Cas9 knockout of glo2 in zebrafish was created and analyzed. Consistent with its function in methylglyoxal detoxification SD Lactoylglutathione but not methylglyoxal accumulated in glo2 / larvae with no change in longevity. Adult glo2 / livers developed an impaired insulin signaling indicated by a reduced hepatic P70 S6 kinase activation and reduced hepatic hexose concentration. In contrast glo2 / skeletal muscle remained functionally intact compensating for the dysfunctional liver through increased glucose uptake thereby maintaining euglycemia and preventing damage of the retina and kidney. In conclusion the data identified Glo2 to fulfill similar but unique functions compared to Glo1 and established Glo2 as a novel target in diabetes research regulating hepatic insulin signaling. Overall design: A CRISPR based knockout of Glyoxalase 2 was created in zebrafish. The development of the fish was analyzed as well as organ specific glucose metabolism in skeletal muscle and liver. Imaging studies of Retina kidney liver and skeletal muscle were conducted. RNA sequencing was performed on adult liver tissue of glo2+/+ and glo2 / fish by BGI in collaboration with the NGS Core facility in Mannheim University of Heidelberg.   pubmed:36535130   Glo2 +/+ 3 GSM6205022   source name:Tgfli1:EGFP|tissue:whole liver|trained:no|genotype:WT Glo2 +/+ 3 trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Assembly: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. Tgfli1:EGFP   Total RNA was extracted using TRIzol method RNA libraries were prepared for sequencing using standard BGISeq 500 protocols   tissue:whole liver|trained:no|genotype:WT GSM6205022 GSM6205022: Glo2 +/+ 3; Danio rerio; RNA Seq GSM6205022 r1 GSM6205022 1 Total RNA was extracted using TRIzol method RNA libraries were prepared for sequencing using standard BGISeq 500 protocols   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED BGISEQ BGISEQ-500   SRP377632     5.1_1.fq.gz 5.1_2.fq.gz fastq fastq 4165235600.0 41652356.0 GSM6205022 r1 0:100 1:100 A:1072104475;C:989511105;G:1023359503;T:1080260517;N:0 100 100     1072104475 989511105 1023359503 1080260517 0 SRX15499115 SRS13213999 SRA1428824 ZMF, University Heidelberg ZMF, University Heidelberg 1 0.95194   0.03798   0.82087   0.54781   100   B   usable mapping rate bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Germany 2022-05-30 Undetermined Larval Liver Liver and Biliary System
70088 70088 SRR19445946 SRX15499114 SRS13213998 SRP377632 PRJNA843695 Loss of Glo2 alters the glucose metabolism in zebrafish GSE205085 Transcriptome Analysis Glyoxalase 2 is the second enzyme of the glyoxalase system catalyzing the detoxification of methylglyoxal to D lactate via SD Lactoylglutathione. Recent studies have suggested Glo2 as a regulator of glycolysis but the physiological functions of Glo2 in vivo and organ specific functions of the enzyme have not yet been evaluated. Therefore a CRISPR/Cas9 knockout of glo2 in zebrafish was created and analyzed. Consistent with its function in methylglyoxal detoxification SD Lactoylglutathione but not methylglyoxal accumulated in glo2 / larvae with no change in longevity. Adult glo2 / livers developed an impaired insulin signaling indicated by a reduced hepatic P70 S6 kinase activation and reduced hepatic hexose concentration. In contrast glo2 / skeletal muscle remained functionally intact compensating for the dysfunctional liver through increased glucose uptake thereby maintaining euglycemia and preventing damage of the retina and kidney. In conclusion the data identified Glo2 to fulfill similar but unique functions compared to Glo1 and established Glo2 as a novel target in diabetes research regulating hepatic insulin signaling. Overall design: A CRISPR based knockout of Glyoxalase 2 was created in zebrafish. The development of the fish was analyzed as well as organ specific glucose metabolism in skeletal muscle and liver. Imaging studies of Retina kidney liver and skeletal muscle were conducted. RNA sequencing was performed on adult liver tissue of glo2+/+ and glo2 / fish by BGI in collaboration with the NGS Core facility in Mannheim University of Heidelberg.   pubmed:36535130   Glo2 / 2 GSM6205021   source name:Tgfli1:EGFP|tissue:whole liver|trained:no|genotype:KO Glo2 / 2 trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Assembly: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. Tgfli1:EGFP   Total RNA was extracted using TRIzol method RNA libraries were prepared for sequencing using standard BGISeq 500 protocols   tissue:whole liver|trained:no|genotype:KO GSM6205021 GSM6205021: Glo2 / 2; Danio rerio; RNA Seq GSM6205021 r1 GSM6205021 1 Total RNA was extracted using TRIzol method RNA libraries were prepared for sequencing using standard BGISeq 500 protocols   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED BGISEQ BGISEQ-500   SRP377632     4.1_1.fq.gz 4.1_2.fq.gz fastq fastq 4171018400.0 41710184.0 GSM6205021 r1 0:100 1:100 A:1073769040;C:990042636;G:1019695979;T:1087510745;N:0 100 100     1073769040 990042636 1019695979 1087510745 0 SRX15499114 SRS13213998 SRA1428824 ZMF, University Heidelberg ZMF, University Heidelberg 1 0.95183   0.04539   0.81134   0.51505   100   B   usable mapping rate bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Germany 2022-05-30 Undetermined Larval Liver Liver and Biliary System
70089 70089 SRR19445947 SRX15499113 SRS13213997 SRP377632 PRJNA843695 Loss of Glo2 alters the glucose metabolism in zebrafish GSE205085 Transcriptome Analysis Glyoxalase 2 is the second enzyme of the glyoxalase system catalyzing the detoxification of methylglyoxal to D lactate via SD Lactoylglutathione. Recent studies have suggested Glo2 as a regulator of glycolysis but the physiological functions of Glo2 in vivo and organ specific functions of the enzyme have not yet been evaluated. Therefore a CRISPR/Cas9 knockout of glo2 in zebrafish was created and analyzed. Consistent with its function in methylglyoxal detoxification SD Lactoylglutathione but not methylglyoxal accumulated in glo2 / larvae with no change in longevity. Adult glo2 / livers developed an impaired insulin signaling indicated by a reduced hepatic P70 S6 kinase activation and reduced hepatic hexose concentration. In contrast glo2 / skeletal muscle remained functionally intact compensating for the dysfunctional liver through increased glucose uptake thereby maintaining euglycemia and preventing damage of the retina and kidney. In conclusion the data identified Glo2 to fulfill similar but unique functions compared to Glo1 and established Glo2 as a novel target in diabetes research regulating hepatic insulin signaling. Overall design: A CRISPR based knockout of Glyoxalase 2 was created in zebrafish. The development of the fish was analyzed as well as organ specific glucose metabolism in skeletal muscle and liver. Imaging studies of Retina kidney liver and skeletal muscle were conducted. RNA sequencing was performed on adult liver tissue of glo2+/+ and glo2 / fish by BGI in collaboration with the NGS Core facility in Mannheim University of Heidelberg.   pubmed:36535130   Glo2 +/+ 2 GSM6205020   source name:Tgfli1:EGFP|tissue:whole liver|trained:no|genotype:WT Glo2 +/+ 2 trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Assembly: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. Tgfli1:EGFP   Total RNA was extracted using TRIzol method RNA libraries were prepared for sequencing using standard BGISeq 500 protocols   tissue:whole liver|trained:no|genotype:WT GSM6205020 GSM6205020: Glo2 +/+ 2; Danio rerio; RNA Seq GSM6205020 r1 GSM6205020 1 Total RNA was extracted using TRIzol method RNA libraries were prepared for sequencing using standard BGISeq 500 protocols   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED BGISEQ BGISEQ-500   SRP377632     3.1_1.fq.gz 3.1_2.fq.gz fastq fastq 4145841000.0 41458410.0 GSM6205020 r1 0:100 1:100 A:1051425067;C:998554505;G:1029593084;T:1066268344;N:0 100 100     1051425067 998554505 1029593084 1066268344 0 SRX15499113 SRS13213997 SRA1428824 ZMF, University Heidelberg ZMF, University Heidelberg 1 0.96363   0.03563   0.81994   0.49336   100   B   usable mapping rate bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Germany 2022-05-30 Undetermined Larval Liver Liver and Biliary System
70090 70090 SRR19445948 SRX15499112 SRS13213996 SRP377632 PRJNA843695 Loss of Glo2 alters the glucose metabolism in zebrafish GSE205085 Transcriptome Analysis Glyoxalase 2 is the second enzyme of the glyoxalase system catalyzing the detoxification of methylglyoxal to D lactate via SD Lactoylglutathione. Recent studies have suggested Glo2 as a regulator of glycolysis but the physiological functions of Glo2 in vivo and organ specific functions of the enzyme have not yet been evaluated. Therefore a CRISPR/Cas9 knockout of glo2 in zebrafish was created and analyzed. Consistent with its function in methylglyoxal detoxification SD Lactoylglutathione but not methylglyoxal accumulated in glo2 / larvae with no change in longevity. Adult glo2 / livers developed an impaired insulin signaling indicated by a reduced hepatic P70 S6 kinase activation and reduced hepatic hexose concentration. In contrast glo2 / skeletal muscle remained functionally intact compensating for the dysfunctional liver through increased glucose uptake thereby maintaining euglycemia and preventing damage of the retina and kidney. In conclusion the data identified Glo2 to fulfill similar but unique functions compared to Glo1 and established Glo2 as a novel target in diabetes research regulating hepatic insulin signaling. Overall design: A CRISPR based knockout of Glyoxalase 2 was created in zebrafish. The development of the fish was analyzed as well as organ specific glucose metabolism in skeletal muscle and liver. Imaging studies of Retina kidney liver and skeletal muscle were conducted. RNA sequencing was performed on adult liver tissue of glo2+/+ and glo2 / fish by BGI in collaboration with the NGS Core facility in Mannheim University of Heidelberg.   pubmed:36535130   Glo2 / 1 GSM6205019   source name:Tgfli1:EGFP|tissue:whole liver|trained:no|genotype:KO Glo2 / 1 trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Assembly: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. Tgfli1:EGFP   Total RNA was extracted using TRIzol method RNA libraries were prepared for sequencing using standard BGISeq 500 protocols   tissue:whole liver|trained:no|genotype:KO GSM6205019 GSM6205019: Glo2 / 1; Danio rerio; RNA Seq GSM6205019 r1 GSM6205019 1 Total RNA was extracted using TRIzol method RNA libraries were prepared for sequencing using standard BGISeq 500 protocols   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED BGISEQ BGISEQ-500   SRP377632     2.1_1.fq.gz 2.1_2.fq.gz fastq fastq 4147644400.0 41476444.0 GSM6205019 r1 0:100 1:100 A:1103014496;C:947498522;G:988532296;T:1108599086;N:0 100 100     1103014496 947498522 988532296 1108599086 0 SRX15499112 SRS13213996 SRA1428824 ZMF, University Heidelberg ZMF, University Heidelberg 1 0.94203   0.05616   0.81268   0.5326   100   B   usable mapping rate bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Germany 2022-05-30 Undetermined Larval Liver Liver and Biliary System
70091 70091 SRR19445949 SRX15499111 SRS13213995 SRP377632 PRJNA843695 Loss of Glo2 alters the glucose metabolism in zebrafish GSE205085 Transcriptome Analysis Glyoxalase 2 is the second enzyme of the glyoxalase system catalyzing the detoxification of methylglyoxal to D lactate via SD Lactoylglutathione. Recent studies have suggested Glo2 as a regulator of glycolysis but the physiological functions of Glo2 in vivo and organ specific functions of the enzyme have not yet been evaluated. Therefore a CRISPR/Cas9 knockout of glo2 in zebrafish was created and analyzed. Consistent with its function in methylglyoxal detoxification SD Lactoylglutathione but not methylglyoxal accumulated in glo2 / larvae with no change in longevity. Adult glo2 / livers developed an impaired insulin signaling indicated by a reduced hepatic P70 S6 kinase activation and reduced hepatic hexose concentration. In contrast glo2 / skeletal muscle remained functionally intact compensating for the dysfunctional liver through increased glucose uptake thereby maintaining euglycemia and preventing damage of the retina and kidney. In conclusion the data identified Glo2 to fulfill similar but unique functions compared to Glo1 and established Glo2 as a novel target in diabetes research regulating hepatic insulin signaling. Overall design: A CRISPR based knockout of Glyoxalase 2 was created in zebrafish. The development of the fish was analyzed as well as organ specific glucose metabolism in skeletal muscle and liver. Imaging studies of Retina kidney liver and skeletal muscle were conducted. RNA sequencing was performed on adult liver tissue of glo2+/+ and glo2 / fish by BGI in collaboration with the NGS Core facility in Mannheim University of Heidelberg.   pubmed:36535130   Glo2 +/+ 1 GSM6205018   source name:Tgfli1:EGFP|tissue:whole liver|trained:no|genotype:WT Glo2 +/+ 1 trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Assembly: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. Tgfli1:EGFP   Total RNA was extracted using TRIzol method RNA libraries were prepared for sequencing using standard BGISeq 500 protocols   tissue:whole liver|trained:no|genotype:WT GSM6205018 GSM6205018: Glo2 +/+ 1; Danio rerio; RNA Seq GSM6205018 r1 GSM6205018 1 Total RNA was extracted using TRIzol method RNA libraries were prepared for sequencing using standard BGISeq 500 protocols   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED BGISEQ BGISEQ-500   SRP377632     1.1_1.fq.gz 1.1_2.fq.gz fastq fastq 4155343800.0 41553438.0 GSM6205018 r1 0:100 1:100 A:1072547817;C:985284919;G:1008557411;T:1088953653;N:0 100 100     1072547817 985284919 1008557411 1088953653 0 SRX15499111 SRS13213995 SRA1428824 ZMF, University Heidelberg ZMF, University Heidelberg 1 0.96135   0.04666   0.80543   0.51213   100   B   usable mapping rate bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Germany 2022-05-30 Undetermined Larval Liver Liver and Biliary System

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