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169 rows where experiment.library_selection = "PolyA", technology = "unknown" and tissue_curation_coarse = "Liver and Biliary System"

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devstage_curation_coarse 3

devstage_curation 3

experiment.platform 2

experiment.library_layout 2

tissue_curation_coarse 1

  • Liver and Biliary System · 169 ✖

tissue_curation 1

technology 1

  • unknown · 169 ✖

experiment.library_strategy 1

experiment.library_source 1

experiment.library_selection 1

  • PolyA · 169 ✖
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
26525 26525 SRR26078869 SRX21793734 SRS18895475 SRP461206 PRJNA1018104 Global liver transcriptome assay of WT Igfbp7 null mutant and Igfbp7 LOE animals PRJNA1018104 Other The global increased expression of Insulin like growth factor binding protein 7 IGFBP7 has been detected in non alcoholic fatty liver disease NAFLD patients however its roles in NAFLD and the mechanism remain largely unclear. The goal of this study is to investigate the effect and mechanism of Igfbp7 using a zebrafish NAFLD model. The igfbp7 / null zebrafish mutant and the Igfbp7 liver overexpressed LOE transgenic zebrafish based on Gal4/UAS system were generated by CRISPR/Cas9 and Tol2 transgenic technique respectively. The zebrafish NAFLD models in wildtypes igfbp7 / mutants and Igfbp7 LOE fishes have been established by high fat diet feeding. The Igfbp7 dynamic expression and its effects on NAFLD progression have been detected and analyzed in both human NAFLD patients and zebrafish models. And the potential mechanism has been investigated through transcriptome analysis and subsequent detection and verification.       liver specific overexpression of Igfbp7 3 LOE replicate 3   strain:transgenic strain|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 mpf|dev stage:adult|collection date:2021 10 09|geo loc name:China:Shanxi|sex:male|tissue:Liver|biomaterial provider:Zebrafish Facility of the Institute of Biomedical Sciences Shanxi University|birth date:09 Jun 2021|birth location:China:Shanxi|breeding history:Fishes were fed 4 times per day with a high fat diet|breeding method:a high fat diet in which 5% cholesterol was added to the standard diet feed type:Marvbeni C1 corresponding to 40 mg/fish/day|replicate:LOE replicate=biological replicate3|BioSampleModel:Model organism or animal                 liver specific overexpression of Igfbp7 3 LOE3 LOE3 liver specific overexpression of Igfbp7 3     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP461206     LOE3_1.fq.gz LOE3_2.fq.gz fastq fastq 7457209500.0 24857365.0 LOE3 1.fq.gz 0:150 1:150 A:1965670426;C:1773372970;G:1762457648;T:1955346803;N:361653 150 150     1965670426 1773372970 1762457648 1955346803 361653 SRX21793734 SRS18895475 SRA1713671 First Hospital of Shanxi Medical University|Department of Gastroenterology and Hepatology First Hospital of Shanxi Medical University 2 0.89541 0.89576 0.04195 0.04177 0.82536 0.82375 0.53368 0.5374 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-09-16 Adult Adult Liver Liver and Biliary System
26526 26526 SRR26078870 SRX21793733 SRS18895474 SRP461206 PRJNA1018104 Global liver transcriptome assay of WT Igfbp7 null mutant and Igfbp7 LOE animals PRJNA1018104 Other The global increased expression of Insulin like growth factor binding protein 7 IGFBP7 has been detected in non alcoholic fatty liver disease NAFLD patients however its roles in NAFLD and the mechanism remain largely unclear. The goal of this study is to investigate the effect and mechanism of Igfbp7 using a zebrafish NAFLD model. The igfbp7 / null zebrafish mutant and the Igfbp7 liver overexpressed LOE transgenic zebrafish based on Gal4/UAS system were generated by CRISPR/Cas9 and Tol2 transgenic technique respectively. The zebrafish NAFLD models in wildtypes igfbp7 / mutants and Igfbp7 LOE fishes have been established by high fat diet feeding. The Igfbp7 dynamic expression and its effects on NAFLD progression have been detected and analyzed in both human NAFLD patients and zebrafish models. And the potential mechanism has been investigated through transcriptome analysis and subsequent detection and verification.       liver specific overexpression of Igfbp7 2 LOE replicate 2   strain:transgenic strain|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 mpf|dev stage:adult|collection date:2021 10 09|geo loc name:China:Shanxi|sex:male|tissue:Liver|biomaterial provider:Zebrafish Facility of the Institute of Biomedical Sciences Shanxi University|birth date:09 Jun 2021|birth location:China:Shanxi|breeding history:Fishes were fed 4 times per day with a high fat diet|breeding method:a high fat diet in which 5% cholesterol was added to the standard diet feed type:Marvbeni C1 corresponding to 40 mg/fish/day|replicate:LOE replicate=biological replicate2|BioSampleModel:Model organism or animal                 liver specific overexpression of Igfbp7 2 LOE2 LOE2 liver specific overexpression of Igfbp7 2     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP461206     LOE2_1.fq.gz LOE2_2.fq.gz fastq fastq 7069059900.0 23563533.0 LOE2 1.fq.gz 0:150 1:150 A:1835774064;C:1704925495;G:1698942360;T:1829075424;N:342557 150 150     1835774064 1704925495 1698942360 1829075424 342557 SRX21793733 SRS18895474 SRA1713671 First Hospital of Shanxi Medical University|Department of Gastroenterology and Hepatology First Hospital of Shanxi Medical University 2 0.89965 0.90019 0.0524 0.05247 0.80669 0.80525 0.53582 0.49543 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-09-16 Adult Adult Liver Liver and Biliary System
26527 26527 SRR26078871 SRX21793732 SRS18895473 SRP461206 PRJNA1018104 Global liver transcriptome assay of WT Igfbp7 null mutant and Igfbp7 LOE animals PRJNA1018104 Other The global increased expression of Insulin like growth factor binding protein 7 IGFBP7 has been detected in non alcoholic fatty liver disease NAFLD patients however its roles in NAFLD and the mechanism remain largely unclear. The goal of this study is to investigate the effect and mechanism of Igfbp7 using a zebrafish NAFLD model. The igfbp7 / null zebrafish mutant and the Igfbp7 liver overexpressed LOE transgenic zebrafish based on Gal4/UAS system were generated by CRISPR/Cas9 and Tol2 transgenic technique respectively. The zebrafish NAFLD models in wildtypes igfbp7 / mutants and Igfbp7 LOE fishes have been established by high fat diet feeding. The Igfbp7 dynamic expression and its effects on NAFLD progression have been detected and analyzed in both human NAFLD patients and zebrafish models. And the potential mechanism has been investigated through transcriptome analysis and subsequent detection and verification.       liver specific overexpression of Igfbp7 1 LOE replicate 1   strain:transgenic strain|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 mpf|dev stage:adult|collection date:2021 10 09|geo loc name:China:Shanxi|sex:male|tissue:Liver|biomaterial provider:Zebrafish Facility of the Institute of Biomedical Sciences Shanxi University|birth date:09 Jun 2021|birth location:China:Shanxi|breeding history:Fishes were fed 4 times per day with a high fat diet|breeding method:a high fat diet in which 5% cholesterol was added to the standard diet feed type:Marvbeni C1 corresponding to 40 mg/fish/day|replicate:LOE replicate=biological replicate1|BioSampleModel:Model organism or animal                 liver specific overexpression of Igfbp7 1 LOE1 LOE1 liver specific overexpression of Igfbp7 1     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP461206     LOE1_1.fq.gz LOE1_2.fq.gz fastq fastq 7110174300.0 23700581.0 LOE1 1.fq.gz 0:150 1:150 A:1847016218;C:1713941614;G:1708466537;T:1840442742;N:307189 150 150     1847016218 1713941614 1708466537 1840442742 307189 SRX21793732 SRS18895473 SRA1713671 First Hospital of Shanxi Medical University|Department of Gastroenterology and Hepatology First Hospital of Shanxi Medical University 2 0.8999 0.89917 0.04883 0.04874 0.80858 0.80716 0.51686 0.52442 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-09-16 Adult Adult Liver Liver and Biliary System
26528 26528 SRR26078872 SRX21793731 SRS18895469 SRP461206 PRJNA1018104 Global liver transcriptome assay of WT Igfbp7 null mutant and Igfbp7 LOE animals PRJNA1018104 Other The global increased expression of Insulin like growth factor binding protein 7 IGFBP7 has been detected in non alcoholic fatty liver disease NAFLD patients however its roles in NAFLD and the mechanism remain largely unclear. The goal of this study is to investigate the effect and mechanism of Igfbp7 using a zebrafish NAFLD model. The igfbp7 / null zebrafish mutant and the Igfbp7 liver overexpressed LOE transgenic zebrafish based on Gal4/UAS system were generated by CRISPR/Cas9 and Tol2 transgenic technique respectively. The zebrafish NAFLD models in wildtypes igfbp7 / mutants and Igfbp7 LOE fishes have been established by high fat diet feeding. The Igfbp7 dynamic expression and its effects on NAFLD progression have been detected and analyzed in both human NAFLD patients and zebrafish models. And the potential mechanism has been investigated through transcriptome analysis and subsequent detection and verification.       Igfbp7 Konckout 3 KO replicate 3   strain:mutant|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 mpf|dev stage:adult|collection date:2021 10 09|geo loc name:China:Shanxi|sex:male|tissue:Liver|biomaterial provider:Zebrafish Facility of the Institute of Biomedical Sciences Shanxi University|birth date:09 Jun 2021|birth location:China:Shanxi|breeding history:Fishes were fed 4 times per day with a high fat diet|breeding method:a high fat diet in which 5% cholesterol was added to the standard diet feed type:Marvbeni C1 corresponding to 40 mg/fish/day|replicate:KO replicate=biological replicate3|BioSampleModel:Model organism or animal                 Igfbp7 Konckout 3 KO3 KO3 Igfbp7 Konckout 3     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP461206     KO3_1.fq.gz KO3_2.fq.gz fastq fastq 6966225300.0 23220751.0 KO3 1.fq.gz 0:150 1:150 A:1854162705;C:1635332068;G:1634647432;T:1841746656;N:336439 150 150     1854162705 1635332068 1634647432 1841746656 336439 SRX21793731 SRS18895469 SRA1713671 First Hospital of Shanxi Medical University|Department of Gastroenterology and Hepatology First Hospital of Shanxi Medical University 2 0.94279 0.94294 0.0551 0.05481 0.78861 0.78739 0.54327 0.50468 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-09-16 Adult Adult Liver Liver and Biliary System
26529 26529 SRR26078873 SRX21793730 SRS18895470 SRP461206 PRJNA1018104 Global liver transcriptome assay of WT Igfbp7 null mutant and Igfbp7 LOE animals PRJNA1018104 Other The global increased expression of Insulin like growth factor binding protein 7 IGFBP7 has been detected in non alcoholic fatty liver disease NAFLD patients however its roles in NAFLD and the mechanism remain largely unclear. The goal of this study is to investigate the effect and mechanism of Igfbp7 using a zebrafish NAFLD model. The igfbp7 / null zebrafish mutant and the Igfbp7 liver overexpressed LOE transgenic zebrafish based on Gal4/UAS system were generated by CRISPR/Cas9 and Tol2 transgenic technique respectively. The zebrafish NAFLD models in wildtypes igfbp7 / mutants and Igfbp7 LOE fishes have been established by high fat diet feeding. The Igfbp7 dynamic expression and its effects on NAFLD progression have been detected and analyzed in both human NAFLD patients and zebrafish models. And the potential mechanism has been investigated through transcriptome analysis and subsequent detection and verification.       Igfbp7 Konckout 2 KO replicate 2   strain:mutant|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 mpf|dev stage:adult|collection date:2021 10 09|geo loc name:China:Shanxi|sex:male|tissue:Liver|biomaterial provider:Zebrafish Facility of the Institute of Biomedical Sciences Shanxi University|birth date:09 Jun 2021|birth location:China:Shanxi|breeding history:Fishes were fed 4 times per day with a high fat diet|breeding method:a high fat diet in which 5% cholesterol was added to the standard diet feed type:Marvbeni C1 corresponding to 40 mg/fish/day|replicate:KO replicate=biological replicate2|BioSampleModel:Model organism or animal                 Igfbp7 Konckout 2 KO2 KO2 Igfbp7 Konckout 2     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP461206     KO2_1.fq.gz KO2_2.fq.gz fastq fastq 7465655100.0 24885517.0 KO2 1.fq.gz 0:150 1:150 A:1988715771;C:1750416778;G:1753335257;T:1972838856;N:348438 150 150     1988715771 1750416778 1753335257 1972838856 348438 SRX21793730 SRS18895470 SRA1713671 First Hospital of Shanxi Medical University|Department of Gastroenterology and Hepatology First Hospital of Shanxi Medical University 2 0.94231 0.94227 0.04975 0.04965 0.802 0.80018 0.50781 0.54557 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-09-16 Adult Adult Liver Liver and Biliary System
26530 26530 SRR26078874 SRX21793729 SRS18895472 SRP461206 PRJNA1018104 Global liver transcriptome assay of WT Igfbp7 null mutant and Igfbp7 LOE animals PRJNA1018104 Other The global increased expression of Insulin like growth factor binding protein 7 IGFBP7 has been detected in non alcoholic fatty liver disease NAFLD patients however its roles in NAFLD and the mechanism remain largely unclear. The goal of this study is to investigate the effect and mechanism of Igfbp7 using a zebrafish NAFLD model. The igfbp7 / null zebrafish mutant and the Igfbp7 liver overexpressed LOE transgenic zebrafish based on Gal4/UAS system were generated by CRISPR/Cas9 and Tol2 transgenic technique respectively. The zebrafish NAFLD models in wildtypes igfbp7 / mutants and Igfbp7 LOE fishes have been established by high fat diet feeding. The Igfbp7 dynamic expression and its effects on NAFLD progression have been detected and analyzed in both human NAFLD patients and zebrafish models. And the potential mechanism has been investigated through transcriptome analysis and subsequent detection and verification.       Igfbp7 Konckout 1 KO replicate 1   strain:mutant|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 mpf|dev stage:adult|collection date:2021 10 09|geo loc name:China:Shanxi|sex:male|tissue:Liver|biomaterial provider:Zebrafish Facility of the Institute of Biomedical Sciences Shanxi University|birth date:09 Jun 2021|birth location:China:Shanxi|breeding history:Fishes were fed 4 times per day with a high fat diet|breeding method:a high fat diet in which 5% cholesterol was added to the standard diet feed type:Marvbeni C1 corresponding to 40 mg/fish/day|replicate:KO replicate=biological replicate1|BioSampleModel:Model organism or animal                 Igfbp7 Konckout 1 KO1 KO1 Igfbp7 Konckout 1     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP461206     KO1_1.fq.gz KO1_2.fq.gz fastq fastq 7208655000.0 24028850.0 KO1 1.fq.gz 0:150 1:150 A:1937720737;C:1672178897;G:1677582029;T:1920894866;N:278471 150 150     1937720737 1672178897 1677582029 1920894866 278471 SRX21793729 SRS18895472 SRA1713671 First Hospital of Shanxi Medical University|Department of Gastroenterology and Hepatology First Hospital of Shanxi Medical University 2 0.93429 0.93361 0.05126 0.05122 0.80827 0.80718 0.48739 0.49469 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-09-16 Adult Adult Liver Liver and Biliary System
26531 26531 SRR26078875 SRX21793728 SRS18895471 SRP461206 PRJNA1018104 Global liver transcriptome assay of WT Igfbp7 null mutant and Igfbp7 LOE animals PRJNA1018104 Other The global increased expression of Insulin like growth factor binding protein 7 IGFBP7 has been detected in non alcoholic fatty liver disease NAFLD patients however its roles in NAFLD and the mechanism remain largely unclear. The goal of this study is to investigate the effect and mechanism of Igfbp7 using a zebrafish NAFLD model. The igfbp7 / null zebrafish mutant and the Igfbp7 liver overexpressed LOE transgenic zebrafish based on Gal4/UAS system were generated by CRISPR/Cas9 and Tol2 transgenic technique respectively. The zebrafish NAFLD models in wildtypes igfbp7 / mutants and Igfbp7 LOE fishes have been established by high fat diet feeding. The Igfbp7 dynamic expression and its effects on NAFLD progression have been detected and analyzed in both human NAFLD patients and zebrafish models. And the potential mechanism has been investigated through transcriptome analysis and subsequent detection and verification.       wild type 3 WT replicate 3   strain:wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 mpf|dev stage:adult|collection date:2021 10 09|geo loc name:China:Shanxi|sex:male|tissue:Liver|biomaterial provider:Zebrafish Facility of the Institute of Biomedical Sciences Shanxi University|birth date:09 Jun 2021|birth location:China:Shanxi|breeding history:Fishes were fed 4 times per day with a high fat diet|breeding method:a high fat diet in which 5% cholesterol was added to the standard diet feed type:Marvbeni C1 corresponding to 40 mg/fish/day|replicate:WT replicate=biological replicate3|BioSampleModel:Model organism or animal                 wild type 3 WT3 WT3 wild type 3     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP461206     WT3_1.fq.gz WT3_2.fq.gz fastq fastq 7267116600.0 24223722.0 WT3 1.fq.gz 0:150 1:150 A:1946606247;C:1693037772;G:1694230444;T:1932894815;N:347322 150 150     1946606247 1693037772 1694230444 1932894815 347322 SRX21793728 SRS18895471 SRA1713671 First Hospital of Shanxi Medical University|Department of Gastroenterology and Hepatology First Hospital of Shanxi Medical University 2 0.94026 0.94007 0.05203 0.05132 0.79622 0.79393 0.52332 0.51051 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-09-16 Adult Adult Liver Liver and Biliary System
26532 26532 SRR26078876 SRX21793727 SRS18895467 SRP461206 PRJNA1018104 Global liver transcriptome assay of WT Igfbp7 null mutant and Igfbp7 LOE animals PRJNA1018104 Other The global increased expression of Insulin like growth factor binding protein 7 IGFBP7 has been detected in non alcoholic fatty liver disease NAFLD patients however its roles in NAFLD and the mechanism remain largely unclear. The goal of this study is to investigate the effect and mechanism of Igfbp7 using a zebrafish NAFLD model. The igfbp7 / null zebrafish mutant and the Igfbp7 liver overexpressed LOE transgenic zebrafish based on Gal4/UAS system were generated by CRISPR/Cas9 and Tol2 transgenic technique respectively. The zebrafish NAFLD models in wildtypes igfbp7 / mutants and Igfbp7 LOE fishes have been established by high fat diet feeding. The Igfbp7 dynamic expression and its effects on NAFLD progression have been detected and analyzed in both human NAFLD patients and zebrafish models. And the potential mechanism has been investigated through transcriptome analysis and subsequent detection and verification.       wild type 2 WT replicate 2   strain:wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 mpf|dev stage:adult|collection date:2021 10 09|geo loc name:China:Shanxi|sex:male|tissue:Liver|biomaterial provider:Zebrafish Facility of the Institute of Biomedical Sciences Shanxi University|birth date:09 Jun 2021|birth location:China:Shanxi|breeding history:Fishes were fed 4 times per day with a high fat diet|breeding method:a high fat diet in which 5% cholesterol was added to the standard diet feed type:Marvbeni C1 corresponding to 40 mg/fish/day|replicate:WT replicate=biological replicate2|BioSampleModel:Model organism or animal                 wild type 2 WT2 WT2 wild type 2     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP461206     WT2_1.fq.gz WT2_2.fq.gz fastq fastq 7206849900.0 24022833.0 WT2 1.fq.gz 0:150 1:150 A:1947268148;C:1660088486;G:1665583448;T:1933561073;N:348745 150 150     1947268148 1660088486 1665583448 1933561073 348745 SRX21793727 SRS18895467 SRA1713671 First Hospital of Shanxi Medical University|Department of Gastroenterology and Hepatology First Hospital of Shanxi Medical University 2 0.93368 0.93327 0.06754 0.06713 0.78681 0.7861 0.53133 0.53795 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-09-16 Adult Adult Liver Liver and Biliary System
26533 26533 SRR26078877 SRX21793726 SRS18895468 SRP461206 PRJNA1018104 Global liver transcriptome assay of WT Igfbp7 null mutant and Igfbp7 LOE animals PRJNA1018104 Other The global increased expression of Insulin like growth factor binding protein 7 IGFBP7 has been detected in non alcoholic fatty liver disease NAFLD patients however its roles in NAFLD and the mechanism remain largely unclear. The goal of this study is to investigate the effect and mechanism of Igfbp7 using a zebrafish NAFLD model. The igfbp7 / null zebrafish mutant and the Igfbp7 liver overexpressed LOE transgenic zebrafish based on Gal4/UAS system were generated by CRISPR/Cas9 and Tol2 transgenic technique respectively. The zebrafish NAFLD models in wildtypes igfbp7 / mutants and Igfbp7 LOE fishes have been established by high fat diet feeding. The Igfbp7 dynamic expression and its effects on NAFLD progression have been detected and analyzed in both human NAFLD patients and zebrafish models. And the potential mechanism has been investigated through transcriptome analysis and subsequent detection and verification.       wild type 1 WT replicate 1   strain:wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 mpf|dev stage:adult|collection date:2021 10 09|geo loc name:China:Shanxi|sex:male|tissue:Liver|biomaterial provider:Zebrafish Facility of the Institute of Biomedical Sciences Shanxi University|birth date:09 Jun 2021|birth location:China:Shanxi|breeding history:Fishes were fed 4 times per day with a high fat diet|breeding method:a high fat diet in which 5% cholesterol was added to the standard diet feed type:Marvbeni C1 corresponding to 40 mg/fish/day|replicate:WT replicate=biological replicate1|BioSampleModel:Model organism or animal                 wild type 1 WT1 WT1 wild type 1     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP461206     WT1_1.fq.gz WT1_2.fq.gz fastq fastq 7170532200.0 23901774.0 WT1 1.fq.gz 0:150 1:150 A:1931584106;C:1658793663;G:1662799956;T:1917012316;N:342159 150 150     1931584106 1658793663 1662799956 1917012316 342159 SRX21793726 SRS18895468 SRA1713671 First Hospital of Shanxi Medical University|Department of Gastroenterology and Hepatology First Hospital of Shanxi Medical University 2 0.93456 0.93372 0.06482 0.06467 0.77327 0.77266 0.52308 0.53023 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-09-16 Adult Adult Liver Liver and Biliary System
29581 29581 SRR27387424 SRX23063703 SRS20023725 SRP480720 PRJNA1059246 Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish PRJNA1059246 Other Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves TWPs contain many harmful chemicals including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.       Control Liver control liver 5   strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:liver|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:control liver replicate5|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish T1 5 T1 5 PCR enrichment of adaptor ligated DNA     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 550   SRP480720     A7_1.fastq.gz A7_2.fastq.gz fastq fastq 7139648700.0 23798829.0 A7 1.fastq.gz 0:150 1:150 A:1898040242;C:1678584917;G:1680422296;T:1882535161;N:66084 150 150     1898040242 1678584917 1680422296 1882535161 66084 SRX23063703 SRS20023725 SRA1777576 Nord University|Faculty of Biosciences and Aquaculture Nord University 2 0.94633 0.94658 0.04866 0.0489 0.77098 0.77041 0.48393 0.49328 150 150 B B biological fallback assumption illumina nextseq unknown poly_a unknown bulk unknown unknown   Norway 2023-12-30 Adult Adult Liver Liver and Biliary System
29592 29592 SRR27387435 SRX23063692 SRS20023714 SRP480720 PRJNA1059246 Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish PRJNA1059246 Other Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves TWPs contain many harmful chemicals including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.       Control Liver control liver 4   strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:liver|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:control liver replicate4|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish T1 4 T1 4 PCR enrichment of adaptor ligated DNA     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 550   SRP480720     A6_1.fastq.gz A6_2.fastq.gz fastq fastq 7080291000.0 23600970.0 A6 1.fastq.gz 0:150 1:150 A:1890410803;C:1656924196;G:1658022500;T:1874867839;N:65662 150 150     1890410803 1656924196 1658022500 1874867839 65662 SRX23063692 SRS20023714 SRA1777576 Nord University|Faculty of Biosciences and Aquaculture Nord University 2 0.94344 0.94345 0.05044 0.05028 0.7683 0.76838 0.48933 0.49113 150 150 B B biological fallback assumption illumina nextseq unknown poly_a unknown bulk unknown unknown   Norway 2023-12-30 Adult Adult Liver Liver and Biliary System
29600 29600 SRR27387443 SRX23063684 SRS20023706 SRP480720 PRJNA1059246 Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish PRJNA1059246 Other Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves TWPs contain many harmful chemicals including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.       Combined Liver combined liver 6   strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:liver|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:combined liver replicate6|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish T4 6 T4 6 PCR enrichment of adaptor ligated DNA     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 550   SRP480720     A21_1.fastq.gz A21_2.fastq.gz fastq fastq 8613810000.0 28712700.0 A21 1.fastq.gz 0:150 1:150 A:2301535821;C:2013247658;G:2021540738;T:2277424933;N:60850 150 150     2301535821 2013247658 2021540738 2277424933 60850 SRX23063684 SRS20023706 SRA1777576 Nord University|Faculty of Biosciences and Aquaculture Nord University 2 0.94372 0.94375 0.04559 0.04554 0.80397 0.80446 0.54615 0.54931 150 150 B B biological fallback assumption illumina nextseq unknown poly_a unknown bulk unknown unknown   Norway 2023-12-30 Adult Adult Liver Liver and Biliary System
29601 29601 SRR27387444 SRX23063683 SRS20023705 SRP480720 PRJNA1059246 Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish PRJNA1059246 Other Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves TWPs contain many harmful chemicals including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.       Combined Liver combined liver 5   strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:liver|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:combined liver replicate5|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish T4 5 T4 5 PCR enrichment of adaptor ligated DNA     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 550   SRP480720     A20_1.fastq.gz A20_2.fastq.gz fastq fastq 7660898400.0 25536328.0 A20 1.fastq.gz 0:150 1:150 A:2045662664;C:1793844486;G:1797425064;T:2023911614;N:54572 150 150     2045662664 1793844486 1797425064 2023911614 54572 SRX23063683 SRS20023705 SRA1777576 Nord University|Faculty of Biosciences and Aquaculture Nord University 2 0.94307 0.94399 0.04996 0.04972 0.79916 0.79967 0.55321 0.55159 150 150 B B biological fallback assumption illumina nextseq unknown poly_a unknown bulk unknown unknown   Norway 2023-12-30 Adult Adult Liver Liver and Biliary System
29602 29602 SRR27387445 SRX23063682 SRS20023704 SRP480720 PRJNA1059246 Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish PRJNA1059246 Other Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves TWPs contain many harmful chemicals including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.       Combined Liver combined liver 4   strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:liver|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:combined liver replicate4|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish T4 4 T4 4 PCR enrichment of adaptor ligated DNA     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 550   SRP480720     A19_1.fastq.gz A19_2.fastq.gz fastq fastq 8492667000.0 28308890.0 A19 1.fastq.gz 0:150 1:150 A:2287240764;C:1972022212;G:1977128547;T:2256183819;N:91658 150 150     2287240764 1972022212 1977128547 2256183819 91658 SRX23063682 SRS20023704 SRA1777576 Nord University|Faculty of Biosciences and Aquaculture Nord University 2 0.94222 0.94087 0.05048 0.05023 0.78847 0.7876 0.54394 0.54327 150 150 B B biological fallback assumption illumina nextseq unknown poly_a unknown bulk unknown unknown   Norway 2023-12-30 Adult Adult Liver Liver and Biliary System
29603 29603 SRR27387446 SRX23063681 SRS20023703 SRP480720 PRJNA1059246 Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish PRJNA1059246 Other Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves TWPs contain many harmful chemicals including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.       Control Liver control liver 3   strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:liver|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:control liver replicate3|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish T1 3 T1 3 PCR enrichment of adaptor ligated DNA     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 550   SRP480720     A5_1.fastq.gz A5_2.fastq.gz fastq fastq 6365746500.0 21219155.0 A5 1.fastq.gz 0:150 1:150 A:1680943294;C:1504416528;G:1516780057;T:1663547544;N:59077 150 150     1680943294 1504416528 1516780057 1663547544 59077 SRX23063681 SRS20023703 SRA1777576 Nord University|Faculty of Biosciences and Aquaculture Nord University 2 0.96138 0.96072 0.01946 0.01949 0.84372 0.84437 0.21657 0.2162 150 150 B B biological fallback assumption illumina nextseq unknown poly_a unknown bulk unknown unknown   Norway 2023-12-30 Adult Adult Liver Liver and Biliary System
29604 29604 SRR27387447 SRX23063680 SRS20023702 SRP480720 PRJNA1059246 Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish PRJNA1059246 Other Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves TWPs contain many harmful chemicals including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.       Combined Liver combined liver 3   strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:liver|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:combined liver replicate3|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish T4 3 T4 3 PCR enrichment of adaptor ligated DNA     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 550   SRP480720     A18_1.fastq.gz A18_2.fastq.gz fastq fastq 6080801100.0 20269337.0 A18 1.fastq.gz 0:150 1:150 A:1625543543;C:1426271281;G:1432771006;T:1596174300;N:40970 150 150     1625543543 1426271281 1432771006 1596174300 40970 SRX23063680 SRS20023702 SRA1777576 Nord University|Faculty of Biosciences and Aquaculture Nord University 2 0.94461 0.94384 0.04104 0.04107 0.81294 0.81369 0.55086 0.55066 150 150 B B biological fallback assumption illumina nextseq unknown poly_a unknown bulk unknown unknown   Norway 2023-12-30 Adult Adult Liver Liver and Biliary System
29605 29605 SRR27387448 SRX23063679 SRS20023701 SRP480720 PRJNA1059246 Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish PRJNA1059246 Other Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves TWPs contain many harmful chemicals including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.       Combined Liver combined liver 2   strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:liver|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:combined liver replicate2|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish T4 2 T4 2 PCR enrichment of adaptor ligated DNA     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 550   SRP480720     A17_1.fastq.gz A17_2.fastq.gz fastq fastq 8357049600.0 27856832.0 A17 1.fastq.gz 0:150 1:150 A:2228408702;C:1962845144;G:1962818306;T:2202917758;N:59690 150 150     2228408702 1962845144 1962818306 2202917758 59690 SRX23063679 SRS20023701 SRA1777576 Nord University|Faculty of Biosciences and Aquaculture Nord University 2 0.94277 0.9436 0.0454 0.04526 0.76039 0.76012 0.53857 0.49252 150 150 B B biological fallback assumption illumina nextseq unknown poly_a unknown bulk unknown unknown   Norway 2023-12-30 Adult Adult Liver Liver and Biliary System
29606 29606 SRR27387449 SRX23063678 SRS20023700 SRP480720 PRJNA1059246 Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish PRJNA1059246 Other Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves TWPs contain many harmful chemicals including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.       Combined Liver combined liver 1   strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:liver|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:combined liver replicate1|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish T4 1 T4 1 PCR enrichment of adaptor ligated DNA     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 550   SRP480720     A16_1.fastq.gz A16_2.fastq.gz fastq fastq 8697886500.0 28992955.0 A16 1.fastq.gz 0:150 1:150 A:2308292580;C:2052173268;G:2056418654;T:2280941830;N:60168 150 150     2308292580 2052173268 2056418654 2280941830 60168 SRX23063678 SRS20023700 SRA1777576 Nord University|Faculty of Biosciences and Aquaculture Nord University 2 0.94941 0.95075 0.03814 0.03814 0.80359 0.80511 0.45866 0.46697 150 150 B B biological fallback assumption illumina nextseq unknown poly_a unknown bulk unknown unknown   Norway 2023-12-30 Adult Adult Liver Liver and Biliary System
29607 29607 SRR27387450 SRX23063677 SRS20023699 SRP480720 PRJNA1059246 Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish PRJNA1059246 Other Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves TWPs contain many harmful chemicals including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.       Nanoplastics Liver nps liver 6   strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:liver|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:nps liver replicate6|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish T3 6 T3 6 PCR enrichment of adaptor ligated DNA     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 550   SRP480720     A14_1.fastq.gz A14_2.fastq.gz fastq fastq 6328078200.0 21093594.0 A14 1.fastq.gz 0:150 1:150 A:1651110799;C:1522543378;G:1523353407;T:1631026281;N:44335 150 150     1651110799 1522543378 1523353407 1631026281 44335 SRX23063677 SRS20023699 SRA1777576 Nord University|Faculty of Biosciences and Aquaculture Nord University 2 0.95918 0.95893 0.03288 0.03279 0.7989 0.79892 0.46602 0.44771 150 150 B B biological fallback assumption illumina nextseq unknown poly_a unknown bulk unknown unknown   Norway 2023-12-30 Adult Adult Liver Liver and Biliary System
29608 29608 SRR27387451 SRX23063676 SRS20023698 SRP480720 PRJNA1059246 Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish PRJNA1059246 Other Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves TWPs contain many harmful chemicals including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.       Nanoplastics Liver nps liver 5   strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:liver|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:nps liver replicate5|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish T3 5 T3 5 PCR enrichment of adaptor ligated DNA     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 550   SRP480720     A13_1.fastq.gz A13_2.fastq.gz fastq fastq 6682736400.0 22275788.0 A13 1.fastq.gz 0:150 1:150 A:1770006493;C:1580541555;G:1583340681;T:1748799643;N:48028 150 150     1770006493 1580541555 1583340681 1748799643 48028 SRX23063676 SRS20023698 SRA1777576 Nord University|Faculty of Biosciences and Aquaculture Nord University 2 0.94674 0.94767 0.04088 0.04069 0.79362 0.79326 0.51807 0.55709 150 150 B B biological fallback assumption illumina nextseq unknown poly_a unknown bulk unknown unknown   Norway 2023-12-30 Adult Adult Liver Liver and Biliary System
29609 29609 SRR27387452 SRX23063675 SRS20023697 SRP480720 PRJNA1059246 Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish PRJNA1059246 Other Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves TWPs contain many harmful chemicals including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.       Nanoplastics Liver nps liver 4   strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:liver|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:nps liver replicate4|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish T3 4 T3 4 PCR enrichment of adaptor ligated DNA     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 550   SRP480720     A12_1.fastq.gz A12_2.fastq.gz fastq fastq 7223844300.0 24079481.0 A12 1.fastq.gz 0:150 1:150 A:1898044988;C:1723221670;G:1728581768;T:1873946251;N:49623 150 150     1898044988 1723221670 1728581768 1873946251 49623 SRX23063675 SRS20023697 SRA1777576 Nord University|Faculty of Biosciences and Aquaculture Nord University 2 0.95897 0.9583 0.03099 0.03094 0.81359 0.81414 0.36697 0.38046 150 150 B B biological fallback assumption illumina nextseq unknown poly_a unknown bulk unknown unknown   Norway 2023-12-30 Adult Adult Liver Liver and Biliary System
29610 29610 SRR27387453 SRX23063674 SRS20023696 SRP480720 PRJNA1059246 Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish PRJNA1059246 Other Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves TWPs contain many harmful chemicals including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.       Nanoplastics Liver nps liver 3   strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:liver|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:nps liver replicate3|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish T3 3 T3 3 PCR enrichment of adaptor ligated DNA     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 550   SRP480720     A11_1.fastq.gz A11_2.fastq.gz fastq fastq 7712327100.0 25707757.0 A11 1.fastq.gz 0:150 1:150 A:2078269634;C:1786227652;G:1790988947;T:2056786923;N:53944 150 150     2078269634 1786227652 1790988947 2056786923 53944 SRX23063674 SRS20023696 SRA1777576 Nord University|Faculty of Biosciences and Aquaculture Nord University 2 0.93754 0.93849 0.05229 0.05261 0.79762 0.79841 0.52961 0.55954 150 150 B B biological fallback assumption illumina nextseq unknown poly_a unknown bulk unknown unknown   Norway 2023-12-30 Adult Adult Liver Liver and Biliary System
29611 29611 SRR27387454 SRX23063673 SRS20023695 SRP480720 PRJNA1059246 Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish PRJNA1059246 Other Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves TWPs contain many harmful chemicals including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.       Nanoplastics Liver nps liver 2   strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:liver|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:nps liver replicate2|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish T3 2 T3 2 PCR enrichment of adaptor ligated DNA     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 550   SRP480720     A10_1.fastq.gz A10_2.fastq.gz fastq fastq 9006367500.0 30021225.0 A10 1.fastq.gz 0:150 1:150 A:2405095208;C:2108519804;G:2119356079;T:2373332498;N:63911 150 150     2405095208 2108519804 2119356079 2373332498 63911 SRX23063673 SRS20023695 SRA1777576 Nord University|Faculty of Biosciences and Aquaculture Nord University 2 0.93857 0.93907 0.04235 0.04254 0.74401 0.74442 0.53865 0.54012 150 150 B B biological fallback assumption illumina nextseq unknown poly_a unknown bulk unknown unknown   Norway 2023-12-30 Adult Adult Liver Liver and Biliary System
29612 29612 SRR27387455 SRX23063672 SRS20023694 SRP480720 PRJNA1059246 Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish PRJNA1059246 Other Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves TWPs contain many harmful chemicals including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.       Nanoplastics Liver nps liver 1   strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:liver|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:nps liver replicate1|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish T3 1 T3 1 PCR enrichment of adaptor ligated DNA     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 550   SRP480720     A8_1.fastq.gz A8_2.fastq.gz fastq fastq 9705357300.0 32351191.0 A8 1.fastq.gz 0:150 1:150 A:2549361250;C:2315598558;G:2319533236;T:2520797865;N:66391 150 150     2549361250 2315598558 2319533236 2520797865 66391 SRX23063672 SRS20023694 SRA1777576 Nord University|Faculty of Biosciences and Aquaculture Nord University 2 0.95257 0.95219 0.03953 0.03882 0.80085 0.80052 0.5024 0.50544 150 150 B B biological fallback assumption illumina nextseq unknown poly_a unknown bulk unknown unknown   Norway 2023-12-30 Adult Adult Liver Liver and Biliary System
29613 29613 SRR27387456 SRX23063671 SRS20023693 SRP480720 PRJNA1059246 Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish PRJNA1059246 Other Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves TWPs contain many harmful chemicals including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.       6PPDQ Liver 6ppdq liver 6   strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:liver|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:6ppdq liver replicate6|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish T2 6 T2 6 PCR enrichment of adaptor ligated DNA     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 550   SRP480720     A28_1.fastq.gz A28_2.fastq.gz fastq fastq 7312027200.0 24373424.0 A28 1.fastq.gz 0:150 1:150 A:1933027768;C:1734543239;G:1734058319;T:1910343929;N:53945 150 150     1933027768 1734543239 1734058319 1910343929 53945 SRX23063671 SRS20023693 SRA1777576 Nord University|Faculty of Biosciences and Aquaculture Nord University 2 0.94984 0.95024 0.04435 0.04424 0.77804 0.77869 0.5448 0.51681 150 150 B B biological fallback assumption illumina nextseq unknown poly_a unknown bulk unknown unknown   Norway 2023-12-30 Adult Adult Liver Liver and Biliary System
29614 29614 SRR27387457 SRX23063670 SRS20023692 SRP480720 PRJNA1059246 Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish PRJNA1059246 Other Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves TWPs contain many harmful chemicals including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.       Control Liver control liver 2   strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:liver|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:control liver replicate2|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish T1 2 T1 2 PCR enrichment of adaptor ligated DNA     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 550   SRP480720     A3_1.fastq.gz A3_2.fastq.gz fastq fastq 10383955200.0 34613184.0 A3 1.fastq.gz 0:150 1:150 A:2778093066;C:2424701453;G:2429080701;T:2751982231;N:97749 150 150     2778093066 2424701453 2429080701 2751982231 97749 SRX23063670 SRS20023692 SRA1777576 Nord University|Faculty of Biosciences and Aquaculture Nord University 2 0.94514 0.94539 0.05128 0.05171 0.80697 0.80669 0.55446 0.54855 150 150 B B biological fallback assumption illumina nextseq unknown poly_a unknown bulk unknown unknown   Norway 2023-12-30 Adult Adult Liver Liver and Biliary System
29615 29615 SRR27387458 SRX23063669 SRS20023691 SRP480720 PRJNA1059246 Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish PRJNA1059246 Other Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves TWPs contain many harmful chemicals including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.       Control Liver control liver 1   strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:liver|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:control liver replicate1|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish T1 1 T1 1 PCR enrichment of adaptor ligated DNA     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 550   SRP480720     A1_1.fastq.gz A1_2.fastq.gz fastq fastq 6990799500.0 23302665.0 A1 1.fastq.gz 0:150 1:150 A:1852168539;C:1650230337;G:1654609197;T:1833725714;N:65713 150 150     1852168539 1650230337 1654609197 1833725714 65713 SRX23063669 SRS20023691 SRA1777576 Nord University|Faculty of Biosciences and Aquaculture Nord University 2 0.95142 0.95049 0.03481 0.03455 0.80955 0.81089 0.42523 0.42786 150 150 B B biological fallback assumption illumina nextseq unknown poly_a unknown bulk unknown unknown   Norway 2023-12-30 Adult Adult Liver Liver and Biliary System
29616 29616 SRR27387459 SRX23063668 SRS20023690 SRP480720 PRJNA1059246 Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish PRJNA1059246 Other Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves TWPs contain many harmful chemicals including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.       6PPDQ Liver 6ppdq liver 5   strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:liver|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:6ppdq liver replicate5|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish T2 5 T2 5 PCR enrichment of adaptor ligated DNA     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 550   SRP480720     A27_1.fastq.gz A27_2.fastq.gz fastq fastq 8327205000.0 27757350.0 A27 1.fastq.gz 0:150 1:150 A:2188059959;C:1983666022;G:1992428805;T:2162994610;N:55604 150 150     2188059959 1983666022 1992428805 2162994610 55604 SRX23063668 SRS20023690 SRA1777576 Nord University|Faculty of Biosciences and Aquaculture Nord University 2 0.95557 0.95521 0.03496 0.035 0.81377 0.81428 0.44899 0.45358 150 150 B B biological fallback assumption illumina nextseq unknown poly_a unknown bulk unknown unknown   Norway 2023-12-30 Adult Adult Liver Liver and Biliary System
29617 29617 SRR27387460 SRX23063667 SRS20023689 SRP480720 PRJNA1059246 Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish PRJNA1059246 Other Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves TWPs contain many harmful chemicals including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.       6PPDQ Liver 6ppdq liver 4   strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:liver|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:6ppdq liver replicate4|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish T2 4 T2 4 PCR enrichment of adaptor ligated DNA     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 550   SRP480720     A26_1.fastq.gz A26_2.fastq.gz fastq fastq 6407337900.0 21357793.0 A26 1.fastq.gz 0:150 1:150 A:1685351213;C:1524796223;G:1531286302;T:1665857949;N:46213 150 150     1685351213 1524796223 1531286302 1665857949 46213 SRX23063667 SRS20023689 SRA1777576 Nord University|Faculty of Biosciences and Aquaculture Nord University 2 0.96413 0.96363 0.02797 0.02805 0.8505 0.85194 0.38255 0.38447 150 150 B B biological fallback assumption illumina nextseq unknown poly_a unknown bulk unknown unknown   Norway 2023-12-30 Adult Adult Liver Liver and Biliary System
29618 29618 SRR27387461 SRX23063666 SRS20023688 SRP480720 PRJNA1059246 Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish PRJNA1059246 Other Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves TWPs contain many harmful chemicals including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.       6PPDQ Liver 6ppdq liver 3   strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:liver|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:6ppdq liver replicate3|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish T2 3 T2 3 PCR enrichment of adaptor ligated DNA     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 550   SRP480720     A25_1.fastq.gz A25_2.fastq.gz fastq fastq 8578160400.0 28593868.0 A25 1.fastq.gz 0:150 1:150 A:2253186424;C:2047305045;G:2050974170;T:2226633669;N:61092 150 150     2253186424 2047305045 2050974170 2226633669 61092 SRX23063666 SRS20023688 SRA1777576 Nord University|Faculty of Biosciences and Aquaculture Nord University 2 0.95088 0.95107 0.04217 0.04231 0.77875 0.77922 0.5388 0.53743 150 150 B B biological fallback assumption illumina nextseq unknown poly_a unknown bulk unknown unknown   Norway 2023-12-30 Adult Adult Liver Liver and Biliary System
29619 29619 SRR27387462 SRX23063665 SRS20023687 SRP480720 PRJNA1059246 Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish PRJNA1059246 Other Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves TWPs contain many harmful chemicals including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.       6PPDQ Liver 6ppdq liver 2   strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:liver|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:6ppdq liver replicate2|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish T2 2 T2 2 PCR enrichment of adaptor ligated DNA     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 550   SRP480720     A23_1.fastq.gz A23_2.fastq.gz fastq fastq 7606031100.0 25353437.0 A23 1.fastq.gz 0:150 1:150 A:2040128163;C:1774614072;G:1775629532;T:2015605795;N:53538 150 150     2040128163 1774614072 1775629532 2015605795 53538 SRX23063665 SRS20023687 SRA1777576 Nord University|Faculty of Biosciences and Aquaculture Nord University 2 0.945 0.94581 0.04313 0.04324 0.81617 0.8172 0.55094 0.55944 150 150 B B biological fallback assumption illumina nextseq unknown poly_a unknown bulk unknown unknown   Norway 2023-12-30 Adult Adult Liver Liver and Biliary System
29620 29620 SRR27387463 SRX23063664 SRS20023686 SRP480720 PRJNA1059246 Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish PRJNA1059246 Other Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves TWPs contain many harmful chemicals including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.       6PPDQ Liver 6ppdq liver 1   strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:liver|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:6ppdq liver replicate1|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish T2 1 T2 1 PCR enrichment of adaptor ligated DNA     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 550   SRP480720     A22_1.fastq.gz A22_2.fastq.gz fastq fastq 6116767200.0 20389224.0 A22 1.fastq.gz 0:150 1:150 A:1642510559;C:1422754642;G:1431247073;T:1620185548;N:69378 150 150     1642510559 1422754642 1431247073 1620185548 69378 SRX23063664 SRS20023686 SRA1777576 Nord University|Faculty of Biosciences and Aquaculture Nord University 2 0.94746 0.9454 0.0432 0.04289 0.80748 0.80752 0.56194 0.55666 150 150 B B biological fallback assumption illumina nextseq unknown poly_a unknown bulk unknown unknown   Norway 2023-12-30 Adult Adult Liver Liver and Biliary System
31932 31932 SRR28776262 SRX24341224 SRS21101374 SRP503449 PRJNA1103351 Characterization of liver pancreas crosstalk following beta cell loss reveals a role for the molybdenum cofactor in beta cell regeneration PRJNA1103351 Other Understanding beta cell regeneration and how inter organ communication can contribute to that is crucial for developing new approaches for diabetes treatment. With this dataste we characterized the hepatocyte beta cell axis and how it can contribute to beta cell regeneration in a zebrafish model of beta cell loss. This data provide a transcriptomics analysis of isolated hepatocytes following beta cell ablation.       Ablated 3 Ablated rep3   strain:AB|age:2 mpf date:2015 06 11|geo loc name:Sweden|sex:mixed|tissue:Liver|cell type:Hepatocytes|collected by:Christos Karampelias|genotype:Tgins:flag NTR|treatment:Metronidazole|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish hepatocytes P2276 105 P2276 105 RNA was extracted from the sorted cells using the RNAqueous micro total isolation kit. The quality of the RNA was assessed and the first control sample was discarded as the RIN value was too low. Libraries were prepared using the TRUSeq stranded mRNA kit Illumina and sequenced on an Illumina HiSeq2500 instrument.     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2500   SRP503449     5_150903_BC7FRTANXX_P2276_105_1.fastq.gz 5_150903_BC7FRTANXX_P2276_105_2.fastq.gz fastq fastq 12443422824.0 49378662.0 5 150903 BC7FRTANXX P2276 105 1.fastq.gz 0:126 1:126 A:3354062616;C:2842732118;G:2899611331;T:3337717349;N:9299410 126 126     3354062616 2842732118 2899611331 3337717349 9299410 SRX24341224 SRS21101374 SRA1851016 Karolinska Institutet|Cell and Molecular Biology Karolinska Institutet                       B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Sweden 2024-04-23 Juvenile Juvenile Liver Liver and Biliary System
31933 31933 SRR28776263 SRX24341223 SRS21101373 SRP503449 PRJNA1103351 Characterization of liver pancreas crosstalk following beta cell loss reveals a role for the molybdenum cofactor in beta cell regeneration PRJNA1103351 Other Understanding beta cell regeneration and how inter organ communication can contribute to that is crucial for developing new approaches for diabetes treatment. With this dataste we characterized the hepatocyte beta cell axis and how it can contribute to beta cell regeneration in a zebrafish model of beta cell loss. This data provide a transcriptomics analysis of isolated hepatocytes following beta cell ablation.       Ablated 2 Ablated rep2   strain:AB|age:2 mpf date:2015 06 09|geo loc name:Sweden|sex:mixed|tissue:Liver|cell type:Hepatocytes|collected by:Christos Karampelias|genotype:Tgins:flag NTR|treatment:Metronidazole|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish hepatocytes P2276 103 P2276 103 RNA was extracted from the sorted cells using the RNAqueous micro total isolation kit. The quality of the RNA was assessed and the first control sample was discarded as the RIN value was too low. Libraries were prepared using the TRUSeq stranded mRNA kit Illumina and sequenced on an Illumina HiSeq2500 instrument.     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2500   SRP503449     5_150903_BC7FRTANXX_P2276_103_1.fastq.gz 5_150903_BC7FRTANXX_P2276_103_2.fastq.gz fastq fastq 12508569612.0 49637181.0 5 150903 BC7FRTANXX P2276 103 1.fastq.gz 0:126 1:126 A:3285561592;C:2941406523;G:2987518362;T:3285515692;N:8567443 126 126     3285561592 2941406523 2987518362 3285515692 8567443 SRX24341223 SRS21101373 SRA1851016 Karolinska Institutet|Cell and Molecular Biology Karolinska Institutet                       B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Sweden 2024-04-23 Juvenile Juvenile Liver Liver and Biliary System
31934 31934 SRR28776264 SRX24341222 SRS21101372 SRP503449 PRJNA1103351 Characterization of liver pancreas crosstalk following beta cell loss reveals a role for the molybdenum cofactor in beta cell regeneration PRJNA1103351 Other Understanding beta cell regeneration and how inter organ communication can contribute to that is crucial for developing new approaches for diabetes treatment. With this dataste we characterized the hepatocyte beta cell axis and how it can contribute to beta cell regeneration in a zebrafish model of beta cell loss. This data provide a transcriptomics analysis of isolated hepatocytes following beta cell ablation.       Ablated 1 Ablated rep1   strain:AB|age:2 mpf date:2015 06 04|geo loc name:Sweden|sex:mixed|tissue:Liver|cell type:Hepatocytes|collected by:Christos Karampelias|genotype:Tgins:flag NTR|treatment:Metronidazole|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish hepatocytes P2276 101 P2276 101 RNA was extracted from the sorted cells using the RNAqueous micro total isolation kit. The quality of the RNA was assessed and the first control sample was discarded as the RIN value was too low. Libraries were prepared using the TRUSeq stranded mRNA kit Illumina and sequenced on an Illumina HiSeq2500 instrument.     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2500   SRP503449     5_150903_BC7FRTANXX_P2276_101_1.fastq.gz 5_150903_BC7FRTANXX_P2276_101_2.fastq.gz fastq fastq 12536188812.0 49746781.0 5 150903 BC7FRTANXX P2276 101 1.fastq.gz 0:126 1:126 A:3281688237;C:2958476935;G:3022979051;T:3265495888;N:7548701 126 126     3281688237 2958476935 3022979051 3265495888 7548701 SRX24341222 SRS21101372 SRA1851016 Karolinska Institutet|Cell and Molecular Biology Karolinska Institutet                       B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Sweden 2024-04-23 Juvenile Juvenile Liver Liver and Biliary System
31935 31935 SRR28776265 SRX24341221 SRS21101375 SRP503449 PRJNA1103351 Characterization of liver pancreas crosstalk following beta cell loss reveals a role for the molybdenum cofactor in beta cell regeneration PRJNA1103351 Other Understanding beta cell regeneration and how inter organ communication can contribute to that is crucial for developing new approaches for diabetes treatment. With this dataste we characterized the hepatocyte beta cell axis and how it can contribute to beta cell regeneration in a zebrafish model of beta cell loss. This data provide a transcriptomics analysis of isolated hepatocytes following beta cell ablation.       Control 2 Control rep2   strain:AB|age:2 mpf date:2015 06 11|geo loc name:Sweden|sex:mixed|tissue:Liver|cell type:Hepatocytes|collected by:Christos Karampelias|genotype:Wild type|treatment:Metronidazole|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish hepatocytes P2276 106 P2276 106 RNA was extracted from the sorted cells using the RNAqueous micro total isolation kit. The quality of the RNA was assessed and the first control sample was discarded as the RIN value was too low. Libraries were prepared using the TRUSeq stranded mRNA kit Illumina and sequenced on an Illumina HiSeq2500 instrument.     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2500   SRP503449     5_150903_BC7FRTANXX_P2276_106_1.fastq.gz 5_150903_BC7FRTANXX_P2276_106_2.fastq.gz fastq fastq 11797087680.0 46813840.0 5 150903 BC7FRTANXX P2276 106 1.fastq.gz 0:126 1:126 A:3087253274;C:2787897503;G:2841312816;T:3072716302;N:7907785 126 126     3087253274 2787897503 2841312816 3072716302 7907785 SRX24341221 SRS21101375 SRA1851016 Karolinska Institutet|Cell and Molecular Biology Karolinska Institutet                       B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Sweden 2024-04-23 Juvenile Juvenile Liver Liver and Biliary System
31936 31936 SRR28776266 SRX24341220 SRS21101371 SRP503449 PRJNA1103351 Characterization of liver pancreas crosstalk following beta cell loss reveals a role for the molybdenum cofactor in beta cell regeneration PRJNA1103351 Other Understanding beta cell regeneration and how inter organ communication can contribute to that is crucial for developing new approaches for diabetes treatment. With this dataste we characterized the hepatocyte beta cell axis and how it can contribute to beta cell regeneration in a zebrafish model of beta cell loss. This data provide a transcriptomics analysis of isolated hepatocytes following beta cell ablation.       Control 1 Control rep1   strain:AB|age:2 mpf date:2015 06 09|geo loc name:Sweden|sex:mixed|tissue:Liver|cell type:Hepatocytes|collected by:Christos Karampelias|genotype:Wild type|treatment:Metronidazole|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish hepatocytes P2276 104 P2276 104 RNA was extracted from the sorted cells using the RNAqueous micro total isolation kit. The quality of the RNA was assessed and the first control sample was discarded as the RIN value was too low. Libraries were prepared using the TRUSeq stranded mRNA kit Illumina and sequenced on an Illumina HiSeq2500 instrument.     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2500   SRP503449     5_150903_BC7FRTANXX_P2276_104_1.fastq.gz 5_150903_BC7FRTANXX_P2276_104_2.fastq.gz fastq fastq 13294186416.0 52754708.0 5 150903 BC7FRTANXX P2276 104 1.fastq.gz 0:126 1:126 A:3544892164;C:3073022881;G:3106419492;T:3559768207;N:10083672 126 126     3544892164 3073022881 3106419492 3559768207 10083672 SRX24341220 SRS21101371 SRA1851016 Karolinska Institutet|Cell and Molecular Biology Karolinska Institutet                       B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Sweden 2024-04-23 Juvenile Juvenile Liver Liver and Biliary System
31980 31980 SRR28892728 SRX24451189 SRS21204958 SRP505641 PRJNA1107713 Tea polyphenols induce hepatotoxicity by interfering with adult zebrafish lipid metabolism and gut microbiota through the gut liver axis PRJNA1107713 Other High dose tea polyphenols may promote fatty acid absorption by hepatocytes by up regulating FABP CD36 and SRB1 genes inhibiting fatty acid efflux by down regulating ABCA1 genes and inhibiting fatty acid beta oxidation by down regulating CPT1 and ACAA2 genes resulting in fat accumulation in hepatocytes upregulation of inflammatory pathways and increased expression of pro inflammatory factors TNF a and IL1 b.         TP3   strain:not applicable|isolate:not applicable|breed:not collected|cultivar:not applicable|ecotype:AB ecotype|age:5 month|collection date:2022 11 24|geo loc name:China|sex:male|tissue:liver|replicate:replicate=biological replicate 6|BioSampleModel:Model organism or animal                 Adult zebrafish liver TP3 TP3 mRNAseq of zebrafish liver replication 3 of TP     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED DNBSEQ DNBSEQ-T7   SRP505641     TP3_1.fq.gz TP3_2.fq.gz fastq fastq 6657069900.0 22190233.0 TP3 1.fq.gz 0:150 1:150 A:1808410149;C:1512668682;G:1536153888;T:1799837181;N:0 150 150     1808410149 1512668682 1536153888 1799837181 0 SRX24451189 SRS21204958 SRA1858747 Beibu Gulf University|college of Food Engineering Beibu Gulf University                       B B biological fallback assumption bgi bgi unknown poly_a unknown bulk unknown unknown   China 2024-05-04 Adult Adult Liver Liver and Biliary System
31981 31981 SRR28892729 SRX24451188 SRS21204959 SRP505641 PRJNA1107713 Tea polyphenols induce hepatotoxicity by interfering with adult zebrafish lipid metabolism and gut microbiota through the gut liver axis PRJNA1107713 Other High dose tea polyphenols may promote fatty acid absorption by hepatocytes by up regulating FABP CD36 and SRB1 genes inhibiting fatty acid efflux by down regulating ABCA1 genes and inhibiting fatty acid beta oxidation by down regulating CPT1 and ACAA2 genes resulting in fat accumulation in hepatocytes upregulation of inflammatory pathways and increased expression of pro inflammatory factors TNF a and IL1 b.         TP2   strain:not applicable|isolate:not applicable|breed:not collected|cultivar:not applicable|ecotype:AB ecotype|age:5 month|collection date:2022 11 24|geo loc name:China|sex:male|tissue:liver|replicate:replicate=biological replicate 5|BioSampleModel:Model organism or animal                 Adult zebrafish liver TP2 TP2 mRNAseq of zebrafish liver replication 2 of TP     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED DNBSEQ DNBSEQ-T7   SRP505641     TP2_1.fq.gz TP2_2.fq.gz fastq fastq 6617368500.0 22057895.0 TP2 1.fq.gz 0:150 1:150 A:1799646726;C:1503407966;G:1523443584;T:1790870224;N:0 150 150     1799646726 1503407966 1523443584 1790870224 0 SRX24451188 SRS21204959 SRA1858747 Beibu Gulf University|college of Food Engineering Beibu Gulf University                       B B biological fallback assumption bgi bgi unknown poly_a unknown bulk unknown unknown   China 2024-05-04 Adult Adult Liver Liver and Biliary System
31982 31982 SRR28892730 SRX24451187 SRS21204956 SRP505641 PRJNA1107713 Tea polyphenols induce hepatotoxicity by interfering with adult zebrafish lipid metabolism and gut microbiota through the gut liver axis PRJNA1107713 Other High dose tea polyphenols may promote fatty acid absorption by hepatocytes by up regulating FABP CD36 and SRB1 genes inhibiting fatty acid efflux by down regulating ABCA1 genes and inhibiting fatty acid beta oxidation by down regulating CPT1 and ACAA2 genes resulting in fat accumulation in hepatocytes upregulation of inflammatory pathways and increased expression of pro inflammatory factors TNF a and IL1 b.         TP1   strain:not applicable|isolate:not applicable|breed:not collected|cultivar:not applicable|ecotype:AB ecotype|age:5 month|collection date:2022 11 24|geo loc name:China|sex:male|tissue:liver|replicate:replicate=biological replicate 4|BioSampleModel:Model organism or animal                 Adult zebrafish liver TP1 TP1 mRNAseq of zebrafish liver replication 1 of TP     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED DNBSEQ DNBSEQ-T7   SRP505641     TP1_1.fq.gz TP1_2.fq.gz fastq fastq 6432586800.0 21441956.0 TP1 1.fq.gz 0:150 1:150 A:1743341515;C:1465440262;G:1488109144;T:1735695879;N:0 150 150     1743341515 1465440262 1488109144 1735695879 0 SRX24451187 SRS21204956 SRA1858747 Beibu Gulf University|college of Food Engineering Beibu Gulf University                       B B biological fallback assumption bgi bgi unknown poly_a unknown bulk unknown unknown   China 2024-05-04 Adult Adult Liver Liver and Biliary System
31983 31983 SRR28892731 SRX24451186 SRS21204957 SRP505641 PRJNA1107713 Tea polyphenols induce hepatotoxicity by interfering with adult zebrafish lipid metabolism and gut microbiota through the gut liver axis PRJNA1107713 Other High dose tea polyphenols may promote fatty acid absorption by hepatocytes by up regulating FABP CD36 and SRB1 genes inhibiting fatty acid efflux by down regulating ABCA1 genes and inhibiting fatty acid beta oxidation by down regulating CPT1 and ACAA2 genes resulting in fat accumulation in hepatocytes upregulation of inflammatory pathways and increased expression of pro inflammatory factors TNF a and IL1 b.         CONT3   strain:not applicable|isolate:not applicable|breed:not collected|cultivar:not applicable|ecotype:AB ecotype|age:5 month|collection date:2022 11 24|geo loc name:China|sex:male|tissue:liver|replicate:replicate=biological replicate 3|BioSampleModel:Model organism or animal                 Adult zebrafish liver CON3 CON3 mRNAseq of zebrafish liver replication 3 of CONT     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED DNBSEQ DNBSEQ-T7   SRP505641     CONT3_1.fq.gz CONT3_2.fq.gz fastq fastq 6595768200.0 21985894.0 CONT3 1.fq.gz 0:150 1:150 A:1762107185;C:1525175684;G:1547321856;T:1761163475;N:0 150 150     1762107185 1525175684 1547321856 1761163475 0 SRX24451186 SRS21204957 SRA1858747 Beibu Gulf University|college of Food Engineering Beibu Gulf University                       B B biological fallback assumption bgi bgi unknown poly_a unknown bulk unknown unknown   China 2024-05-04 Adult Adult Liver Liver and Biliary System
31984 31984 SRR28892732 SRX24451185 SRS21204954 SRP505641 PRJNA1107713 Tea polyphenols induce hepatotoxicity by interfering with adult zebrafish lipid metabolism and gut microbiota through the gut liver axis PRJNA1107713 Other High dose tea polyphenols may promote fatty acid absorption by hepatocytes by up regulating FABP CD36 and SRB1 genes inhibiting fatty acid efflux by down regulating ABCA1 genes and inhibiting fatty acid beta oxidation by down regulating CPT1 and ACAA2 genes resulting in fat accumulation in hepatocytes upregulation of inflammatory pathways and increased expression of pro inflammatory factors TNF a and IL1 b.         CONT2   strain:not applicable|isolate:not applicable|breed:not collected|cultivar:not applicable|ecotype:AB ecotype|age:5 month|collection date:2022 11 24|geo loc name:China|sex:male|tissue:liver|replicate:replicate=biological replicate 2|BioSampleModel:Model organism or animal                 Adult zebrafish liver CON2 CON2 mRNAseq of zebrafish liver replication 2 of CONT     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED DNBSEQ DNBSEQ-T7   SRP505641     CONT2_1.fq.gz CONT2_2.fq.gz fastq fastq 6175346400.0 20584488.0 CONT2 1.fq.gz 0:150 1:150 A:1656546719;C:1421990443;G:1442409824;T:1654399414;N:0 150 150     1656546719 1421990443 1442409824 1654399414 0 SRX24451185 SRS21204954 SRA1858747 Beibu Gulf University|college of Food Engineering Beibu Gulf University                       B B biological fallback assumption bgi bgi unknown poly_a unknown bulk unknown unknown   China 2024-05-04 Adult Adult Liver Liver and Biliary System
31985 31985 SRR28892733 SRX24451184 SRS21204955 SRP505641 PRJNA1107713 Tea polyphenols induce hepatotoxicity by interfering with adult zebrafish lipid metabolism and gut microbiota through the gut liver axis PRJNA1107713 Other High dose tea polyphenols may promote fatty acid absorption by hepatocytes by up regulating FABP CD36 and SRB1 genes inhibiting fatty acid efflux by down regulating ABCA1 genes and inhibiting fatty acid beta oxidation by down regulating CPT1 and ACAA2 genes resulting in fat accumulation in hepatocytes upregulation of inflammatory pathways and increased expression of pro inflammatory factors TNF a and IL1 b.         CONT1   strain:not applicable|isolate:not applicable|breed:not collected|cultivar:not applicable|ecotype:AB ecotype|age:5 month|collection date:2022 11 24|geo loc name:China|sex:male|tissue:liver|replicate:replicate=biological replicate 1|BioSampleModel:Model organism or animal                 Adult zebrafish liver CON1 CON1 mRNAseq of zebrafish liver replication 1 of CONT     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED DNBSEQ DNBSEQ-T7   SRP505641     CONT1_1.fq.gz CONT1_2.fq.gz fastq fastq 6342828300.0 21142761.0 CONT1 1.fq.gz 0:150 1:150 A:1698306803;C:1464261565;G:1482929449;T:1697330483;N:0 150 150     1698306803 1464261565 1482929449 1697330483 0 SRX24451184 SRS21204955 SRA1858747 Beibu Gulf University|college of Food Engineering Beibu Gulf University                       B B biological fallback assumption bgi bgi unknown poly_a unknown bulk unknown unknown   China 2024-05-04 Adult Adult Liver Liver and Biliary System
31986 31986 SRR28894021 SRX24452441 SRS21206092 SRP505663 PRJNA1107798 liver PRJNA1107798 Other wt and elovl2 mutant liver         elovl2 4   strain:elovl2 4|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|collection date:not collected|geo loc name:not collected|sex:male|tissue:liver|BioSampleModel:Model organism or animal                 elovl2 4 8 8 liver     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq X   SRP505663     elovl2-4 fastq 4367010000.0 29113400.0 elovl2 4.gz 0:150 A:1161921878;C:1015107709;G:1012841192;T:1177020487;N:118734 150       1161921878 1015107709 1012841192 1177020487 118734 SRX24452441 SRS21206092 SRA1858809 Chinese Academy of Sciences (CAS)|The Institute of Hydrobiology Chinese Academy of Sciences (CAS)                       B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2024-05-04 Undetermined Undetermined Liver Liver and Biliary System
31987 31987 SRR28894022 SRX24452440 SRS21206091 SRP505663 PRJNA1107798 liver PRJNA1107798 Other wt and elovl2 mutant liver         elovl2 3   strain:elovl2 3|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|collection date:not collected|geo loc name:not collected|sex:male|tissue:liver|BioSampleModel:Model organism or animal                 elovl2 3 7 7 liver     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq X   SRP505663     elovl2-3 fastq 5125533150.0 34170221.0 elovl2 3.gz 0:150 A:1365645170;C:1189846405;G:1184721703;T:1385180096;N:139776 150       1365645170 1189846405 1184721703 1385180096 139776 SRX24452440 SRS21206091 SRA1858809 Chinese Academy of Sciences (CAS)|The Institute of Hydrobiology Chinese Academy of Sciences (CAS)                       B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2024-05-04 Undetermined Undetermined Liver Liver and Biliary System
31988 31988 SRR28894023 SRX24452439 SRS21206090 SRP505663 PRJNA1107798 liver PRJNA1107798 Other wt and elovl2 mutant liver         elovl2 2   strain:elovl2 2|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|collection date:not collected|geo loc name:not collected|sex:male|tissue:liver|BioSampleModel:Model organism or animal                 elovl2 2 6 6 liver     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq X   SRP505663     elovl2-2 fastq 3261375750.0 21742505.0 elovl2 2.gz 0:150 A:878478836;C:747963062;G:743760185;T:891083235;N:90432 150       878478836 747963062 743760185 891083235 90432 SRX24452439 SRS21206090 SRA1858809 Chinese Academy of Sciences (CAS)|The Institute of Hydrobiology Chinese Academy of Sciences (CAS)                       B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2024-05-04 Undetermined Undetermined Liver Liver and Biliary System
31989 31989 SRR28894024 SRX24452438 SRS21206089 SRP505663 PRJNA1107798 liver PRJNA1107798 Other wt and elovl2 mutant liver         elovl2 1   strain:elovl2 1|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|collection date:not collected|geo loc name:not collected|sex:male|tissue:liver|BioSampleModel:Model organism or animal                 elovl2 1 5 5 liver     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq X   SRP505663     elovl2-1 fastq 3629422950.0 24196153.0 elovl2 1.gz 0:150 A:974034477;C:836070594;G:831068189;T:988151010;N:98680 150       974034477 836070594 831068189 988151010 98680 SRX24452438 SRS21206089 SRA1858809 Chinese Academy of Sciences (CAS)|The Institute of Hydrobiology Chinese Academy of Sciences (CAS)                       B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2024-05-04 Undetermined Undetermined Liver Liver and Biliary System
31990 31990 SRR28894025 SRX24452437 SRS21206088 SRP505663 PRJNA1107798 liver PRJNA1107798 Other wt and elovl2 mutant liver         WT 4   strain:WT 4|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|collection date:not collected|geo loc name:not collected|sex:male|tissue:liver|BioSampleModel:Model organism or animal                 WT 4 4 4 liver     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq X   SRP505663     WT-4 fastq 4037472900.0 26916486.0 WT 4.gz 0:150 A:1083383010;C:932278459;G:925831402;T:1095868616;N:111413 150       1083383010 932278459 925831402 1095868616 111413 SRX24452437 SRS21206088 SRA1858809 Chinese Academy of Sciences (CAS)|The Institute of Hydrobiology Chinese Academy of Sciences (CAS)                       B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2024-05-04 Undetermined Undetermined Liver Liver and Biliary System
31991 31991 SRR28894026 SRX24452436 SRS21206087 SRP505663 PRJNA1107798 liver PRJNA1107798 Other wt and elovl2 mutant liver         WT 3   strain:WT 3|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|collection date:not collected|geo loc name:not collected|sex:male|tissue:liver|BioSampleModel:Model organism or animal                 WT 3 3 3 liver     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq X   SRP505663     WT-3 fastq 3651994200.0 24346628.0 WT 3.gz 0:150 A:978819903;C:844506880;G:836704943;T:991863415;N:99059 150       978819903 844506880 836704943 991863415 99059 SRX24452436 SRS21206087 SRA1858809 Chinese Academy of Sciences (CAS)|The Institute of Hydrobiology Chinese Academy of Sciences (CAS)                       B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2024-05-04 Undetermined Undetermined Liver Liver and Biliary System
31992 31992 SRR28894027 SRX24452435 SRS21206086 SRP505663 PRJNA1107798 liver PRJNA1107798 Other wt and elovl2 mutant liver         WT 2   strain:WT 2|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|collection date:not collected|geo loc name:not collected|sex:male|tissue:liver|BioSampleModel:Model organism or animal                 WT 2 2 2 liver     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq X   SRP505663     WT-2 fastq 3845338950.0 25635593.0 WT 2.gz 0:150 A:1033991995;C:885977441;G:878907105;T:1046356459;N:105950 150       1033991995 885977441 878907105 1046356459 105950 SRX24452435 SRS21206086 SRA1858809 Chinese Academy of Sciences (CAS)|The Institute of Hydrobiology Chinese Academy of Sciences (CAS)                       B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2024-05-04 Undetermined Undetermined Liver Liver and Biliary System
31993 31993 SRR28894028 SRX24452434 SRS21206085 SRP505663 PRJNA1107798 liver PRJNA1107798 Other wt and elovl2 mutant liver         WT 1   strain:WT 1|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|collection date:not collected|geo loc name:not collected|sex:male|tissue:liver|BioSampleModel:Model organism or animal                 WT 1 1 1 liver     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq X   SRP505663     WT-1 fastq 3756883050.0 25045887.0 WT 1.gz 0:150 A:1005244721;C:868304979;G:865360007;T:1017811504;N:161839 150       1005244721 868304979 865360007 1017811504 161839 SRX24452434 SRS21206085 SRA1858809 Chinese Academy of Sciences (CAS)|The Institute of Hydrobiology Chinese Academy of Sciences (CAS)                       B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2024-05-04 Undetermined Undetermined Liver Liver and Biliary System
34397 34397 SRR31719829 SRX27082407 SRS23541575 SRP551495 PRJNA1198392 RNA seq data of zebrafish with gmfb knockout and overexpression in MASLD PRJNA1198392 Other Glia maturation factor beta Gmfb an actin filament debrancher was first identified in the brain and has more recently been associated with liver diseases. However the potential direct role of Gmfb in hepatocytes post chronic liver injury remains largely uninvestigated. In this study total RNA was extracted from wild type or gmfb knockout and overexpression zebrafish liver in MASLD. And then RNA sequencing was performed in Novogene Co. Ltd. Beijing China using the Illumina NovaSeq 6000 platform to unravel gmfb transcriptome changes in MASLD.     hepatocyte specific gmfb overexpression normal diet for 35 days RNAseq MASLD HepGOE ND rep2 HepGOE ND rep2   strain:not collected|isolate:not collected|breed:AB|cultivar:not collected|ecotype:not collected|age:40 dpf stage:juvenile|collection date:2023 12 21|geo loc name:China:Guangzhou|sex:pooled male and female|tissue:liver|sample type:Total RNA|replicate:replicate = biological replicate 10|BioSampleModel:Model organism or animal                 Transcriptome of liver tissues in HepGOE zebrafish of normal diet. HepGOE ND rep2 HepGOE ND rep2 Total RNA was extracted from liver tissue for RNA sequencing     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP551495     RNAseq_MASLD_HepGOE_ND_rep2_1.fq.gz RNAseq_MASLD_HepGOE_ND_rep2_2.fq.gz fastq fastq 7177536600.0 23925122.0 RNAseq MASLD HepGOE ND rep2 1.fq.gz 0:150 1:150 A:1917334205;C:1668595888;G:1703080664;T:1887679182;N:846661 150 150     1917334205 1668595888 1703080664 1887679182 846661 SRX27082407 SRS23541575 SRA2034386 Southern Medical University|Biomedical Research Center Southern Medical University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   United States 2024-12-15 Juvenile Juvenile Liver Liver and Biliary System
34398 34398 SRR31719830 SRX27082406 SRS23541574 SRP551495 PRJNA1198392 RNA seq data of zebrafish with gmfb knockout and overexpression in MASLD PRJNA1198392 Other Glia maturation factor beta Gmfb an actin filament debrancher was first identified in the brain and has more recently been associated with liver diseases. However the potential direct role of Gmfb in hepatocytes post chronic liver injury remains largely uninvestigated. In this study total RNA was extracted from wild type or gmfb knockout and overexpression zebrafish liver in MASLD. And then RNA sequencing was performed in Novogene Co. Ltd. Beijing China using the Illumina NovaSeq 6000 platform to unravel gmfb transcriptome changes in MASLD.     hepatocyte specific gmfb overexpression normal diet for 35 days RNAseq MASLD HepGOE ND rep1 HepGOE ND rep1   strain:not collected|isolate:not collected|breed:AB|cultivar:not collected|ecotype:not collected|age:40 dpf stage:juvenile|collection date:2023 12 21|geo loc name:China:Guangzhou|sex:pooled male and female|tissue:liver|sample type:Total RNA|replicate:replicate = biological replicate 9|BioSampleModel:Model organism or animal                 Transcriptome of liver tissues in HepGOE zebrafish of normal diet. HepGOE ND rep1 HepGOE ND rep1 Total RNA was extracted from liver tissue for RNA sequencing     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP551495     RNAseq_MASLD_HepGOE_ND_rep1_1.fq.gz RNAseq_MASLD_HepGOE_ND_rep1_2.fq.gz fastq fastq 6621268500.0 22070895.0 RNAseq MASLD HepGOE ND rep1 1.fq.gz 0:150 1:150 A:1711419517;C:1595902037;G:1611514825;T:1702282385;N:149736 150 150     1711419517 1595902037 1611514825 1702282385 149736 SRX27082406 SRS23541574 SRA2034386 Southern Medical University|Biomedical Research Center Southern Medical University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   United States 2024-12-15 Juvenile Juvenile Liver Liver and Biliary System
34399 34399 SRR31719831 SRX27082405 SRS23541573 SRP551495 PRJNA1198392 RNA seq data of zebrafish with gmfb knockout and overexpression in MASLD PRJNA1198392 Other Glia maturation factor beta Gmfb an actin filament debrancher was first identified in the brain and has more recently been associated with liver diseases. However the potential direct role of Gmfb in hepatocytes post chronic liver injury remains largely uninvestigated. In this study total RNA was extracted from wild type or gmfb knockout and overexpression zebrafish liver in MASLD. And then RNA sequencing was performed in Novogene Co. Ltd. Beijing China using the Illumina NovaSeq 6000 platform to unravel gmfb transcriptome changes in MASLD.     hepatocyte specific gmfb knockout high fat high cholesterol diet for 35 days RNAseq MASLD HepGKO HFC rep2 HepGKO HFC rep2   strain:not collected|isolate:not collected|breed:AB|cultivar:not collected|ecotype:not collected|age:40 dpf stage:juvenile|collection date:2023 12 21|geo loc name:China:Guangzhou|sex:pooled male and female|tissue:liver|sample type:Total RNA|replicate:replicate = biological replicate 8|BioSampleModel:Model organism or animal                 Transcriptome of liver tissues in HepGKO zebrafish of high fat high cholesterol diet. HepGKO HFC rep2 HepGKO HFC rep2 Total RNA was extracted from liver tissue for RNA sequencing     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP551495     RNAseq_MASLD_HepGKO_HFC_rep2_1.fq.gz RNAseq_MASLD_HepGKO_HFC_rep2_2.fq.gz fastq fastq 5901646500.0 19672155.0 RNAseq MASLD HepGKO HFC rep2 1.fq.gz 0:150 1:150 A:1547939419;C:1401111812;G:1425197669;T:1527300198;N:97402 150 150     1547939419 1401111812 1425197669 1527300198 97402 SRX27082405 SRS23541573 SRA2034386 Southern Medical University|Biomedical Research Center Southern Medical University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   United States 2024-12-15 Juvenile Juvenile Liver Liver and Biliary System
34400 34400 SRR31719832 SRX27082404 SRS23541572 SRP551495 PRJNA1198392 RNA seq data of zebrafish with gmfb knockout and overexpression in MASLD PRJNA1198392 Other Glia maturation factor beta Gmfb an actin filament debrancher was first identified in the brain and has more recently been associated with liver diseases. However the potential direct role of Gmfb in hepatocytes post chronic liver injury remains largely uninvestigated. In this study total RNA was extracted from wild type or gmfb knockout and overexpression zebrafish liver in MASLD. And then RNA sequencing was performed in Novogene Co. Ltd. Beijing China using the Illumina NovaSeq 6000 platform to unravel gmfb transcriptome changes in MASLD.     hepatocyte specific gmfb knockout high fat high cholesterol diet for 35 days RNAseq MASLD HepGKO HFC rep1 HepGKO HFC rep1   strain:not collected|isolate:not collected|breed:AB|cultivar:not collected|ecotype:not collected|age:40 dpf stage:juvenile|collection date:2023 12 21|geo loc name:China:Guangzhou|sex:pooled male and female|tissue:liver|sample type:Total RNA|replicate:replicate = biological replicate 7|BioSampleModel:Model organism or animal                 Transcriptome of liver tissues in HepGKO zebrafish of high fat high cholesterol diet. HepGKO HFC rep1 HepGKO HFC rep1 Total RNA was extracted from liver tissue for RNA sequencing     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP551495     RNAseq_MASLD_HepGKO_HFC_rep1_1.fq.gz RNAseq_MASLD_HepGKO_HFC_rep1_2.fq.gz fastq fastq 6484178700.0 21613929.0 RNAseq MASLD HepGKO HFC rep1 1.fq.gz 0:150 1:150 A:1692850957;C:1545705390;G:1573644279;T:1671871368;N:106706 150 150     1692850957 1545705390 1573644279 1671871368 106706 SRX27082404 SRS23541572 SRA2034386 Southern Medical University|Biomedical Research Center Southern Medical University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   United States 2024-12-15 Juvenile Juvenile Liver Liver and Biliary System
34401 34401 SRR31719833 SRX27082403 SRS23541571 SRP551495 PRJNA1198392 RNA seq data of zebrafish with gmfb knockout and overexpression in MASLD PRJNA1198392 Other Glia maturation factor beta Gmfb an actin filament debrancher was first identified in the brain and has more recently been associated with liver diseases. However the potential direct role of Gmfb in hepatocytes post chronic liver injury remains largely uninvestigated. In this study total RNA was extracted from wild type or gmfb knockout and overexpression zebrafish liver in MASLD. And then RNA sequencing was performed in Novogene Co. Ltd. Beijing China using the Illumina NovaSeq 6000 platform to unravel gmfb transcriptome changes in MASLD.     hepatocyte specific gmfb knockout normal diet for 35 days RNAseq MASLD HepGKO ND rep2 HepGKO ND rep2   strain:not collected|isolate:not collected|breed:AB|cultivar:not collected|ecotype:not collected|age:40 dpf stage:juvenile|collection date:2023 12 21|geo loc name:China:Guangzhou|sex:pooled male and female|tissue:liver|sample type:Total RNA|replicate:replicate = biological replicate 6|BioSampleModel:Model organism or animal                 Transcriptome of liver tissues in HepGKO zebrafish of normal diet. HepGKO ND rep2 HepGKO ND rep2 Total RNA was extracted from liver tissue for RNA sequencing     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP551495     RNAseq_MASLD_HepGKO_ND_rep2_1.fq.gz RNAseq_MASLD_HepGKO_ND_rep2_2.fq.gz fastq fastq 6436941000.0 21456470.0 RNAseq MASLD HepGKO ND rep2 1.fq.gz 0:150 1:150 A:1671402056;C:1543860294;G:1570976721;T:1650596456;N:105473 150 150     1671402056 1543860294 1570976721 1650596456 105473 SRX27082403 SRS23541571 SRA2034386 Southern Medical University|Biomedical Research Center Southern Medical University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   United States 2024-12-15 Juvenile Juvenile Liver Liver and Biliary System
34402 34402 SRR31719834 SRX27082402 SRS23541570 SRP551495 PRJNA1198392 RNA seq data of zebrafish with gmfb knockout and overexpression in MASLD PRJNA1198392 Other Glia maturation factor beta Gmfb an actin filament debrancher was first identified in the brain and has more recently been associated with liver diseases. However the potential direct role of Gmfb in hepatocytes post chronic liver injury remains largely uninvestigated. In this study total RNA was extracted from wild type or gmfb knockout and overexpression zebrafish liver in MASLD. And then RNA sequencing was performed in Novogene Co. Ltd. Beijing China using the Illumina NovaSeq 6000 platform to unravel gmfb transcriptome changes in MASLD.     hepatocyte specific gmfb knockout normal diet for 35 days RNAseq MASLD HepGKO ND rep1 HepGKO ND rep1   strain:not collected|isolate:not collected|breed:AB|cultivar:not collected|ecotype:not collected|age:40 dpf stage:juvenile|collection date:2023 12 21|geo loc name:China:Guangzhou|sex:pooled male and female|tissue:liver|sample type:Total RNA|replicate:replicate = biological replicate 5|BioSampleModel:Model organism or animal                 Transcriptome of liver tissues in HepGKO zebrafish of normal diet. HepGKO ND rep1 HepGKO ND rep1 Total RNA was extracted from liver tissue for RNA sequencing     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP551495     RNAseq_MASLD_HepGKO_ND_rep1_1.fq.gz RNAseq_MASLD_HepGKO_ND_rep1_2.fq.gz fastq fastq 6386174700.0 21287249.0 RNAseq MASLD HepGKO ND rep1 1.fq.gz 0:150 1:150 A:1662767742;C:1527603435;G:1545756971;T:1649944714;N:101838 150 150     1662767742 1527603435 1545756971 1649944714 101838 SRX27082402 SRS23541570 SRA2034386 Southern Medical University|Biomedical Research Center Southern Medical University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   United States 2024-12-15 Juvenile Juvenile Liver Liver and Biliary System
34403 34403 SRR31719835 SRX27082401 SRS23541569 SRP551495 PRJNA1198392 RNA seq data of zebrafish with gmfb knockout and overexpression in MASLD PRJNA1198392 Other Glia maturation factor beta Gmfb an actin filament debrancher was first identified in the brain and has more recently been associated with liver diseases. However the potential direct role of Gmfb in hepatocytes post chronic liver injury remains largely uninvestigated. In this study total RNA was extracted from wild type or gmfb knockout and overexpression zebrafish liver in MASLD. And then RNA sequencing was performed in Novogene Co. Ltd. Beijing China using the Illumina NovaSeq 6000 platform to unravel gmfb transcriptome changes in MASLD.     WT zebrafish high fat high cholesterol diet for 35 days RNAseq MASLD WT HFC rep2 WT HFC rep2   strain:not collected|isolate:not collected|breed:AB|cultivar:not collected|ecotype:not collected|age:40 dpf stage:juvenile|collection date:2023 12 21|geo loc name:China:Guangzhou|sex:pooled male and female|tissue:liver|sample type:Total RNA|replicate:replicate = biological replicate 4|BioSampleModel:Model organism or animal                 Transcriptome of liver tissues in WT zebrafish of high fat high cholesterol diet. WT HFC rep2 WT HFC rep2 Total RNA was extracted from liver tissue for RNA sequencing     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP551495     RNAseq_MASLD_WT_HFC_rep2_1.fq.gz RNAseq_MASLD_WT_HFC_rep2_2.fq.gz fastq fastq 7088163900.0 23627213.0 RNAseq MASLD WT HFC rep2 1.fq.gz 0:150 1:150 A:1904609517;C:1635475353;G:1664944747;T:1882978732;N:155551 150 150     1904609517 1635475353 1664944747 1882978732 155551 SRX27082401 SRS23541569 SRA2034386 Southern Medical University|Biomedical Research Center Southern Medical University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   United States 2024-12-15 Juvenile Juvenile Liver Liver and Biliary System
34404 34404 SRR31719836 SRX27082400 SRS23541568 SRP551495 PRJNA1198392 RNA seq data of zebrafish with gmfb knockout and overexpression in MASLD PRJNA1198392 Other Glia maturation factor beta Gmfb an actin filament debrancher was first identified in the brain and has more recently been associated with liver diseases. However the potential direct role of Gmfb in hepatocytes post chronic liver injury remains largely uninvestigated. In this study total RNA was extracted from wild type or gmfb knockout and overexpression zebrafish liver in MASLD. And then RNA sequencing was performed in Novogene Co. Ltd. Beijing China using the Illumina NovaSeq 6000 platform to unravel gmfb transcriptome changes in MASLD.     WT zebrafish high fat high cholesterol diet for 35 days RNAseq MASLD WT HFC rep1 WT HFC rep1   strain:not collected|isolate:not collected|breed:AB|cultivar:not collected|ecotype:not collected|age:40 dpf stage:juvenile|collection date:2023 12 21|geo loc name:China:Guangzhou|sex:pooled male and female|tissue:liver|sample type:Total RNA|replicate:replicate = biological replicate 3|BioSampleModel:Model organism or animal                 Transcriptome of liver tissues in WT zebrafish of high fat high cholesterol diet. WT HFC rep1 WT HFC rep1 Total RNA was extracted from liver tissue for RNA sequencing     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP551495     RNAseq_MASLD_WT_HFC_rep1_1.fq.gz RNAseq_MASLD_WT_HFC_rep1_2.fq.gz fastq fastq 7053396600.0 23511322.0 RNAseq MASLD WT HFC rep1 1.fq.gz 0:150 1:150 A:1862942395;C:1655266768;G:1688002812;T:1847030526;N:154099 150 150     1862942395 1655266768 1688002812 1847030526 154099 SRX27082400 SRS23541568 SRA2034386 Southern Medical University|Biomedical Research Center Southern Medical University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   United States 2024-12-15 Juvenile Juvenile Liver Liver and Biliary System
34405 34405 SRR31719837 SRX27082399 SRS23541567 SRP551495 PRJNA1198392 RNA seq data of zebrafish with gmfb knockout and overexpression in MASLD PRJNA1198392 Other Glia maturation factor beta Gmfb an actin filament debrancher was first identified in the brain and has more recently been associated with liver diseases. However the potential direct role of Gmfb in hepatocytes post chronic liver injury remains largely uninvestigated. In this study total RNA was extracted from wild type or gmfb knockout and overexpression zebrafish liver in MASLD. And then RNA sequencing was performed in Novogene Co. Ltd. Beijing China using the Illumina NovaSeq 6000 platform to unravel gmfb transcriptome changes in MASLD.     hepatocyte specific gmfb overexpression high fat high cholesterol diet for 35 days RNAseq MASLD HepGOE HFC rep2 HepGOE HFC rep2   strain:not collected|isolate:not collected|breed:AB|cultivar:not collected|ecotype:not collected|age:40 dpf stage:juvenile|collection date:2023 12 21|geo loc name:China:Guangzhou|sex:pooled male and female|tissue:liver|sample type:Total RNA|replicate:replicate = biological replicate 12|BioSampleModel:Model organism or animal                 Transcriptome of liver tissues in HepGOE zebrafish of high fat high cholesterol diet. HepGOE HFC rep2 HepGOE HFC rep2 Total RNA was extracted from liver tissue for RNA sequencing     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP551495     RNAseq_MASLD_HepGOE_HFC_rep2_1.fq.gz RNAseq_MASLD_HepGOE_HFC_rep2_2.fq.gz fastq fastq 7004757600.0 23349192.0 RNAseq MASLD HepGOE HFC rep2 1.fq.gz 0:150 1:150 A:1846708800;C:1647727254;G:1676955416;T:1833207397;N:158733 150 150     1846708800 1647727254 1676955416 1833207397 158733 SRX27082399 SRS23541567 SRA2034386 Southern Medical University|Biomedical Research Center Southern Medical University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   United States 2024-12-15 Juvenile Juvenile Liver Liver and Biliary System
34406 34406 SRR31719838 SRX27082398 SRS23541566 SRP551495 PRJNA1198392 RNA seq data of zebrafish with gmfb knockout and overexpression in MASLD PRJNA1198392 Other Glia maturation factor beta Gmfb an actin filament debrancher was first identified in the brain and has more recently been associated with liver diseases. However the potential direct role of Gmfb in hepatocytes post chronic liver injury remains largely uninvestigated. In this study total RNA was extracted from wild type or gmfb knockout and overexpression zebrafish liver in MASLD. And then RNA sequencing was performed in Novogene Co. Ltd. Beijing China using the Illumina NovaSeq 6000 platform to unravel gmfb transcriptome changes in MASLD.     hepatocyte specific gmfb overexpression high fat high cholesterol diet for 35 days RNAseq MASLD HepGOE HFC rep1 HepGOE HFC rep1   strain:not collected|isolate:not collected|breed:AB|cultivar:not collected|ecotype:not collected|age:40 dpf stage:juvenile|collection date:2023 12 21|geo loc name:China:Guangzhou|sex:pooled male and female|tissue:liver|sample type:Total RNA|replicate:replicate = biological replicate 11|BioSampleModel:Model organism or animal                 Transcriptome of liver tissues in HepGOE zebrafish of high fat high cholesterol diet. HepGOE HFC rep1 HepGOE HFC rep1 Total RNA was extracted from liver tissue for RNA sequencing     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP551495     RNAseq_MASLD_HepGOE_HFC_rep1_1.fq.gz RNAseq_MASLD_HepGOE_HFC_rep1_2.fq.gz fastq fastq 8211524400.0 27371748.0 RNAseq MASLD HepGOE HFC rep1 1.fq.gz 0:150 1:150 A:2217820195;C:1876471113;G:1906298333;T:2210753213;N:181546 150 150     2217820195 1876471113 1906298333 2210753213 181546 SRX27082398 SRS23541566 SRA2034386 Southern Medical University|Biomedical Research Center Southern Medical University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   United States 2024-12-15 Juvenile Juvenile Liver Liver and Biliary System
34407 34407 SRR31719839 SRX27082397 SRS23541565 SRP551495 PRJNA1198392 RNA seq data of zebrafish with gmfb knockout and overexpression in MASLD PRJNA1198392 Other Glia maturation factor beta Gmfb an actin filament debrancher was first identified in the brain and has more recently been associated with liver diseases. However the potential direct role of Gmfb in hepatocytes post chronic liver injury remains largely uninvestigated. In this study total RNA was extracted from wild type or gmfb knockout and overexpression zebrafish liver in MASLD. And then RNA sequencing was performed in Novogene Co. Ltd. Beijing China using the Illumina NovaSeq 6000 platform to unravel gmfb transcriptome changes in MASLD.     WT zebrafish normal diet for 35 days RNAseq MASLD WT ND rep2 WT ND rep2   strain:not collected|isolate:not collected|breed:AB|cultivar:not collected|ecotype:not collected|age:40 dpf stage:juvenile|collection date:2023 12 21|geo loc name:China:Guangzhou|sex:pooled male and female|tissue:liver|sample type:Total RNA|replicate:replicate = biological replicate 2|BioSampleModel:Model organism or animal                 Transcriptome of liver tissues in WT zebrafish of normal diet. WT ND rep2 WT ND rep2 Total RNA was extracted from liver tissue for RNA sequencing     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP551495     RNAseq_MASLD_WT_ND_rep2_1.fq.gz RNAseq_MASLD_WT_ND_rep2_2.fq.gz fastq fastq 6966786300.0 23222621.0 RNAseq MASLD WT ND rep2 1.fq.gz 0:150 1:150 A:1855652140;C:1619780884;G:1651213951;T:1839982276;N:157049 150 150     1855652140 1619780884 1651213951 1839982276 157049 SRX27082397 SRS23541565 SRA2034386 Southern Medical University|Biomedical Research Center Southern Medical University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   United States 2024-12-15 Juvenile Juvenile Liver Liver and Biliary System
34408 34408 SRR31719840 SRX27082396 SRS23541564 SRP551495 PRJNA1198392 RNA seq data of zebrafish with gmfb knockout and overexpression in MASLD PRJNA1198392 Other Glia maturation factor beta Gmfb an actin filament debrancher was first identified in the brain and has more recently been associated with liver diseases. However the potential direct role of Gmfb in hepatocytes post chronic liver injury remains largely uninvestigated. In this study total RNA was extracted from wild type or gmfb knockout and overexpression zebrafish liver in MASLD. And then RNA sequencing was performed in Novogene Co. Ltd. Beijing China using the Illumina NovaSeq 6000 platform to unravel gmfb transcriptome changes in MASLD.     WT zebrafish normal diet for 35 days RNAseq MASLD WT ND rep1 WT ND rep1   strain:not collected|isolate:not collected|breed:AB|cultivar:not collected|ecotype:not collected|age:40 dpf stage:juvenile|collection date:2023 12 21|geo loc name:China:Guangzhou|sex:pooled male and female|tissue:liver|sample type:Total RNA|replicate:replicate = biological replicate 1|BioSampleModel:Model organism or animal                 Transcriptome of liver tissues in WT zebrafish of normal diet. WT ND rep1 WT ND rep1 Total RNA was extracted from liver tissue for RNA sequencing     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP551495     RNAseq_MASLD_WT_ND_rep1_1.fq.gz RNAseq_MASLD_WT_ND_rep1_2.fq.gz fastq fastq 7149668700.0 23832229.0 RNAseq MASLD WT ND rep1 1.fq.gz 0:150 1:150 A:1869145140;C:1695095352;G:1726444600;T:1858824841;N:158767 150 150     1869145140 1695095352 1726444600 1858824841 158767 SRX27082396 SRS23541564 SRA2034386 Southern Medical University|Biomedical Research Center Southern Medical University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   United States 2024-12-15 Juvenile Juvenile Liver Liver and Biliary System
35418 35418 SRR32754071 SRX28039267 SRS24399991 SRP571287 PRJNA1237738 Spliceosome components as the main targets of alternative splicing PRJNA1237738 Other Splicing of transcripts via the spliceosome machinery is a complex process involving a multitude of proteins and short non coding RNAs. Mechanisms responsible for non canonical/alternative splicing of genes are poorly understood although numerous processes and diseases have been associated with aberrant mRNA splicing. We have tried to identify the genes most frequently targeted by alternative splicing. Data from several species and types of tissue indicate that the constituents of the spliceosome itself are the main targets of alternative splicing suggesting a model where high splice variant diversity is a fundamental feature of the spliceosome.       S103 liver10   isolate:103|dev stage:Adult|sex:missing|tissue:Liver|collection date:missing|geo loc name:Norway|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish liver S103 S103 RNA Seq     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP571287     liver10.R1.fastq.gz liver10.R2.fastq.gz fastq fastq 31116884382.0 103036041.0 liver10.R1.fastq.gz 0:151 1:151 A:7624117025;C:7503766265;G:8481819121;T:7505094002;N:2087969 151 151     7624117025 7503766265 8481819121 7505094002 2087969 SRX28039267 SRS24399991 SRA2095732 NOFIMA|Department of Breeding and Genetics NOFIMA                       B B mate2-mate1 similar by mapping diff illumina novaseq_era unknown poly_a unknown bulk unknown unknown   Norway 2025-03-18 Adult Adult Liver Liver and Biliary System
35419 35419 SRR32754072 SRX28039266 SRS24399990 SRP571287 PRJNA1237738 Spliceosome components as the main targets of alternative splicing PRJNA1237738 Other Splicing of transcripts via the spliceosome machinery is a complex process involving a multitude of proteins and short non coding RNAs. Mechanisms responsible for non canonical/alternative splicing of genes are poorly understood although numerous processes and diseases have been associated with aberrant mRNA splicing. We have tried to identify the genes most frequently targeted by alternative splicing. Data from several species and types of tissue indicate that the constituents of the spliceosome itself are the main targets of alternative splicing suggesting a model where high splice variant diversity is a fundamental feature of the spliceosome.       S102 liver9   isolate:102|dev stage:Adult|sex:missing|tissue:Liver|collection date:missing|geo loc name:Norway|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish liver S102 S102 RNA Seq     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP571287     liver9.R1.fastq.gz liver9.R2.fastq.gz fastq fastq 34003123146.0 112593123.0 liver9.R1.fastq.gz 0:151 1:151 A:8730950531;C:8043211766;G:8689254612;T:8537416606;N:2289631 151 151     8730950531 8043211766 8689254612 8537416606 2289631 SRX28039266 SRS24399990 SRA2095732 NOFIMA|Department of Breeding and Genetics NOFIMA                       B B mate2-mate1 similar by mapping diff illumina novaseq_era unknown poly_a unknown bulk unknown unknown   Norway 2025-03-18 Adult Adult Liver Liver and Biliary System
35420 35420 SRR32754073 SRX28039265 SRS24399988 SRP571287 PRJNA1237738 Spliceosome components as the main targets of alternative splicing PRJNA1237738 Other Splicing of transcripts via the spliceosome machinery is a complex process involving a multitude of proteins and short non coding RNAs. Mechanisms responsible for non canonical/alternative splicing of genes are poorly understood although numerous processes and diseases have been associated with aberrant mRNA splicing. We have tried to identify the genes most frequently targeted by alternative splicing. Data from several species and types of tissue indicate that the constituents of the spliceosome itself are the main targets of alternative splicing suggesting a model where high splice variant diversity is a fundamental feature of the spliceosome.       S101 liver8   isolate:101|dev stage:Adult|sex:missing|tissue:Liver|collection date:missing|geo loc name:Norway|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish liver S101 S101 RNA Seq     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP571287     liver8.R1.fastq.gz liver8.R2.fastq.gz fastq fastq 39765841242.0 131674971.0 liver8.R1.fastq.gz 0:151 1:151 A:10237775536;C:9424805191;G:10092482364;T:10008099872;N:2678279 151 151     10237775536 9424805191 10092482364 10008099872 2678279 SRX28039265 SRS24399988 SRA2095732 NOFIMA|Department of Breeding and Genetics NOFIMA 2 0.95418 0.62731 0.09366 0.05664 0.78206 0.81783 0.59167 0.60193 151 151 B B mate2-mate1 similar by mapping diff illumina novaseq_era unknown poly_a unknown bulk unknown unknown   Norway 2025-03-18 Adult Adult Liver Liver and Biliary System
35421 35421 SRR32754074 SRX28039264 SRS24399989 SRP571287 PRJNA1237738 Spliceosome components as the main targets of alternative splicing PRJNA1237738 Other Splicing of transcripts via the spliceosome machinery is a complex process involving a multitude of proteins and short non coding RNAs. Mechanisms responsible for non canonical/alternative splicing of genes are poorly understood although numerous processes and diseases have been associated with aberrant mRNA splicing. We have tried to identify the genes most frequently targeted by alternative splicing. Data from several species and types of tissue indicate that the constituents of the spliceosome itself are the main targets of alternative splicing suggesting a model where high splice variant diversity is a fundamental feature of the spliceosome.       S100 liver7   isolate:100|dev stage:Adult|sex:missing|tissue:Liver|collection date:missing|geo loc name:Norway|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish liver S100 S100 RNA Seq     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP571287     liver7.R1.fastq.gz liver7.R2.fastq.gz fastq fastq 45078803724.0 149267562.0 liver7.R1.fastq.gz 0:151 1:151 A:10896182136;C:10202070103;G:13175371544;T:10802143248;N:3036693 151 151     10896182136 10202070103 13175371544 10802143248 3036693 SRX28039264 SRS24399989 SRA2095732 NOFIMA|Department of Breeding and Genetics NOFIMA 2 0.9672 0.63136 0.05647 0.03264 0.85541 0.88229 0.3215 0.30652 151 151 B B mate2-mate1 similar by mapping diff illumina novaseq_era unknown poly_a unknown bulk unknown unknown   Norway 2025-03-18 Adult Adult Liver Liver and Biliary System
35422 35422 SRR32754075 SRX28039263 SRS24399987 SRP571287 PRJNA1237738 Spliceosome components as the main targets of alternative splicing PRJNA1237738 Other Splicing of transcripts via the spliceosome machinery is a complex process involving a multitude of proteins and short non coding RNAs. Mechanisms responsible for non canonical/alternative splicing of genes are poorly understood although numerous processes and diseases have been associated with aberrant mRNA splicing. We have tried to identify the genes most frequently targeted by alternative splicing. Data from several species and types of tissue indicate that the constituents of the spliceosome itself are the main targets of alternative splicing suggesting a model where high splice variant diversity is a fundamental feature of the spliceosome.       S99 liver6   isolate:99|dev stage:Adult|sex:missing|tissue:Liver|collection date:missing|geo loc name:Norway|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish liver S99 S99 RNA Seq     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP571287     liver6.R1.fastq.gz liver6.R2.fastq.gz fastq fastq 20010565904.0 66260152.0 liver6.R1.fastq.gz 0:151 1:151 A:5046321218;C:4692862900;G:5355961232;T:4914071665;N:1348889 151 151     5046321218 4692862900 5355961232 4914071665 1348889 SRX28039263 SRS24399987 SRA2095732 NOFIMA|Department of Breeding and Genetics NOFIMA                       B B mate2-mate1 similar by mapping diff illumina novaseq_era unknown poly_a unknown bulk unknown unknown   Norway 2025-03-18 Adult Adult Liver Liver and Biliary System
35423 35423 SRR32754076 SRX28039262 SRS24399986 SRP571287 PRJNA1237738 Spliceosome components as the main targets of alternative splicing PRJNA1237738 Other Splicing of transcripts via the spliceosome machinery is a complex process involving a multitude of proteins and short non coding RNAs. Mechanisms responsible for non canonical/alternative splicing of genes are poorly understood although numerous processes and diseases have been associated with aberrant mRNA splicing. We have tried to identify the genes most frequently targeted by alternative splicing. Data from several species and types of tissue indicate that the constituents of the spliceosome itself are the main targets of alternative splicing suggesting a model where high splice variant diversity is a fundamental feature of the spliceosome.       S98 liver5   isolate:98|dev stage:Adult|sex:missing|tissue:Liver|collection date:missing|geo loc name:Norway|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish liver S98 S98 RNA Seq     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP571287     liver5.R1.fastq.gz liver5.R2.fastq.gz fastq fastq 21668259608.0 71749204.0 liver5.R1.fastq.gz 0:151 1:151 A:5478219080;C:5141072641;G:5743751757;T:5303745741;N:1470389 151 151     5478219080 5141072641 5743751757 5303745741 1470389 SRX28039262 SRS24399986 SRA2095732 NOFIMA|Department of Breeding and Genetics NOFIMA                       B B mate2-mate1 similar by mapping diff illumina novaseq_era unknown poly_a unknown bulk unknown unknown   Norway 2025-03-18 Adult Adult Liver Liver and Biliary System
35424 35424 SRR32754077 SRX28039261 SRS24399984 SRP571287 PRJNA1237738 Spliceosome components as the main targets of alternative splicing PRJNA1237738 Other Splicing of transcripts via the spliceosome machinery is a complex process involving a multitude of proteins and short non coding RNAs. Mechanisms responsible for non canonical/alternative splicing of genes are poorly understood although numerous processes and diseases have been associated with aberrant mRNA splicing. We have tried to identify the genes most frequently targeted by alternative splicing. Data from several species and types of tissue indicate that the constituents of the spliceosome itself are the main targets of alternative splicing suggesting a model where high splice variant diversity is a fundamental feature of the spliceosome.       S97 liver4   isolate:97|dev stage:Adult|sex:missing|tissue:Liver|collection date:missing|geo loc name:Norway|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish liver S97 S97 RNA Seq     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP571287     liver4.R1.fastq.gz liver4.R2.fastq.gz fastq fastq 18126139358.0 60020329.0 liver4.R1.fastq.gz 0:151 1:151 A:4382298483;C:4280507238;G:5109402412;T:4352745086;N:1186139 151 151     4382298483 4280507238 5109402412 4352745086 1186139 SRX28039261 SRS24399984 SRA2095732 NOFIMA|Department of Breeding and Genetics NOFIMA                       B B mate2-mate1 similar by mapping diff illumina novaseq_era unknown poly_a unknown bulk unknown unknown   Norway 2025-03-18 Adult Adult Liver Liver and Biliary System
35425 35425 SRR32754078 SRX28039260 SRS24399985 SRP571287 PRJNA1237738 Spliceosome components as the main targets of alternative splicing PRJNA1237738 Other Splicing of transcripts via the spliceosome machinery is a complex process involving a multitude of proteins and short non coding RNAs. Mechanisms responsible for non canonical/alternative splicing of genes are poorly understood although numerous processes and diseases have been associated with aberrant mRNA splicing. We have tried to identify the genes most frequently targeted by alternative splicing. Data from several species and types of tissue indicate that the constituents of the spliceosome itself are the main targets of alternative splicing suggesting a model where high splice variant diversity is a fundamental feature of the spliceosome.       S96 liver3   isolate:96|dev stage:Adult|sex:missing|tissue:Liver|collection date:missing|geo loc name:Norway|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish liver S96 S96 RNA Seq     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP571287     liver3.R1.fastq.gz liver3.R2.fastq.gz fastq fastq 23286044012.0 77106106.0 liver3.R1.fastq.gz 0:151 1:151 A:5720715760;C:5341688034;G:6543246636;T:5678817182;N:1576400 151 151     5720715760 5341688034 6543246636 5678817182 1576400 SRX28039260 SRS24399985 SRA2095732 NOFIMA|Department of Breeding and Genetics NOFIMA                       B B mate2-mate1 similar by mapping diff illumina novaseq_era unknown poly_a unknown bulk unknown unknown   Norway 2025-03-18 Adult Adult Liver Liver and Biliary System
35426 35426 SRR32754079 SRX28039259 SRS24399983 SRP571287 PRJNA1237738 Spliceosome components as the main targets of alternative splicing PRJNA1237738 Other Splicing of transcripts via the spliceosome machinery is a complex process involving a multitude of proteins and short non coding RNAs. Mechanisms responsible for non canonical/alternative splicing of genes are poorly understood although numerous processes and diseases have been associated with aberrant mRNA splicing. We have tried to identify the genes most frequently targeted by alternative splicing. Data from several species and types of tissue indicate that the constituents of the spliceosome itself are the main targets of alternative splicing suggesting a model where high splice variant diversity is a fundamental feature of the spliceosome.       S95 liver2   isolate:95|dev stage:Adult|sex:missing|tissue:Liver|collection date:missing|geo loc name:Norway|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish liver S95 S95 RNA Seq     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP571287     liver2.R1.fastq.gz liver2.R2.fastq.gz fastq fastq 22012368978.0 72888639.0 liver2.R1.fastq.gz 0:151 1:151 A:5606088677;C:5168682847;G:5747322774;T:5488820956;N:1453724 151 151     5606088677 5168682847 5747322774 5488820956 1453724 SRX28039259 SRS24399983 SRA2095732 NOFIMA|Department of Breeding and Genetics NOFIMA                       B B mate2-mate1 similar by mapping diff illumina novaseq_era unknown poly_a unknown bulk unknown unknown   Norway 2025-03-18 Adult Adult Liver Liver and Biliary System
35427 35427 SRR32754080 SRX28039258 SRS24399982 SRP571287 PRJNA1237738 Spliceosome components as the main targets of alternative splicing PRJNA1237738 Other Splicing of transcripts via the spliceosome machinery is a complex process involving a multitude of proteins and short non coding RNAs. Mechanisms responsible for non canonical/alternative splicing of genes are poorly understood although numerous processes and diseases have been associated with aberrant mRNA splicing. We have tried to identify the genes most frequently targeted by alternative splicing. Data from several species and types of tissue indicate that the constituents of the spliceosome itself are the main targets of alternative splicing suggesting a model where high splice variant diversity is a fundamental feature of the spliceosome.       S94 liver1   isolate:94|dev stage:Adult|sex:missing|tissue:Liver|collection date:missing|geo loc name:Norway|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish liver S94 S94 RNA Seq     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP571287     liver1.R1.fastq.gz liver1.R2.fastq.gz fastq fastq 28602378928.0 94709864.0 liver1.R1.fastq.gz 0:151 1:151 A:7474504321;C:6558758775;G:7262889466;T:7304296884;N:1929482 151 151     7474504321 6558758775 7262889466 7304296884 1929482 SRX28039258 SRS24399982 SRA2095732 NOFIMA|Department of Breeding and Genetics NOFIMA                       B B mate2-mate1 similar by mapping diff illumina novaseq_era unknown poly_a unknown bulk unknown unknown   Norway 2025-03-18 Adult Adult Liver Liver and Biliary System
38360 38360 SRR1791570 SRX866239 SRS837299 SRP053216 PRJNA274605 Danio rerio Transcriptome or Gene expression PRJNA274605 Transcriptome Analysis Groups of adult zebrafish 9 male and 9 female were exposed for 7 days ttwo xxx ng/L 168.7 pmol/L of 17a ethinylestradiol EE2. Transcriptome response of EE2 in zebrafish liver were analysed.     9 female were exposed for 7 days ttwo xxx ng/L 168.7 pmol/L of EE2. Transcriptome response of EE2 in zebrafish liver were analysed.   EE2 exposed Female   breed:zebrafish|age:adult|sex:female|tissue:liver|BioSampleModel:Model organism or animal                 Transcriptome response of EE2 in zebrafish EE2 exposed Female EE2 exposed Female Library Construction: Illumina HiSeq 2000 protolcol. Experimental design: Adult zebrafish and juvenile crucian carp Carassius auratus were bred and maintained in 10 L glass aquaria operating with a 14:10 h light:dark cycle at 23–26°C in the laboratory. Fish were acclimated for 1 week prior to use and fed with Tubifex worms once per day. Groups of adult zebrafish 9 male and 9 female were exposed for 7 days ttwo xxx ng/L 168.7 pmol/L of 17α ethinylestradiol EE2; TCI chemicals Tokyo Japan which had been diluted from a concentrated stock solution solubilized in dimethyl sulfoxide DMSO; Sigma Aldrich St. Louis MO USA. DMSO only was added to the water in control group tanks. Transcriptome response of EE2 in zebrafish liver were analysed.     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>180</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>91</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP053216     Expose_Female_L1_2.fq.gz Expose_Female_L1_1.fq.gz fastq fastq 4988787300.0 27715485.0 EE2 exposed Female 0:90 1:90 A:1328523973;C:1152447608;G:1190548781;T:1317135516;N:131422 90 90     1328523973 1152447608 1190548781 1317135516 131422 SRX866239 SRS837299 SRA236477 Yangtze River Fisheries Research Institute|Fisheries resources and environment Institute of hydrobiology Chinese academy of sciences 2 0.94998 0.94966 0.01842 0.01884 0.88335 0.88657 0.11318 0.11185 90 90 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2016-02-05 Adult Adult Liver Liver and Biliary System
38361 38361 SRR1791573 SRX866243 SRS837302 SRP053216 PRJNA274605 Danio rerio Transcriptome or Gene expression PRJNA274605 Transcriptome Analysis Groups of adult zebrafish 9 male and 9 female were exposed for 7 days ttwo xxx ng/L 168.7 pmol/L of 17a ethinylestradiol EE2. Transcriptome response of EE2 in zebrafish liver were analysed.     Groups of adult zebrafish 9 male were exposed for 7 days to DMSO. Transcriptome response of DMSO in zebrafish liver were analysed.   Control Male   breed:zebrafish|age:adult|sex:male|tissue:Liver|BioSampleModel:Model organism or animal                 Transcriptome response of EE2 in zebrafish Control Male Control Male Library Construction: Illumina HiSeq 2000 protolcol. Experimental design: Adult zebrafish and juvenile crucian carp Carassius auratus were bred and maintained in 10 L glass aquaria operating with a 14:10 h light:dark cycle at 23–26°C in the laboratory. Fish were acclimated for 1 week prior to use and fed with Tubifex worms once per day. Groups of adult zebrafish 9 male and 9 female were exposed for 7 days ttwo xxx ng/L 168.7 pmol/L of 17α ethinylestradiol EE2; TCI chemicals Tokyo Japan which had been diluted from a concentrated stock solution solubilized in dimethyl sulfoxide DMSO; Sigma Aldrich St. Louis MO USA. DMSO only was added to the water in control group tanks. Transcriptome response of EE2 in zebrafish liver were analysed.     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>180</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>91</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP053216     Control_Male_L1_1.fq.gz Control_Male_L1_2.fq.gz fastq fastq 4630623300.0 25725685.0 Control Male 0:90 1:90 A:1239458137;C:1044072167;G:1102275499;T:1244745295;N:72202 90 90     1239458137 1044072167 1102275499 1244745295 72202 SRX866243 SRS837302 SRA236477 Yangtze River Fisheries Research Institute|Fisheries resources and environment Institute of hydrobiology Chinese academy of sciences 2 0.92771 0.92723 0.05741 0.05779 0.80318 0.80574 0.62063 0.61561 90 90 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2016-02-05 Adult Adult Liver Liver and Biliary System
38362 38362 SRR1791572 SRX866242 SRS837301 SRP053216 PRJNA274605 Danio rerio Transcriptome or Gene expression PRJNA274605 Transcriptome Analysis Groups of adult zebrafish 9 male and 9 female were exposed for 7 days ttwo xxx ng/L 168.7 pmol/L of 17a ethinylestradiol EE2. Transcriptome response of EE2 in zebrafish liver were analysed.     Groups of adult zebrafish 9 female were exposed for 7 days to DMSO. Transcriptome response of DMSO in zebrafish liver were analysed.   Control Female   breed:zebrafihs|age:adult|sex:female|tissue:Liver|BioSampleModel:Model organism or animal                 Transcriptome response of EE2 in zebrafish Control Female Control Female Library Construction: Illumina HiSeq 2000 protolcol. Experimental design: Adult zebrafish and juvenile crucian carp Carassius auratus were bred and maintained in 10 L glass aquaria operating with a 14:10 h light:dark cycle at 23–26°C in the laboratory. Fish were acclimated for 1 week prior to use and fed with Tubifex worms once per day. Groups of adult zebrafish 9 male and 9 female were exposed for 7 days ttwo xxx ng/L 168.7 pmol/L of 17α ethinylestradiol EE2; TCI chemicals Tokyo Japan which had been diluted from a concentrated stock solution solubilized in dimethyl sulfoxide DMSO; Sigma Aldrich St. Louis MO USA. DMSO only was added to the water in control group tanks. Transcriptome response of EE2 in zebrafish liver were analysed.     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>180</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>91</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP053216     Control_Female_L1_2.fq.gz Control_Female_L1_1.fq.gz fastq fastq 4616088120.0 25644934.0 Control Female 0:90 1:90 A:1224454560;C:1067759750;G:1107547943;T:1216252836;N:73031 90 90     1224454560 1067759750 1107547943 1216252836 73031 SRX866242 SRS837301 SRA236477 Yangtze River Fisheries Research Institute|Fisheries resources and environment Institute of hydrobiology Chinese academy of sciences 2 0.95027 0.95039 0.02174 0.02234 0.86387 0.86574 0.19491 0.19962 90 90 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2015-02-06 Adult Adult Liver Liver and Biliary System
38363 38363 SRR1791571 SRX866240 SRS837300 SRP053216 PRJNA274605 Danio rerio Transcriptome or Gene expression PRJNA274605 Transcriptome Analysis Groups of adult zebrafish 9 male and 9 female were exposed for 7 days ttwo xxx ng/L 168.7 pmol/L of 17a ethinylestradiol EE2. Transcriptome response of EE2 in zebrafish liver were analysed.     Groups of adult zebrafish 9 male were exposed for 7 days ttwo xxx ng/L 168.7 pmol/L of EE2. Transcriptome response of EE2 in zebrafish liver were analysed.   EE2 exposed Male   breed:zebrafish|age:adult|sex:male|tissue:Liver|BioSampleModel:Model organism or animal                 Transcriptome response of EE2 in zebrafish EE2 exposed Male EE2 exposed Male Library Construction: Illumina HiSeq 2000 protolcol. Experimental design: Adult zebrafish and juvenile crucian carp Carassius auratus were bred and maintained in 10 L glass aquaria operating with a 14:10 h light:dark cycle at 23–26°C in the laboratory. Fish were acclimated for 1 week prior to use and fed with Tubifex worms once per day. Groups of adult zebrafish 9 male and 9 female were exposed for 7 days ttwo xxx ng/L 168.7 pmol/L of 17α ethinylestradiol EE2; TCI chemicals Tokyo Japan which had been diluted from a concentrated stock solution solubilized in dimethyl sulfoxide DMSO; Sigma Aldrich St. Louis MO USA. DMSO only was added to the water in control group tanks. Transcriptome response of EE2 in zebrafish liver were analysed.     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>180</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>91</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP053216     Expose_Male_L1_2.fq.gz Expose_Male_L1_1.fq.gz fastq fastq 4629984300.0 25722135.0 EE2 exposed Male 0:90 1:90 A:1232976082;C:1070850605;G:1104409362;T:1221672015;N:76236 90 90     1232976082 1070850605 1104409362 1221672015 76236 SRX866240 SRS837300 SRA236477 Yangtze River Fisheries Research Institute|Fisheries resources and environment Institute of hydrobiology Chinese academy of sciences 2 0.94664 0.94487 0.02001 0.02006 0.88838 0.89096 0.11737 0.1189 90 90 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2015-02-06 Adult Adult Liver Liver and Biliary System
40709 40709 SRR3420429 SRX1660365 SRS1360335 SRP072296 PRJNA316313 Codon optimality and mRNA decay in zebrafish and Xenopus PRJNA316313 Other Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.         AG01295 liver   strain:TUAB|age:adult|sex:pooled male and female|tissue:Liver|BioSampleModel:Model organism or animal                 AG01295 liver AG01295 liver 1 1     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>75</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP072296     AG01295_SEQ0273_R1.fastq.gz fastq 887443260.0 11676885.0 AG01295 run 1 0:76 A:230924609;C:202487813;G:205378868;T:248612177;N:39793 76       230924609 202487813 205378868 248612177 39793 SRX1660365 SRS1360335 SRA395141 Yale University|Giraldez Lab Yale University 1 0.95421   0.04352   0.84062   0.23556   76   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2016-06-17 Adult Adult Liver Liver and Biliary System
43824 43824 SRR6152619 SRX3264623 SRS2576849 SRP119651 PRJNA413770 Cross generational effects of a marginal 1 C metabolite deficiency PRJNA413770 Other The effect of a deficiency in one carbon 1 C metabolites in the adult generation on DNA methylation and gene expression in adult offspring livers was investigated through the use of high throughput RNA sequencing and reduced representation bisulfite sequencing.Individuals in the F0 generation were either fed a normal diet or one marginally deficient in 1 C metabolites folate vitamins B12 and B6 methionine and choline from larval stages and mated within each diet group. The resulting offspring were fed the control diet throughout their lives and Livers of adult offspring were harvested post 113 dpf and RNA and DNA extracted for RNA sequencing and RRBS.       F1 livers control 1 rna ctl 1   strain:AB strain|isolate:Male fish tank 1|age:113 dpf|dev stage:adult|sex:male|tissue:liver|biomaterial provider:NIFES Kaja Helvik Skjaerven|birth location:NIFES|breeding method:Ref: Skjaerven K. H. et al. Sci Rep 6 34535 doi:10.1038/srep34535 2016|collected by:Kaja Helvik Skjaerven and Anne Catrin Adam|collection date:2013 11 12|health state:Good|BioSampleModel:Model organism or animal                 F1 livers control 1 rna ctl 1 rna ctl 1 Directional sequencing of mRNA fragments     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 2000   SRP119651         1477820550.0 29556411.0 RZY 323.fastq 0:50 A:341022361;C:372071364;G:361979807;T:401982416;N:764602 50       341022361 372071364 361979807 401982416 764602 SRX3264623 SRS2576849 SRA617983 Nord University|FBA Nord University 1 0.88633   0.09624   0.85886   0.58198   50   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Norway 2017-10-10 Adult Adult Liver Liver and Biliary System
43825 43825 SRR6152620 SRX3264622 SRS2576848 SRP119651 PRJNA413770 Cross generational effects of a marginal 1 C metabolite deficiency PRJNA413770 Other The effect of a deficiency in one carbon 1 C metabolites in the adult generation on DNA methylation and gene expression in adult offspring livers was investigated through the use of high throughput RNA sequencing and reduced representation bisulfite sequencing.Individuals in the F0 generation were either fed a normal diet or one marginally deficient in 1 C metabolites folate vitamins B12 and B6 methionine and choline from larval stages and mated within each diet group. The resulting offspring were fed the control diet throughout their lives and Livers of adult offspring were harvested post 113 dpf and RNA and DNA extracted for RNA sequencing and RRBS.       F1 livers control 2 rna ctl 2   strain:AB strain|isolate:Male fish tank 2|age:113 dpf|dev stage:adult|sex:male|tissue:liver|biomaterial provider:NIFES Kaja Helvik Skjaerven|birth location:NIFES|breeding method:Ref: Skjaerven K. H. et al. Sci Rep 6 34535 doi:10.1038/srep34535 2016|collected by:Kaja Helvik Skjaerven and Anne Catrin Adam|collection date:2013 11 12|health state:Good|BioSampleModel:Model organism or animal                 F1 livers control 2 rna ctl 2 rna ctl 2 Directional sequencing of mRNA fragments     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 2000   SRP119651         1267834350.0 25356687.0 RZY 324.fastq 0:50 A:294105777;C:312048823;G:312619877;T:348380931;N:678942 50       294105777 312048823 312619877 348380931 678942 SRX3264622 SRS2576848 SRA617983 Nord University|FBA Nord University 1 0.90606   0.10033   0.83309   0.58402   50   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Norway 2017-10-10 Adult Adult Liver Liver and Biliary System
43826 43826 SRR6152623 SRX3264619 SRS2576845 SRP119651 PRJNA413770 Cross generational effects of a marginal 1 C metabolite deficiency PRJNA413770 Other The effect of a deficiency in one carbon 1 C metabolites in the adult generation on DNA methylation and gene expression in adult offspring livers was investigated through the use of high throughput RNA sequencing and reduced representation bisulfite sequencing.Individuals in the F0 generation were either fed a normal diet or one marginally deficient in 1 C metabolites folate vitamins B12 and B6 methionine and choline from larval stages and mated within each diet group. The resulting offspring were fed the control diet throughout their lives and Livers of adult offspring were harvested post 113 dpf and RNA and DNA extracted for RNA sequencing and RRBS.       F1 livers low 1C 1 rna low 1C 1   strain:AB strain|isolate:Male fish tank 7|age:113 dpf|dev stage:adult|sex:male|tissue:liver|biomaterial provider:NIFES Kaja Helvik Skjaerven|birth location:NIFES|breeding method:Ref: Skjaerven K. H. et al. Sci Rep 6 34535 doi:10.1038/srep34535 2016|collected by:Kaja Helvik Skjaerven and Anne Catrin Adam|collection date:2013 11 12|health state:Good|BioSampleModel:Model organism or animal                 F1 livers low 1C 1 rna low 1C 1 rna low 1C 1 Directional sequencing of mRNA fragments     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 2000   SRP119651         1477820550.0 29556411.0 RZY 319.fastq 0:50 A:341022361;C:372071364;G:361979807;T:401982416;N:764602 50       341022361 372071364 361979807 401982416 764602 SRX3264619 SRS2576845 SRA617983 Nord University|FBA Nord University 1 0.88641   0.09616   0.85882   0.58903   50   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Norway 2017-10-10 Adult Adult Liver Liver and Biliary System
43827 43827 SRR6152624 SRX3264618 SRS2576843 SRP119651 PRJNA413770 Cross generational effects of a marginal 1 C metabolite deficiency PRJNA413770 Other The effect of a deficiency in one carbon 1 C metabolites in the adult generation on DNA methylation and gene expression in adult offspring livers was investigated through the use of high throughput RNA sequencing and reduced representation bisulfite sequencing.Individuals in the F0 generation were either fed a normal diet or one marginally deficient in 1 C metabolites folate vitamins B12 and B6 methionine and choline from larval stages and mated within each diet group. The resulting offspring were fed the control diet throughout their lives and Livers of adult offspring were harvested post 113 dpf and RNA and DNA extracted for RNA sequencing and RRBS.       F1 livers low 1C 2 rna low 1C 2   strain:AB strain|isolate:Male fish tank 8|age:113 dpf|dev stage:adult|sex:male|tissue:liver|biomaterial provider:NIFES Kaja Helvik Skjaerven|birth location:NIFES|breeding method:Ref: Skjaerven K. H. et al. Sci Rep 6 34535 doi:10.1038/srep34535 2016|collected by:Kaja Helvik Skjaerven and Anne Catrin Adam|collection date:2013 11 12|health state:Good|BioSampleModel:Model organism or animal                 F1 livers low 1C 2 rna low 1C 2 rna low 1C 2 Directional sequencing of mRNA fragments     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 2000   SRP119651         1250104800.0 25002096.0 RZY 320.fastq 0:50 A:298225313;C:301950518;G:305099451;T:344161142;N:668376 50       298225313 301950518 305099451 344161142 668376 SRX3264618 SRS2576843 SRA617983 Nord University|FBA Nord University 1 0.88702   0.09849   0.82548   0.57466   50   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Norway 2017-10-10 Adult Adult Liver Liver and Biliary System
43828 43828 SRR6152625 SRX3264617 SRS2576844 SRP119651 PRJNA413770 Cross generational effects of a marginal 1 C metabolite deficiency PRJNA413770 Other The effect of a deficiency in one carbon 1 C metabolites in the adult generation on DNA methylation and gene expression in adult offspring livers was investigated through the use of high throughput RNA sequencing and reduced representation bisulfite sequencing.Individuals in the F0 generation were either fed a normal diet or one marginally deficient in 1 C metabolites folate vitamins B12 and B6 methionine and choline from larval stages and mated within each diet group. The resulting offspring were fed the control diet throughout their lives and Livers of adult offspring were harvested post 113 dpf and RNA and DNA extracted for RNA sequencing and RRBS.       F1 livers control 3 rna ctl 3   strain:AB strain|isolate:Male fish tank 3|age:113 dpf|dev stage:adult|sex:male|tissue:liver|biomaterial provider:NIFES Kaja Helvik Skjaerven|birth location:NIFES|breeding method:Ref: Skjaerven K. H. et al. Sci Rep 6 34535 doi:10.1038/srep34535 2016|collected by:Kaja Helvik Skjaerven and Anne Catrin Adam|collection date:2013 11 12|health state:Good|BioSampleModel:Model organism or animal                 F1 livers control 3 rna ctl 3 rna ctl 3 Directional sequencing of mRNA fragments     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 2000   SRP119651         1375388050.0 27507761.0 RZY 325.fastq 0:50 A:331719333;C:330944665;G:333352358;T:378627997;N:743697 50       331719333 330944665 333352358 378627997 743697 SRX3264617 SRS2576844 SRA617983 Nord University|FBA Nord University 1 0.89565   0.12552   0.83189   0.57988   50   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Norway 2017-10-10 Adult Adult Liver Liver and Biliary System
43829 43829 SRR6152626 SRX3264616 SRS2576842 SRP119651 PRJNA413770 Cross generational effects of a marginal 1 C metabolite deficiency PRJNA413770 Other The effect of a deficiency in one carbon 1 C metabolites in the adult generation on DNA methylation and gene expression in adult offspring livers was investigated through the use of high throughput RNA sequencing and reduced representation bisulfite sequencing.Individuals in the F0 generation were either fed a normal diet or one marginally deficient in 1 C metabolites folate vitamins B12 and B6 methionine and choline from larval stages and mated within each diet group. The resulting offspring were fed the control diet throughout their lives and Livers of adult offspring were harvested post 113 dpf and RNA and DNA extracted for RNA sequencing and RRBS.       F1 livers control 4 rna ctl 4   strain:AB strain|isolate:Male fish tank 4|age:113 dpf|dev stage:adult|sex:male|tissue:liver|biomaterial provider:NIFES Kaja Helvik Skjaerven|birth location:NIFES|breeding method:Ref: Skjaerven K. H. et al. Sci Rep 6 34535 doi:10.1038/srep34535 2016|collected by:Kaja Helvik Skjaerven and Anne Catrin Adam|collection date:2013 11 12|health state:Good|BioSampleModel:Model organism or animal                 F1 livers control 4 rna ctl 4 rna ctl 4 Directional sequencing of mRNA fragments     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 2000   SRP119651         1433558100.0 28671162.0 RZY 326.fastq 0:50 A:340242659;C:350821208;G:346146280;T:395614030;N:733923 50       340242659 350821208 346146280 395614030 733923 SRX3264616 SRS2576842 SRA617983 Nord University|FBA Nord University 1 0.90327   0.11496   0.82335   0.57528   50   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Norway 2017-10-10 Adult Adult Liver Liver and Biliary System
43830 43830 SRR6152627 SRX3264615 SRS2576841 SRP119651 PRJNA413770 Cross generational effects of a marginal 1 C metabolite deficiency PRJNA413770 Other The effect of a deficiency in one carbon 1 C metabolites in the adult generation on DNA methylation and gene expression in adult offspring livers was investigated through the use of high throughput RNA sequencing and reduced representation bisulfite sequencing.Individuals in the F0 generation were either fed a normal diet or one marginally deficient in 1 C metabolites folate vitamins B12 and B6 methionine and choline from larval stages and mated within each diet group. The resulting offspring were fed the control diet throughout their lives and Livers of adult offspring were harvested post 113 dpf and RNA and DNA extracted for RNA sequencing and RRBS.       F1 livers low 1C 3 rna low 1C 3   strain:AB strain|isolate:Male fish tank 9|age:113 dpf|dev stage:adult|sex:male|tissue:liver|biomaterial provider:NIFES Kaja Helvik Skjaerven|birth location:NIFES|breeding method:Ref: Skjaerven K. H. et al. Sci Rep 6 34535 doi:10.1038/srep34535 2016|collected by:Kaja Helvik Skjaerven and Anne Catrin Adam|collection date:2013 11 12|health state:Good|BioSampleModel:Model organism or animal                 F1 livers low 1C 3 rna low 1C 3 rna low 1C 3 Directional sequencing of mRNA fragments     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 2000   SRP119651         1453888750.0 29077775.0 RZY 321.fastq 0:50 A:335835385;C:357658223;G:359480232;T:400135740;N:779170 50       335835385 357658223 359480232 400135740 779170 SRX3264615 SRS2576841 SRA617983 Nord University|FBA Nord University 1 0.89454   0.08578   0.84009   0.584   50   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Norway 2017-10-10 Adult Adult Liver Liver and Biliary System
43831 43831 SRR6152628 SRX3264614 SRS2576840 SRP119651 PRJNA413770 Cross generational effects of a marginal 1 C metabolite deficiency PRJNA413770 Other The effect of a deficiency in one carbon 1 C metabolites in the adult generation on DNA methylation and gene expression in adult offspring livers was investigated through the use of high throughput RNA sequencing and reduced representation bisulfite sequencing.Individuals in the F0 generation were either fed a normal diet or one marginally deficient in 1 C metabolites folate vitamins B12 and B6 methionine and choline from larval stages and mated within each diet group. The resulting offspring were fed the control diet throughout their lives and Livers of adult offspring were harvested post 113 dpf and RNA and DNA extracted for RNA sequencing and RRBS.       F1 livers low 1C 4 rna low 1C 4   strain:AB strain|isolate:Male fish tank 10|age:113 dpf|dev stage:adult|sex:male|tissue:liver|biomaterial provider:NIFES Kaja Helvik Skjaerven|birth location:NIFES|breeding method:Ref: Skjaerven K. H. et al. Sci Rep 6 34535 doi:10.1038/srep34535 2016|collected by:Kaja Helvik Skjaerven and Anne Catrin Adam|collection date:2013 11 12|health state:Good|BioSampleModel:Model organism or animal                 F1 livers low 1C 4 rna low 1C 4 rna low 1C 4 Directional sequencing of mRNA fragments     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 2000   SRP119651         1336779650.0 26735593.0 RZY 322.fastq 0:50 A:310390083;C:329159312;G:327197131;T:369319794;N:713330 50       310390083 329159312 327197131 369319794 713330 SRX3264614 SRS2576840 SRA617983 Nord University|FBA Nord University 1 0.91491   0.10744   0.81773   0.57357   50   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Norway 2017-10-10 Adult Adult Liver Liver and Biliary System
63821 63821 SRR14075695 SRX10449991 SRS8581367 SRP312266 PRJNA717374 TBBPA and BPA in zebrafish liver PRJNA717374 Other         10 T5002   strain:AB|isolate:10|ecotype:China|age:5 months|sex:male|tissue:liver|BioSampleModel:Model organism or animal                 zebrafish liver 19 19 paired end 150 bp sequencing strategy PE168 on Illumina sequencing platform     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2000   SRP312266     T5002_R1.fq.gz T5002_R2.fq.gz fastq fastq 7182190800.0 23940636.0 T5002 R1.fq.gz 0:150 1:150 A:1926957044;C:1644662133;G:1702083526;T:1908468526;N:19571 150 150     1926957044 1644662133 1702083526 1908468526 19571 SRX10449991 SRS8581367 SRA1210832 China Agricultural University|Science China Agricultural University 2 0.94109 0.93953 0.03638 0.0361 0.78039 0.78064 0.359 0.3582 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2021-03-26 Adult Adult Liver Liver and Biliary System
63822 63822 SRR14075696 SRX10449990 SRS8581366 SRP312266 PRJNA717374 TBBPA and BPA in zebrafish liver PRJNA717374 Other         9 T5001   strain:AB|isolate:9|ecotype:China|age:5 months|sex:male|tissue:liver|BioSampleModel:Model organism or animal                 zebrafish liver 17 17 paired end 150 bp sequencing strategy PE166 on Illumina sequencing platform     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2000   SRP312266     T5001_R1.fq.gz T5001_R2.fq.gz fastq fastq 7559023200.0 25196744.0 T5001 R1.fq.gz 0:150 1:150 A:2012816619;C:1746396782;G:1805351517;T:1994436007;N:22275 150 150     2012816619 1746396782 1805351517 1994436007 22275 SRX10449990 SRS8581366 SRA1210832 China Agricultural University|Science China Agricultural University 2 0.93997 0.93942 0.0484 0.04841 0.81322 0.81316 0.44088 0.43338 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2021-03-26 Adult Adult Liver Liver and Biliary System
63823 63823 SRR14075697 SRX10449989 SRS8581365 SRP312266 PRJNA717374 TBBPA and BPA in zebrafish liver PRJNA717374 Other         8 B5004   strain:AB|isolate:8|ecotype:China|age:5 months|sex:male|tissue:liver|BioSampleModel:Model organism or animal                 zebrafish liver 15 15 paired end 150 bp sequencing strategy PE164 on Illumina sequencing platform     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2000   SRP312266     B5004_R1.fq.gz B5004_R2.fq.gz fastq fastq 7425571500.0 24751905.0 B5004 R1.fq.gz 0:150 1:150 A:2019517882;C:1666984264;G:1758468016;T:1980578552;N:22786 150 150     2019517882 1666984264 1758468016 1980578552 22786 SRX10449989 SRS8581365 SRA1210832 China Agricultural University|Science China Agricultural University 2 0.94186 0.93931 0.03821 0.03767 0.77266 0.77331 0.41877 0.42762 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2021-03-26 Adult Adult Liver Liver and Biliary System
63824 63824 SRR14075698 SRX10449988 SRS8581364 SRP312266 PRJNA717374 TBBPA and BPA in zebrafish liver PRJNA717374 Other         7 B5003   strain:AB|isolate:7|ecotype:China|age:5 months|sex:male|tissue:liver|BioSampleModel:Model organism or animal                 zebrafish liver 13 13 paired end 150 bp sequencing strategy PE162 on Illumina sequencing platform     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2000   SRP312266     B5003_R1.fq.gz B5003_R2.fq.gz fastq fastq 7374404100.0 24581347.0 B5003 R1.fq.gz 0:150 1:150 A:1899614476;C:1736676478;G:1878418205;T:1859673053;N:21888 150 150     1899614476 1736676478 1878418205 1859673053 21888 SRX10449988 SRS8581364 SRA1210832 China Agricultural University|Science China Agricultural University 2 0.95308 0.95248 0.08134 0.08066 0.80351 0.80517 0.66972 0.66984 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2021-03-26 Adult Adult Liver Liver and Biliary System
63825 63825 SRR14075699 SRX10449987 SRS8581363 SRP312266 PRJNA717374 TBBPA and BPA in zebrafish liver PRJNA717374 Other         6 B5002   strain:AB|isolate:6|ecotype:China|age:5 months|sex:male|tissue:liver|BioSampleModel:Model organism or animal                 zebrafish liver 11 11 paired end 150 bp sequencing strategy PE160 on Illumina sequencing platform     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2000   SRP312266     B5002_R1.fq.gz B5002_R2.fq.gz fastq fastq 7113584400.0 23711948.0 B5002 R1.fq.gz 0:150 1:150 A:1938775036;C:1582561544;G:1692583448;T:1899643206;N:21166 150 150     1938775036 1582561544 1692583448 1899643206 21166 SRX10449987 SRS8581363 SRA1210832 China Agricultural University|Science China Agricultural University 2 0.94948 0.91723 0.04562 0.04356 0.77177 0.77565 0.58354 0.59857 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2021-03-26 Adult Adult Liver Liver and Biliary System
63826 63826 SRR14075700 SRX10449986 SRS8581361 SRP312266 PRJNA717374 TBBPA and BPA in zebrafish liver PRJNA717374 Other         5 B5001   strain:AB|isolate:5|ecotype:China|age:5 months|sex:male|tissue:liver|BioSampleModel:Model organism or animal                 zebrafish liver 9 9 paired end 150 bp sequencing strategy PE158 on Illumina sequencing platform     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2000   SRP312266     B5001_R1.fq.gz B5001_R2.fq.gz fastq fastq 7543863300.0 25146211.0 B5001 R1.fq.gz 0:150 1:150 A:2056584280;C:1680753330;G:1794647709;T:2011855925;N:22056 150 150     2056584280 1680753330 1794647709 2011855925 22056 SRX10449986 SRS8581361 SRA1210832 China Agricultural University|Science China Agricultural University 2 0.91263 0.95048 0.03837 0.03928 0.78524 0.78514 0.45938 0.46 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2021-03-26 Adult Adult Liver Liver and Biliary System
63827 63827 SRR14075701 SRX10449985 SRS8581360 SRP312266 PRJNA717374 TBBPA and BPA in zebrafish liver PRJNA717374 Other         4 CK4   strain:AB|isolate:4|ecotype:China|age:5 months|sex:male|tissue:liver|BioSampleModel:Model organism or animal                 zebrafish liver 7 7 paired end 150 bp sequencing strategy PE156 on Illumina sequencing platform     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2000   SRP312266     CK4_R1.fq.gz CK4_R2.fq.gz fastq fastq 6750095700.0 22500319.0 CK4 R1.fq.gz 0:150 1:150 A:1792406362;C:1558261336;G:1621333697;T:1778074458;N:19847 150 150     1792406362 1558261336 1621333697 1778074458 19847 SRX10449985 SRS8581360 SRA1210832 China Agricultural University|Science China Agricultural University 2 0.93923 0.93732 0.05139 0.05074 0.81156 0.81306 0.43829 0.44367 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2021-03-26 Adult Adult Liver Liver and Biliary System
63828 63828 SRR14075702 SRX10449984 SRS8581359 SRP312266 PRJNA717374 TBBPA and BPA in zebrafish liver PRJNA717374 Other         3 CK3   strain:AB|isolate:3|ecotype:China|age:5 months|sex:male|tissue:liver|BioSampleModel:Model organism or animal                 zebrafish liver 5 5 paired end 150 bp sequencing strategy PE154 on Illumina sequencing platform     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2000   SRP312266     CK3_R1.fq.gz CK3_R2.fq.gz fastq fastq 7319041800.0 24396806.0 CK3 R1.fq.gz 0:150 1:150 A:1968208626;C:1663075891;G:1745039198;T:1942696410;N:21675 150 150     1968208626 1663075891 1745039198 1942696410 21675 SRX10449984 SRS8581359 SRA1210832 China Agricultural University|Science China Agricultural University 2 0.92912 0.92666 0.0568 0.05694 0.76189 0.76303 0.49038 0.49002 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2021-03-26 Adult Adult Liver Liver and Biliary System
63829 63829 SRR14075703 SRX10449983 SRS8581358 SRP312266 PRJNA717374 TBBPA and BPA in zebrafish liver PRJNA717374 Other         12 T5004   strain:AB|isolate:12|ecotype:China|age:5 months|sex:male|tissue:liver|BioSampleModel:Model organism or animal                 zebrafish liver 23 23 paired end 150 bp sequencing strategy PE172 on Illumina sequencing platform     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2000   SRP312266     T5004_R1.fq.gz T5004_R2.fq.gz fastq fastq 7204351200.0 24014504.0 T5004 R1.fq.gz 0:150 1:150 A:1968101800;C:1609306677;G:1681354261;T:1945567211;N:21251 150 150     1968101800 1609306677 1681354261 1945567211 21251 SRX10449983 SRS8581358 SRA1210832 China Agricultural University|Science China Agricultural University 2 0.93519 0.93443 0.06275 0.06279 0.79719 0.79904 0.37514 0.37575 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2021-03-26 Adult Adult Liver Liver and Biliary System
63830 63830 SRR14075704 SRX10449982 SRS8581357 SRP312266 PRJNA717374 TBBPA and BPA in zebrafish liver PRJNA717374 Other         11 T5003   strain:AB|isolate:11|ecotype:China|age:5 months|sex:male|tissue:liver|BioSampleModel:Model organism or animal                 zebrafish liver 21 21 paired end 150 bp sequencing strategy PE170 on Illumina sequencing platform     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2000   SRP312266     T5003_R1.fq.gz T5003_R2.fq.gz fastq fastq 7289788200.0 24299294.0 T5003 R1.fq.gz 0:150 1:150 A:1967144656;C:1653336932;G:1740636597;T:1928648641;N:21374 150 150     1967144656 1653336932 1740636597 1928648641 21374 SRX10449982 SRS8581357 SRA1210832 China Agricultural University|Science China Agricultural University 2 0.9404 0.94062 0.08176 0.08109 0.78058 0.78263 0.52125 0.51873 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2021-03-26 Adult Adult Liver Liver and Biliary System
63831 63831 SRR14075705 SRX10449981 SRS8581362 SRP312266 PRJNA717374 TBBPA and BPA in zebrafish liver PRJNA717374 Other         2 CK2   strain:AB|isolate:2|ecotype:China|age:5 months|sex:male|tissue:liver|BioSampleModel:Model organism or animal                 zebrafish liver 3 3 paired end 150 bp sequencing strategy PE152 on Illumina sequencing platform     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2000   SRP312266     CK2_R1.fq.gz CK2_R2.fq.gz fastq fastq 6645681000.0 22152270.0 CK2 R1.fq.gz 0:150 1:150 A:1796375985;C:1501679668;G:1569660812;T:1777944318;N:20217 150 150     1796375985 1501679668 1569660812 1777944318 20217 SRX10449981 SRS8581362 SRA1210832 China Agricultural University|Science China Agricultural University 2 0.92626 0.92481 0.05736 0.05778 0.78062 0.78088 0.45165 0.45172 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2021-03-26 Adult Adult Liver Liver and Biliary System
63832 63832 SRR14075706 SRX10449980 SRS8581356 SRP312266 PRJNA717374 TBBPA and BPA in zebrafish liver PRJNA717374 Other         1 CK1   strain:AB|isolate:1|ecotype:China|age:5 months|sex:male|tissue:liver|BioSampleModel:Model organism or animal                 zebrafish liver 1 1 paired end 150 bp sequencing strategy PE150 on Illumina sequencing platform     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2000   SRP312266     CK1_R1.fq.gz CK1_R2.fq.gz fastq fastq 6565856400.0 21886188.0 CK1 R1.fq.gz 0:150 1:150 A:1772868328;C:1492177204;G:1560207661;T:1740583511;N:19696 150 150     1772868328 1492177204 1560207661 1740583511 19696 SRX10449980 SRS8581356 SRA1210832 China Agricultural University|Science China Agricultural University 2 0.93201 0.93139 0.07051 0.06893 0.76027 0.76094 0.46903 0.46132 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2021-03-26 Adult Adult Liver Liver and Biliary System
68336 68336 SRR17714679 SRX13877730 SRS11747904 SRP356388 PRJNA799842 RNA seq of CRISPR/Cas9 mediated genome editing zebrafishes; the alligator pipefish spleen and the small white organ of the lined seahorse. PRJNA799842 Other To explore the function of the gene in spleen development we generated a knockout zebrafish line. To investigate whether the phenotypic consequences in the seahorses were caused by a missense mutation in this gene we generated a point mutation zebrafish line by CRISPR/Cas9 mediated homologous recombination HR. RNA seq of these samples tissues brain liver kidney and intestine were analyzed. In addition to clarify the splenic phenotype of the Syngnathidaes the transcriptomic profiles of the S. biaculeatus spleens and the H. erectus small white organ were also sampled and sequenced.         WT li 4   strain:AB type|isolate:wild type|breed:WT li 4|age:3 month|dev stage:NA|sex:NA|tissue:liver|BioSampleModel:Model organism or animal                 RNA seq of zebrafish WT li 4 WT li 4 RNA seq     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2500   SRP356388   loader:fastq load.py Daniorerio_WT-li-4_good_1.fq.gz Daniorerio_WT-li-4_good_2.fq.gz fastq fastq 6430134868.0 21486047.0 Daniorerio WT li 4 good 1.fq.gz 0:149.64 1:149.64 A:1680825158;C:1514161489;G:1548997244;T:1685824955;N:326022 149 149     1680825158 1514161489 1548997244 1685824955 326022 SRX13877730 SRS11747904 SRA1360632 South China Sea Institute of Oceanology|CAS Key Laboratory of Tropical Marine Bio-Resource South China Sea Institute of Oceanology 2 0.9611 0.95868 0.03418 0.03413 0.83759 0.83725 0.32633 0.32384 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2022-01-27 Adult Adult Liver Liver and Biliary System
68337 68337 SRR17714680 SRX13877729 SRS11747902 SRP356388 PRJNA799842 RNA seq of CRISPR/Cas9 mediated genome editing zebrafishes; the alligator pipefish spleen and the small white organ of the lined seahorse. PRJNA799842 Other To explore the function of the gene in spleen development we generated a knockout zebrafish line. To investigate whether the phenotypic consequences in the seahorses were caused by a missense mutation in this gene we generated a point mutation zebrafish line by CRISPR/Cas9 mediated homologous recombination HR. RNA seq of these samples tissues brain liver kidney and intestine were analyzed. In addition to clarify the splenic phenotype of the Syngnathidaes the transcriptomic profiles of the S. biaculeatus spleens and the H. erectus small white organ were also sampled and sequenced.         WT li 3   strain:AB type|isolate:wild type|breed:WT li 3|age:3 month|dev stage:NA|sex:NA|tissue:liver|BioSampleModel:Model organism or animal                 RNA seq of zebrafish WT li 3 WT li 3 RNA seq     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2500   SRP356388   loader:fastq load.py Daniorerio_WT-li-3_good_1.fq.gz Daniorerio_WT-li-3_good_2.fq.gz fastq fastq 5906881770.0 19720245.0 Daniorerio WT li 3 good 1.fq.gz 0:149.77 1:149.77 A:1597082554;C:1335335327;G:1375451240;T:1598710937;N:301712 149 149     1597082554 1335335327 1375451240 1598710937 301712 SRX13877729 SRS11747902 SRA1360632 South China Sea Institute of Oceanology|CAS Key Laboratory of Tropical Marine Bio-Resource South China Sea Institute of Oceanology 2 0.9081 0.90685 0.06939 0.06922 0.80633 0.80736 0.57398 0.56534 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2022-01-27 Adult Adult 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");;