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 30650,SRR28054745,SRX23704460,SRS20534455,SRP491086,PRJNA1078753,Integrated mRNA and miRNA sequencing analyses unveil the underlying mechanism of tobacco pollutant induced developmental toxicity in zebrafish embryos,PRJNA1078753,Other,Tobacco pollutants are prevalent in the environment leading to inadvertent exposure of pregnant females. Studies of these pollutants' toxic effects on development have not fully elucidated the potential underlying mechanisms. Therefore in this study we aim at investigate the developmental toxicity induced by cigarette smoke extract CSE at concentrations of 0.25% 1% and 2.5% using a zebrafish embryo toxicity test and integrated transcriptomic analysis of microRNA miRNA and messenger RNA mRNA. The findings revealed that CSE caused developmental toxicity including increased mortality and decreased incubation rate in a dose dependent manner. Moreover CSE induced malformations and apoptosis specifically in the head and heart of zebrafish larvae. We used mRNA and miRNA sequencing analyses to compare changes in the expression of genes and miRNAs in zebrafish larvae. The bioinformatics analysis indicates that the mechanism underlying CSE induced developmental toxicity was associated with genetic repair impairment apoptosis disorder and lipid metabolism disturbance. The enrichment analysis and RT qPCR show that the ctsba gene plays a crucial function in embryo developmental apoptosis and the fads2 gene mainly regulates lipid metabolic toxicity. The results of this study improve the understanding of CSE induced developmental toxicity in zebrafish embryos and contribute insights into the formulation of novel preventive strategies against tobacco pollutants during early embryonic development.,,,,,S21K1228,,library ID:H 1|title:High 1|library strategy:OTHER|library source:METATRANSCRIPTIOMIC|library selection:other|library layout:paired|platform:ILLUMINA|instrument model:RNA seq|filetype:fastq|filename:S21K1228 rep1 1 URNA S72 L003 R1 001.fastq|filename2:S21K1228 rep1 1 URNA S72 L003 R2 001.fastq|host:missing|isolation source:missing|collection date:missing|geographic location:missing|latitude and longitude:missing|age:missing|breed:missing|cultivar:missing|dev stage:missing|ecotype:missing|isolate:missing|sex:missing|strain:missing|tissue:missing|BioSampleModel:Model organism or animal,,,,,,,,,High 1,H 1,H 1,missing,,,RNA-Seq,METATRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP491086,,,S21K1228_rep1_1_URNA_S72_L003_R1_001.fastq.gz S21K1228_rep1_1_URNA_S72_L003_R2_001.fastq.gz,fastq fastq,6506930400.0,21689768.0,S21K1228 rep1 1 URNA S72 L003 R1 001.fastq.gz,0:150 1:150,A:1750770382;C:1473474222;G:1551729505;T:1730941027;N:15264,150,150,,,1750770382,1473474222,1551729505,1730941027,15264,SRX23704460,SRS20534455,SRA1806456,The Second Affiliated Hospital of Shantou University Medical College|Department of Burns and Plastic Surgery,The Second Affiliated Hospital of Shantou University Medical College,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,China,2024-02-22,Undetermined,Multi-stage,Undetermined,Undetermined 30651,SRR28054746,SRX23704459,SRS20534452,SRP491086,PRJNA1078753,Integrated mRNA and miRNA sequencing analyses unveil the underlying mechanism of tobacco pollutant induced developmental toxicity in zebrafish embryos,PRJNA1078753,Other,Tobacco pollutants are prevalent in the environment leading to inadvertent exposure of pregnant females. Studies of these pollutants' toxic effects on development have not fully elucidated the potential underlying mechanisms. Therefore in this study we aim at investigate the developmental toxicity induced by cigarette smoke extract CSE at concentrations of 0.25% 1% and 2.5% using a zebrafish embryo toxicity test and integrated transcriptomic analysis of microRNA miRNA and messenger RNA mRNA. The findings revealed that CSE caused developmental toxicity including increased mortality and decreased incubation rate in a dose dependent manner. Moreover CSE induced malformations and apoptosis specifically in the head and heart of zebrafish larvae. We used mRNA and miRNA sequencing analyses to compare changes in the expression of genes and miRNAs in zebrafish larvae. The bioinformatics analysis indicates that the mechanism underlying CSE induced developmental toxicity was associated with genetic repair impairment apoptosis disorder and lipid metabolism disturbance. The enrichment analysis and RT qPCR show that the ctsba gene plays a crucial function in embryo developmental apoptosis and the fads2 gene mainly regulates lipid metabolic toxicity. The results of this study improve the understanding of CSE induced developmental toxicity in zebrafish embryos and contribute insights into the formulation of novel preventive strategies against tobacco pollutants during early embryonic development.,,,,,S21K1227,,library ID:M 3|title:Medium 3|library strategy:OTHER|library source:METATRANSCRIPTIOMIC|library selection:other|library layout:paired|platform:ILLUMINA|instrument model:RNA seq|filetype:fastq|filename:S21K1227 rep1 1 URNA S71 L003 R1 001.fastq|filename2:S21K1227 rep1 1 URNA S71 L003 R2 001.fastq|host:missing|isolation source:missing|collection date:missing|geographic location:missing|latitude and longitude:missing|age:missing|breed:missing|cultivar:missing|dev stage:missing|ecotype:missing|isolate:missing|sex:missing|strain:missing|tissue:missing|BioSampleModel:Model organism or animal,,,,,,,,,Medium 3,M 3,M 3,missing,,,RNA-Seq,METATRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP491086,,,S21K1227_rep1_1_URNA_S71_L003_R1_001.fastq.gz S21K1227_rep1_1_URNA_S71_L003_R2_001.fastq.gz,fastq fastq,6899268300.0,22997561.0,S21K1227 rep1 1 URNA S71 L003 R1 001.fastq.gz,0:150 1:150,A:1858425383;C:1565856426;G:1639602501;T:1835367744;N:16246,150,150,,,1858425383,1565856426,1639602501,1835367744,16246,SRX23704459,SRS20534452,SRA1806456,The Second Affiliated Hospital of Shantou University Medical College|Department of Burns and Plastic Surgery,The Second Affiliated Hospital of Shantou University Medical College,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,China,2024-02-22,Undetermined,Multi-stage,Undetermined,Undetermined 30652,SRR28054747,SRX23704458,SRS20534453,SRP491086,PRJNA1078753,Integrated mRNA and miRNA sequencing analyses unveil the underlying mechanism of tobacco pollutant induced developmental toxicity in zebrafish embryos,PRJNA1078753,Other,Tobacco pollutants are prevalent in the environment leading to inadvertent exposure of pregnant females. Studies of these pollutants' toxic effects on development have not fully elucidated the potential underlying mechanisms. Therefore in this study we aim at investigate the developmental toxicity induced by cigarette smoke extract CSE at concentrations of 0.25% 1% and 2.5% using a zebrafish embryo toxicity test and integrated transcriptomic analysis of microRNA miRNA and messenger RNA mRNA. The findings revealed that CSE caused developmental toxicity including increased mortality and decreased incubation rate in a dose dependent manner. Moreover CSE induced malformations and apoptosis specifically in the head and heart of zebrafish larvae. We used mRNA and miRNA sequencing analyses to compare changes in the expression of genes and miRNAs in zebrafish larvae. The bioinformatics analysis indicates that the mechanism underlying CSE induced developmental toxicity was associated with genetic repair impairment apoptosis disorder and lipid metabolism disturbance. The enrichment analysis and RT qPCR show that the ctsba gene plays a crucial function in embryo developmental apoptosis and the fads2 gene mainly regulates lipid metabolic toxicity. The results of this study improve the understanding of CSE induced developmental toxicity in zebrafish embryos and contribute insights into the formulation of novel preventive strategies against tobacco pollutants during early embryonic development.,,,,,S21K1226,,library ID:M 2|title:Medium 2|library strategy:OTHER|library source:METATRANSCRIPTIOMIC|library selection:other|library layout:paired|platform:ILLUMINA|instrument model:RNA seq|filetype:fastq|filename:S21K1226 rep1 1 URNA S70 L003 R1 001.fastq|filename2:S21K1226 rep1 1 URNA S70 L003 R2 001.fastq|host:missing|isolation source:missing|collection date:missing|geographic location:missing|latitude and longitude:missing|age:missing|breed:missing|cultivar:missing|dev stage:missing|ecotype:missing|isolate:missing|sex:missing|strain:missing|tissue:missing|BioSampleModel:Model organism or animal,,,,,,,,,Medium 2,M 2,M 2,missing,,,RNA-Seq,METATRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP491086,,,S21K1226_rep1_1_URNA_S70_L003_R1_001.fastq.gz S21K1226_rep1_1_URNA_S70_L003_R2_001.fastq.gz,fastq fastq,6310969500.0,21036565.0,S21K1226 rep1 1 URNA S70 L003 R1 001.fastq.gz,0:150 1:150,A:1688391347;C:1451351943;G:1503321023;T:1667755412;N:149775,150,150,,,1688391347,1451351943,1503321023,1667755412,149775,SRX23704458,SRS20534453,SRA1806456,The Second Affiliated Hospital of Shantou University Medical College|Department of Burns and Plastic Surgery,The Second Affiliated Hospital of Shantou University Medical College,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,China,2024-02-22,Undetermined,Multi-stage,Undetermined,Undetermined 30653,SRR28054748,SRX23704457,SRS20534454,SRP491086,PRJNA1078753,Integrated mRNA and miRNA sequencing analyses unveil the underlying mechanism of tobacco pollutant induced developmental toxicity in zebrafish embryos,PRJNA1078753,Other,Tobacco pollutants are prevalent in the environment leading to inadvertent exposure of pregnant females. Studies of these pollutants' toxic effects on development have not fully elucidated the potential underlying mechanisms. Therefore in this study we aim at investigate the developmental toxicity induced by cigarette smoke extract CSE at concentrations of 0.25% 1% and 2.5% using a zebrafish embryo toxicity test and integrated transcriptomic analysis of microRNA miRNA and messenger RNA mRNA. The findings revealed that CSE caused developmental toxicity including increased mortality and decreased incubation rate in a dose dependent manner. Moreover CSE induced malformations and apoptosis specifically in the head and heart of zebrafish larvae. We used mRNA and miRNA sequencing analyses to compare changes in the expression of genes and miRNAs in zebrafish larvae. The bioinformatics analysis indicates that the mechanism underlying CSE induced developmental toxicity was associated with genetic repair impairment apoptosis disorder and lipid metabolism disturbance. The enrichment analysis and RT qPCR show that the ctsba gene plays a crucial function in embryo developmental apoptosis and the fads2 gene mainly regulates lipid metabolic toxicity. The results of this study improve the understanding of CSE induced developmental toxicity in zebrafish embryos and contribute insights into the formulation of novel preventive strategies against tobacco pollutants during early embryonic development.,,,,,S21K1225,,library ID:M 1|title:Medium 1|library strategy:OTHER|library source:METATRANSCRIPTIOMIC|library selection:other|library layout:paired|platform:ILLUMINA|instrument model:RNA seq|filetype:fastq|filename:S21K1225 rep1 1 URNA S69 L003 R1 001.fastq|filename2:S21K1225 rep1 1 URNA S69 L003 R2 001.fastq|host:missing|isolation source:missing|collection date:missing|geographic location:missing|latitude and longitude:missing|age:missing|breed:missing|cultivar:missing|dev stage:missing|ecotype:missing|isolate:missing|sex:missing|strain:missing|tissue:missing|BioSampleModel:Model organism or animal,,,,,,,,,Medium 1,M 1,M 1,missing,,,RNA-Seq,METATRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP491086,,,S21K1225_rep1_1_URNA_S69_L003_R1_001.fastq.gz S21K1225_rep1_1_URNA_S69_L003_R2_001.fastq.gz,fastq fastq,8677007700.0,28923359.0,S21K1225 rep1 1 URNA S69 L003 R1 001.fastq.gz,0:150 1:150,A:2318840740;C:1999375306;G:2068690840;T:2290080340;N:20474,150,150,,,2318840740,1999375306,2068690840,2290080340,20474,SRX23704457,SRS20534454,SRA1806456,The Second Affiliated Hospital of Shantou University Medical College|Department of Burns and Plastic Surgery,The Second Affiliated Hospital of Shantou University Medical College,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,China,2024-02-22,Undetermined,Multi-stage,Undetermined,Undetermined 30654,SRR28054749,SRX23704456,SRS20534450,SRP491086,PRJNA1078753,Integrated mRNA and miRNA sequencing analyses unveil the underlying mechanism of tobacco pollutant induced developmental toxicity in zebrafish embryos,PRJNA1078753,Other,Tobacco pollutants are prevalent in the environment leading to inadvertent exposure of pregnant females. Studies of these pollutants' toxic effects on development have not fully elucidated the potential underlying mechanisms. Therefore in this study we aim at investigate the developmental toxicity induced by cigarette smoke extract CSE at concentrations of 0.25% 1% and 2.5% using a zebrafish embryo toxicity test and integrated transcriptomic analysis of microRNA miRNA and messenger RNA mRNA. The findings revealed that CSE caused developmental toxicity including increased mortality and decreased incubation rate in a dose dependent manner. Moreover CSE induced malformations and apoptosis specifically in the head and heart of zebrafish larvae. We used mRNA and miRNA sequencing analyses to compare changes in the expression of genes and miRNAs in zebrafish larvae. The bioinformatics analysis indicates that the mechanism underlying CSE induced developmental toxicity was associated with genetic repair impairment apoptosis disorder and lipid metabolism disturbance. The enrichment analysis and RT qPCR show that the ctsba gene plays a crucial function in embryo developmental apoptosis and the fads2 gene mainly regulates lipid metabolic toxicity. The results of this study improve the understanding of CSE induced developmental toxicity in zebrafish embryos and contribute insights into the formulation of novel preventive strategies against tobacco pollutants during early embryonic development.,,,,,S21K1224,,library ID:L 3|title:Low 3|library strategy:OTHER|library source:METATRANSCRIPTIOMIC|library selection:other|library layout:paired|platform:ILLUMINA|instrument model:RNA seq|filetype:fastq|filename:S21K1224 rep1 1 URNA S68 L003 R1 001.fastq|filename2:S21K1224 rep1 1 URNA S68 L003 R2 001.fastq|host:missing|isolation source:missing|collection date:missing|geographic location:missing|latitude and longitude:missing|age:missing|breed:missing|cultivar:missing|dev stage:missing|ecotype:missing|isolate:missing|sex:missing|strain:missing|tissue:missing|BioSampleModel:Model organism or animal,,,,,,,,,Low 3,L 3,L 3,missing,,,RNA-Seq,METATRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP491086,,,S21K1224_rep1_1_URNA_S68_L003_R1_001.fastq.gz S21K1224_rep1_1_URNA_S68_L003_R2_001.fastq.gz,fastq fastq,7160279400.0,23867598.0,S21K1224 rep1 1 URNA S68 L003 R1 001.fastq.gz,0:150 1:150,A:1893984011;C:1641393143;G:1753657602;T:1871228004;N:16640,150,150,,,1893984011,1641393143,1753657602,1871228004,16640,SRX23704456,SRS20534450,SRA1806456,The Second Affiliated Hospital of Shantou University Medical College|Department of Burns and Plastic Surgery,The Second Affiliated Hospital of Shantou University Medical College,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,China,2024-02-22,Undetermined,Multi-stage,Undetermined,Undetermined 30655,SRR28054750,SRX23704455,SRS20534451,SRP491086,PRJNA1078753,Integrated mRNA and miRNA sequencing analyses unveil the underlying mechanism of tobacco pollutant induced developmental toxicity in zebrafish embryos,PRJNA1078753,Other,Tobacco pollutants are prevalent in the environment leading to inadvertent exposure of pregnant females. Studies of these pollutants' toxic effects on development have not fully elucidated the potential underlying mechanisms. Therefore in this study we aim at investigate the developmental toxicity induced by cigarette smoke extract CSE at concentrations of 0.25% 1% and 2.5% using a zebrafish embryo toxicity test and integrated transcriptomic analysis of microRNA miRNA and messenger RNA mRNA. The findings revealed that CSE caused developmental toxicity including increased mortality and decreased incubation rate in a dose dependent manner. Moreover CSE induced malformations and apoptosis specifically in the head and heart of zebrafish larvae. We used mRNA and miRNA sequencing analyses to compare changes in the expression of genes and miRNAs in zebrafish larvae. The bioinformatics analysis indicates that the mechanism underlying CSE induced developmental toxicity was associated with genetic repair impairment apoptosis disorder and lipid metabolism disturbance. The enrichment analysis and RT qPCR show that the ctsba gene plays a crucial function in embryo developmental apoptosis and the fads2 gene mainly regulates lipid metabolic toxicity. The results of this study improve the understanding of CSE induced developmental toxicity in zebrafish embryos and contribute insights into the formulation of novel preventive strategies against tobacco pollutants during early embryonic development.,,,,,S21K1223,,library ID:L 2|title:Low 2|library strategy:OTHER|library source:METATRANSCRIPTIOMIC|library selection:other|library layout:paired|platform:ILLUMINA|instrument model:RNA seq|filetype:fastq|filename:S21K1223 rep1 1 URNA S67 L003 R1 001.fastq|filename2:S21K1223 rep1 1 URNA S67 L003 R2 001.fastq|host:missing|isolation source:missing|collection date:missing|geographic location:missing|latitude and longitude:missing|age:missing|breed:missing|cultivar:missing|dev stage:missing|ecotype:missing|isolate:missing|sex:missing|strain:missing|tissue:missing|BioSampleModel:Model organism or animal,,,,,,,,,Low 2,L 2,L 2,missing,,,RNA-Seq,METATRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP491086,,,S21K1223_rep1_1_URNA_S67_L003_R1_001.fastq.gz S21K1223_rep1_1_URNA_S67_L003_R2_001.fastq.gz,fastq fastq,6779124000.0,22597080.0,S21K1223 rep1 1 URNA S67 L003 R1 001.fastq.gz,0:150 1:150,A:1804338053;C:1556291420;G:1636850001;T:1781628665;N:15861,150,150,,,1804338053,1556291420,1636850001,1781628665,15861,SRX23704455,SRS20534451,SRA1806456,The Second Affiliated Hospital of Shantou University Medical College|Department of Burns and Plastic Surgery,The Second Affiliated Hospital of Shantou University Medical College,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,China,2024-02-22,Undetermined,Multi-stage,Undetermined,Undetermined 30656,SRR28054751,SRX23704454,SRS20534449,SRP491086,PRJNA1078753,Integrated mRNA and miRNA sequencing analyses unveil the underlying mechanism of tobacco pollutant induced developmental toxicity in zebrafish embryos,PRJNA1078753,Other,Tobacco pollutants are prevalent in the environment leading to inadvertent exposure of pregnant females. Studies of these pollutants' toxic effects on development have not fully elucidated the potential underlying mechanisms. Therefore in this study we aim at investigate the developmental toxicity induced by cigarette smoke extract CSE at concentrations of 0.25% 1% and 2.5% using a zebrafish embryo toxicity test and integrated transcriptomic analysis of microRNA miRNA and messenger RNA mRNA. The findings revealed that CSE caused developmental toxicity including increased mortality and decreased incubation rate in a dose dependent manner. Moreover CSE induced malformations and apoptosis specifically in the head and heart of zebrafish larvae. We used mRNA and miRNA sequencing analyses to compare changes in the expression of genes and miRNAs in zebrafish larvae. The bioinformatics analysis indicates that the mechanism underlying CSE induced developmental toxicity was associated with genetic repair impairment apoptosis disorder and lipid metabolism disturbance. The enrichment analysis and RT qPCR show that the ctsba gene plays a crucial function in embryo developmental apoptosis and the fads2 gene mainly regulates lipid metabolic toxicity. The results of this study improve the understanding of CSE induced developmental toxicity in zebrafish embryos and contribute insights into the formulation of novel preventive strategies against tobacco pollutants during early embryonic development.,,,,,S21K1222,,library ID:L 1|title:Low 1|library strategy:OTHER|library source:METATRANSCRIPTIOMIC|library selection:other|library layout:paired|platform:ILLUMINA|instrument model:RNA seq|filetype:fastq|filename:S21K1222 rep1 1 URNA S66 L003 R1 001.fastq|filename2:S21K1222 rep1 1 URNA S66 L003 R2 001.fastq|host:missing|isolation source:missing|collection date:missing|geographic location:missing|latitude and longitude:missing|age:missing|breed:missing|cultivar:missing|dev stage:missing|ecotype:missing|isolate:missing|sex:missing|strain:missing|tissue:missing|BioSampleModel:Model organism or animal,,,,,,,,,Low 1,L 1,L 1,missing,,,RNA-Seq,METATRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP491086,,,S21K1222_rep1_1_URNA_S66_L003_R1_001.fastq.gz S21K1222_rep1_1_URNA_S66_L003_R2_001.fastq.gz,fastq fastq,7484014500.0,24946715.0,S21K1222 rep1 1 URNA S66 L003 R1 001.fastq.gz,0:150 1:150,A:1895991723;C:1633895559;G:2095064183;T:1859045639;N:17396,150,150,,,1895991723,1633895559,2095064183,1859045639,17396,SRX23704454,SRS20534449,SRA1806456,The Second Affiliated Hospital of Shantou University Medical College|Department of Burns and Plastic Surgery,The Second Affiliated Hospital of Shantou University Medical College,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,China,2024-02-22,Undetermined,Multi-stage,Undetermined,Undetermined 30657,SRR28054752,SRX23704453,SRS20534447,SRP491086,PRJNA1078753,Integrated mRNA and miRNA sequencing analyses unveil the underlying mechanism of tobacco pollutant induced developmental toxicity in zebrafish embryos,PRJNA1078753,Other,Tobacco pollutants are prevalent in the environment leading to inadvertent exposure of pregnant females. Studies of these pollutants' toxic effects on development have not fully elucidated the potential underlying mechanisms. Therefore in this study we aim at investigate the developmental toxicity induced by cigarette smoke extract CSE at concentrations of 0.25% 1% and 2.5% using a zebrafish embryo toxicity test and integrated transcriptomic analysis of microRNA miRNA and messenger RNA mRNA. The findings revealed that CSE caused developmental toxicity including increased mortality and decreased incubation rate in a dose dependent manner. Moreover CSE induced malformations and apoptosis specifically in the head and heart of zebrafish larvae. We used mRNA and miRNA sequencing analyses to compare changes in the expression of genes and miRNAs in zebrafish larvae. The bioinformatics analysis indicates that the mechanism underlying CSE induced developmental toxicity was associated with genetic repair impairment apoptosis disorder and lipid metabolism disturbance. The enrichment analysis and RT qPCR show that the ctsba gene plays a crucial function in embryo developmental apoptosis and the fads2 gene mainly regulates lipid metabolic toxicity. The results of this study improve the understanding of CSE induced developmental toxicity in zebrafish embryos and contribute insights into the formulation of novel preventive strategies against tobacco pollutants during early embryonic development.,,,,,S21K1221,,library ID:C 3|title:Control 3|library strategy:OTHER|library source:METATRANSCRIPTIOMIC|library selection:other|library layout:paired|platform:ILLUMINA|instrument model:RNA seq|filetype:fastq|filename:S21K1221 rep1 1 URNA S65 L003 R1 001.fastq|filename2:S21K1221 rep1 1 URNA S65 L003 R2 001.fastq|host:missing|isolation source:missing|collection date:missing|geographic location:missing|latitude and longitude:missing|age:missing|breed:missing|cultivar:missing|dev stage:missing|ecotype:missing|isolate:missing|sex:missing|strain:missing|tissue:missing|BioSampleModel:Model organism or animal,,,,,,,,,Control 3,C 3,C 3,missing,,,RNA-Seq,METATRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP491086,,,S21K1221_rep1_1_URNA_S65_L003_R1_001.fastq.gz S21K1221_rep1_1_URNA_S65_L003_R2_001.fastq.gz,fastq fastq,6562506000.0,21875020.0,S21K1221 rep1 1 URNA S65 L003 R1 001.fastq.gz,0:150 1:150,A:1753018331;C:1507753283;G:1569109292;T:1732610076;N:15018,150,150,,,1753018331,1507753283,1569109292,1732610076,15018,SRX23704453,SRS20534447,SRA1806456,The Second Affiliated Hospital of Shantou University Medical College|Department of Burns and Plastic Surgery,The Second Affiliated Hospital of Shantou University Medical College,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,China,2024-02-22,Undetermined,Multi-stage,Undetermined,Undetermined 30658,SRR28054753,SRX23704452,SRS20534448,SRP491086,PRJNA1078753,Integrated mRNA and miRNA sequencing analyses unveil the underlying mechanism of tobacco pollutant induced developmental toxicity in zebrafish embryos,PRJNA1078753,Other,Tobacco pollutants are prevalent in the environment leading to inadvertent exposure of pregnant females. Studies of these pollutants' toxic effects on development have not fully elucidated the potential underlying mechanisms. Therefore in this study we aim at investigate the developmental toxicity induced by cigarette smoke extract CSE at concentrations of 0.25% 1% and 2.5% using a zebrafish embryo toxicity test and integrated transcriptomic analysis of microRNA miRNA and messenger RNA mRNA. The findings revealed that CSE caused developmental toxicity including increased mortality and decreased incubation rate in a dose dependent manner. Moreover CSE induced malformations and apoptosis specifically in the head and heart of zebrafish larvae. We used mRNA and miRNA sequencing analyses to compare changes in the expression of genes and miRNAs in zebrafish larvae. The bioinformatics analysis indicates that the mechanism underlying CSE induced developmental toxicity was associated with genetic repair impairment apoptosis disorder and lipid metabolism disturbance. The enrichment analysis and RT qPCR show that the ctsba gene plays a crucial function in embryo developmental apoptosis and the fads2 gene mainly regulates lipid metabolic toxicity. The results of this study improve the understanding of CSE induced developmental toxicity in zebrafish embryos and contribute insights into the formulation of novel preventive strategies against tobacco pollutants during early embryonic development.,,,,,S21K1230,,library ID:H 3|title:High 3|library strategy:OTHER|library source:METATRANSCRIPTIOMIC|library selection:other|library layout:paired|platform:ILLUMINA|instrument model:RNA seq|filetype:fastq|filename:S21K1230 rep1 1 URNA S74 L003 R1 001.fastq|filename2:S21K1230 rep1 1 URNA S74 L003 R2 001.fastq|host:missing|isolation source:missing|collection date:missing|geographic location:missing|latitude and longitude:missing|age:missing|breed:missing|cultivar:missing|dev stage:missing|ecotype:missing|isolate:missing|sex:missing|strain:missing|tissue:missing|BioSampleModel:Model organism or animal,,,,,,,,,High 3,H 3,H 3,missing,,,RNA-Seq,METATRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP491086,,,S21K1230_rep1_1_URNA_S74_L003_R1_001.fastq.gz S21K1230_rep1_1_URNA_S74_L003_R2_001.fastq.gz,fastq fastq,6117817800.0,20392726.0,S21K1230 rep1 1 URNA S74 L003 R1 001.fastq.gz,0:150 1:150,A:1635728688;C:1405168032;G:1464072107;T:1612834762;N:14211,150,150,,,1635728688,1405168032,1464072107,1612834762,14211,SRX23704452,SRS20534448,SRA1806456,The Second Affiliated Hospital of Shantou University Medical College|Department of Burns and Plastic Surgery,The Second Affiliated Hospital of Shantou University Medical College,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,China,2024-02-22,Undetermined,Multi-stage,Undetermined,Undetermined 30659,SRR28054754,SRX23704451,SRS20534446,SRP491086,PRJNA1078753,Integrated mRNA and miRNA sequencing analyses unveil the underlying mechanism of tobacco pollutant induced developmental toxicity in zebrafish embryos,PRJNA1078753,Other,Tobacco pollutants are prevalent in the environment leading to inadvertent exposure of pregnant females. Studies of these pollutants' toxic effects on development have not fully elucidated the potential underlying mechanisms. Therefore in this study we aim at investigate the developmental toxicity induced by cigarette smoke extract CSE at concentrations of 0.25% 1% and 2.5% using a zebrafish embryo toxicity test and integrated transcriptomic analysis of microRNA miRNA and messenger RNA mRNA. The findings revealed that CSE caused developmental toxicity including increased mortality and decreased incubation rate in a dose dependent manner. Moreover CSE induced malformations and apoptosis specifically in the head and heart of zebrafish larvae. We used mRNA and miRNA sequencing analyses to compare changes in the expression of genes and miRNAs in zebrafish larvae. The bioinformatics analysis indicates that the mechanism underlying CSE induced developmental toxicity was associated with genetic repair impairment apoptosis disorder and lipid metabolism disturbance. The enrichment analysis and RT qPCR show that the ctsba gene plays a crucial function in embryo developmental apoptosis and the fads2 gene mainly regulates lipid metabolic toxicity. The results of this study improve the understanding of CSE induced developmental toxicity in zebrafish embryos and contribute insights into the formulation of novel preventive strategies against tobacco pollutants during early embryonic development.,,,,,S21K1229,,library ID:H 2|title:High 2|library strategy:OTHER|library source:METATRANSCRIPTIOMIC|library selection:other|library layout:paired|platform:ILLUMINA|instrument model:RNA seq|filetype:fastq|filename:S21K1229 rep1 1 URNA S73 L003 R1 001.fastq|filename2:S21K1229 rep1 1 URNA S73 L003 R2 001.fastq|host:missing|isolation source:missing|collection date:missing|geographic location:missing|latitude and longitude:missing|age:missing|breed:missing|cultivar:missing|dev stage:missing|ecotype:missing|isolate:missing|sex:missing|strain:missing|tissue:missing|BioSampleModel:Model organism or animal,,,,,,,,,High 2,H 2,H 2,missing,,,RNA-Seq,METATRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP491086,,,S21K1229_rep1_1_URNA_S73_L003_R1_001.fastq.gz S21K1229_rep1_1_URNA_S73_L003_R2_001.fastq.gz,fastq fastq,7164803100.0,23882677.0,S21K1229 rep1 1 URNA S73 L003 R1 001.fastq.gz,0:150 1:150,A:1920286881;C:1649856655;G:1697032084;T:1897610671;N:16809,150,150,,,1920286881,1649856655,1697032084,1897610671,16809,SRX23704451,SRS20534446,SRA1806456,The Second Affiliated Hospital of Shantou University Medical College|Department of Burns and Plastic Surgery,The Second Affiliated Hospital of Shantou University Medical College,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,China,2024-02-22,Undetermined,Multi-stage,Undetermined,Undetermined 30660,SRR28054755,SRX23704450,SRS20534445,SRP491086,PRJNA1078753,Integrated mRNA and miRNA sequencing analyses unveil the underlying mechanism of tobacco pollutant induced developmental toxicity in zebrafish embryos,PRJNA1078753,Other,Tobacco pollutants are prevalent in the environment leading to inadvertent exposure of pregnant females. Studies of these pollutants' toxic effects on development have not fully elucidated the potential underlying mechanisms. Therefore in this study we aim at investigate the developmental toxicity induced by cigarette smoke extract CSE at concentrations of 0.25% 1% and 2.5% using a zebrafish embryo toxicity test and integrated transcriptomic analysis of microRNA miRNA and messenger RNA mRNA. The findings revealed that CSE caused developmental toxicity including increased mortality and decreased incubation rate in a dose dependent manner. Moreover CSE induced malformations and apoptosis specifically in the head and heart of zebrafish larvae. We used mRNA and miRNA sequencing analyses to compare changes in the expression of genes and miRNAs in zebrafish larvae. The bioinformatics analysis indicates that the mechanism underlying CSE induced developmental toxicity was associated with genetic repair impairment apoptosis disorder and lipid metabolism disturbance. The enrichment analysis and RT qPCR show that the ctsba gene plays a crucial function in embryo developmental apoptosis and the fads2 gene mainly regulates lipid metabolic toxicity. The results of this study improve the understanding of CSE induced developmental toxicity in zebrafish embryos and contribute insights into the formulation of novel preventive strategies against tobacco pollutants during early embryonic development.,,,,,S21K1220,,library ID:C 2|title:Control 2|library strategy:OTHER|library source:METATRANSCRIPTIOMIC|library selection:other|library layout:paired|platform:ILLUMINA|instrument model:RNA seq|filetype:fastq|filename:S21K1220 rep1 1 URNA S64 L003 R1 001.fastq|filename2:S21K1220 rep1 1 URNA S64 L003 R2 001.fastq|host:missing|isolation source:missing|collection date:missing|geographic location:missing|latitude and longitude:missing|age:missing|breed:missing|cultivar:missing|dev stage:missing|ecotype:missing|isolate:missing|sex:missing|strain:missing|tissue:missing|BioSampleModel:Model organism or animal,,,,,,,,,Control 2,C 2,C 2,missing,,,RNA-Seq,METATRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP491086,,,S21K1220_rep1_1_URNA_S64_L003_R1_001.fastq.gz S21K1220_rep1_1_URNA_S64_L003_R2_001.fastq.gz,fastq fastq,6790504800.0,22635016.0,S21K1220 rep1 1 URNA S64 L003 R1 001.fastq.gz,0:150 1:150,A:1784553430;C:1593393319;G:1650087761;T:1762454671;N:15619,150,150,,,1784553430,1593393319,1650087761,1762454671,15619,SRX23704450,SRS20534445,SRA1806456,The Second Affiliated Hospital of Shantou University Medical College|Department of Burns and Plastic Surgery,The Second Affiliated Hospital of Shantou University Medical College,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,China,2024-02-22,Undetermined,Multi-stage,Undetermined,Undetermined 30661,SRR28054756,SRX23704449,SRS20534444,SRP491086,PRJNA1078753,Integrated mRNA and miRNA sequencing analyses unveil the underlying mechanism of tobacco pollutant induced developmental toxicity in zebrafish embryos,PRJNA1078753,Other,Tobacco pollutants are prevalent in the environment leading to inadvertent exposure of pregnant females. Studies of these pollutants' toxic effects on development have not fully elucidated the potential underlying mechanisms. Therefore in this study we aim at investigate the developmental toxicity induced by cigarette smoke extract CSE at concentrations of 0.25% 1% and 2.5% using a zebrafish embryo toxicity test and integrated transcriptomic analysis of microRNA miRNA and messenger RNA mRNA. The findings revealed that CSE caused developmental toxicity including increased mortality and decreased incubation rate in a dose dependent manner. Moreover CSE induced malformations and apoptosis specifically in the head and heart of zebrafish larvae. We used mRNA and miRNA sequencing analyses to compare changes in the expression of genes and miRNAs in zebrafish larvae. The bioinformatics analysis indicates that the mechanism underlying CSE induced developmental toxicity was associated with genetic repair impairment apoptosis disorder and lipid metabolism disturbance. The enrichment analysis and RT qPCR show that the ctsba gene plays a crucial function in embryo developmental apoptosis and the fads2 gene mainly regulates lipid metabolic toxicity. The results of this study improve the understanding of CSE induced developmental toxicity in zebrafish embryos and contribute insights into the formulation of novel preventive strategies against tobacco pollutants during early embryonic development.,,,,,S21K1219,,library ID:C 1|title:Control 1|library strategy:OTHER|library source:METATRANSCRIPTIOMIC|library selection:other|library layout:paired|platform:ILLUMINA|instrument model:RNA seq|filetype:fastq|filename:S21K1219 rep1 1 URNA S63 L003 R1 001.fastq|filename2:S21K1219 rep1 1 URNA S63 L003 R2 001.fastq|host:missing|isolation source:missing|collection date:missing|geographic location:missing|latitude and longitude:missing|age:missing|breed:missing|cultivar:missing|dev stage:missing|ecotype:missing|isolate:missing|sex:missing|strain:missing|tissue:missing|BioSampleModel:Model organism or animal,,,,,,,,,Control 1,C 1,C 1,missing,,,RNA-Seq,METATRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP491086,,,S21K1219_rep1_1_URNA_S63_L003_R1_001.fastq.gz S21K1219_rep1_1_URNA_S63_L003_R2_001.fastq.gz,fastq fastq,7498264200.0,24994214.0,S21K1219 rep1 1 URNA S63 L003 R1 001.fastq.gz,0:150 1:150,A:2002773492;C:1716996682;G:1800329295;T:1978147319;N:17412,150,150,,,2002773492,1716996682,1800329295,1978147319,17412,SRX23704449,SRS20534444,SRA1806456,The Second Affiliated Hospital of Shantou University Medical College|Department of Burns and Plastic Surgery,The Second Affiliated Hospital of Shantou University Medical College,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,China,2024-02-22,Undetermined,Multi-stage,Undetermined,Undetermined 33123,SRR29672615,SRX25176099,SRS21866000,SRP517393,PRJNA1130538,ac4C transcriptomes of Zebrafish and Worm,GSE271258,Other,ac4C modification appears in mutilple model organisms including Zebrafish and Worm Overall design: To investigate whether ac4C modification is involved in evolution we performed ac4C RIP seq on Zebrafish and Worm.,,,,Zebrafish ac4C,GSM8372406,,tissue:Animal organ cells|cell type:Animal organ cells|genotype:Wild type|rip antibody:anti ac4C Abcam catalog No. ab252215|geo loc name:missing|collection date:missing,Zebrafish ac4C,The raw ac4C RIP seq data were aligned to genome reference sequences by Hisat2. The aligned reads were used for ac4C modification peak calling and the significant methylation was identified by exomepeak2 and the ac4C peak calling can be visualized by IGV software. The MetaTX was used to examine the distribution pattern of epitranscriptome profiles. The STREME was used to determine if the ac4C peaks contained the consensus of ac4C motif sequences. For mRNA seq the mRNA expression level was analyzed by StringTie and differentially expressed mRNAs were calculated by DEseq. The substrates of ac4C regulators were obtained from starBase v2.0. The statistical enrichment analysis of Gene Ontology GO and Kyoto Encyclopedia of Genes and Genomes KEGG pathway for differentially expressed genes DEGs and differentially methylated mRNAs were applied by DAVID. Assembly: danRer10 or WBcel235 Supplementary files format and content: The processed data files is in CSV format containing the expression levels and ac4C status changes for each gene.,Animal organ cells,,Total RNA was extracted according to manufacturer’s instruction. The stranded RNA sequencing library was constructed by KC DigitalTM Stranded mRNA Library Prep Kit for Illumina® Catalog NO. DR08502 Wuhan Seqhealth Co. Ltd. China following the manufacturer’s instruction. The kit eliminates duplication bias in PCR and sequencing steps by using unique molecular identifier UMI of 8 random bases to label the pre amplified cDNA molecules. The library products corresponding to 200 500 bps were enriched,,cell type:Animal organ cells|genotype:Wild type|rip antibody:anti ac4C Abcam catalog No. ab252215,GSM8372406,GSM8372406: Zebrafish ac4C; Danio rerio; RIP Seq,GSM8372406 r1,GSM8372406,1,Total RNA was extracted according to manufacturer's instruction. The stranded RNA sequencing library was constructed by KC DigitalTM Stranded mRNA Library Prep Kit for Illumina® Catalog NO. DR08502 Wuhan Seqhealth Co. Ltd. China following the manufacturer's instruction. The kit eliminates duplication bias in PCR and sequencing steps by using unique molecular identifier UMI of 8 random bases to label the pre amplified cDNA molecules. The library products corresponding to 200 500 bps were enriched,,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP517393,,,Fish_IP.clean.R2.fastq.gz Fish_IP.clean.R1.fastq.gz,fastq fastq,816231517.0,3830403.0,GSM8372406 r1,0:102.34 1:110.76,A:199381841;C:207571478;G:205740791;T:203535549;N:1858,102,110,,,199381841,207571478,205740791,203535549,1858,SRX25176099,SRS21866000,SRA1914369,Fujian Medical University,Fujian Medical University,2,0.60415,0.60545,0.08824,0.08794,0.78796,0.78733,0.43432,0.43842,126,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2024-07-01,Undetermined,Undetermined,Undetermined,Undetermined 52210,SRR9021058,SRX5799154,SRS4730324,SRP195685,PRJNA541367,Global transcriptomic analysis of zebrafish glucagon receptor mutant,PRJNA541367,Other,We performed RNA sequencing RNA seq analysis of whole fish to provide a comprehensive view of its global transcriptomic regulation in this study.,,,,,WT 1,,replicate:biological replicate 1|strain:AB|age:7 days|sex:not applicable|tissue:total|BioSampleModel:Model organism or animal,,,,,,,,,Diano rerio transcriptome,WT 1 20190506 1,WT 1 20190506 1,RNA seq of WT Diano rerio,,,RNA-Seq,TRANSCRIPTOMIC,other,SINGLE,BGISEQ,BGISEQ-500,,SRP195685,,loader:fastq load.py,WT1.1.fq,fastq,1094498950.0,21889979.0,WT1.1.fq,0:50,A:291195764;C:255539280;G:262638316;T:284737693;N:387897,50,,,,291195764,255539280,262638316,284737693,387897,SRX5799154,SRS4730324,SRA883435,Xiamen University|School of Pharmaceutical Sciences,Xiamen University,1,0.94195,,0.09713,,0.66689,,0.47749,,50,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-01-18,Larval,Larval,Undetermined,Undetermined 52211,SRR9021059,SRX5799153,SRS4730323,SRP195685,PRJNA541367,Global transcriptomic analysis of zebrafish glucagon receptor mutant,PRJNA541367,Other,We performed RNA sequencing RNA seq analysis of whole fish to provide a comprehensive view of its global transcriptomic regulation in this study.,,,,,WT 2,,replicate:biological replicate 2|strain:AB|age:7 days|sex:not applicable|tissue:total|BioSampleModel:Model organism or animal,,,,,,,,,Diano rerio transcriptome,WT 2 20190506 2,WT 2 20190506 2,RNA seq of WT Diano rerio,,,RNA-Seq,TRANSCRIPTOMIC,other,SINGLE,BGISEQ,BGISEQ-500,,SRP195685,,loader:fastq load.py,WT2.1.fq,fastq,1095133200.0,21902664.0,WT2.1.fq,0:50,A:290594757;C:255644044;G:259681140;T:288014102;N:1199157,50,,,,290594757,255644044,259681140,288014102,1199157,SRX5799153,SRS4730323,SRA883435,Xiamen University|School of Pharmaceutical Sciences,Xiamen University,1,0.93368,,0.09166,,0.67085,,0.46523,,50,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-01-18,Larval,Larval,Undetermined,Undetermined 52212,SRR9021060,SRX5799152,SRS4730322,SRP195685,PRJNA541367,Global transcriptomic analysis of zebrafish glucagon receptor mutant,PRJNA541367,Other,We performed RNA sequencing RNA seq analysis of whole fish to provide a comprehensive view of its global transcriptomic regulation in this study.,,,,,WT 3,,replicate:biological replicate 3|strain:AB|age:7 days|sex:not applicable|tissue:total|BioSampleModel:Model organism or animal,,,,,,,,,Diano rerio transcriptome,WT 3 20190506 3,WT 3 20190506 3,RNA seq of WT Diano rerio,,,RNA-Seq,TRANSCRIPTOMIC,other,SINGLE,BGISEQ,BGISEQ-500,,SRP195685,,loader:fastq load.py,WT3.1.fq,fastq,1096083900.0,21921678.0,WT3.1.fq,0:50,A:290332094;C:256993500;G:263043956;T:285349722;N:364628,50,,,,290332094,256993500,263043956,285349722,364628,SRX5799152,SRS4730322,SRA883435,Xiamen University|School of Pharmaceutical Sciences,Xiamen University,1,0.94147,,0.10157,,0.66135,,0.47301,,50,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-01-18,Larval,Larval,Undetermined,Undetermined 52213,SRR9021061,SRX5799151,SRS4730320,SRP195685,PRJNA541367,Global transcriptomic analysis of zebrafish glucagon receptor mutant,PRJNA541367,Other,We performed RNA sequencing RNA seq analysis of whole fish to provide a comprehensive view of its global transcriptomic regulation in this study.,,,,,gcgr 1,,replicate:biological replicate 1|strain:AB|age:7 days|sex:not applicable|tissue:total|BioSampleModel:Model organism or animal,,,,,,,,,Diano rerio transcriptome,gcgr 1 20190506 1,gcgr 1 20190506 1,RNA seq of Diano rerio with gcgr mutant,,,RNA-Seq,TRANSCRIPTOMIC,other,SINGLE,BGISEQ,BGISEQ-500,,SRP195685,,loader:fastq load.py,gcgr1.1.fq,fastq,1096307200.0,21926144.0,gcgr1.1.fq,0:50,A:288839446;C:258297625;G:264630675;T:284199738;N:339716,50,,,,288839446,258297625,264630675,284199738,339716,SRX5799151,SRS4730320,SRA883435,Xiamen University|School of Pharmaceutical Sciences,Xiamen University,1,0.94131,,0.09307,,0.67574,,0.46993,,50,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-01-18,Larval,Larval,Undetermined,Undetermined 52214,SRR9021062,SRX5799150,SRS4730321,SRP195685,PRJNA541367,Global transcriptomic analysis of zebrafish glucagon receptor mutant,PRJNA541367,Other,We performed RNA sequencing RNA seq analysis of whole fish to provide a comprehensive view of its global transcriptomic regulation in this study.,,,,,gcgr 2,,replicate:biological replicate 2|strain:AB|age:7 days|sex:not applicable|tissue:total|BioSampleModel:Model organism or animal,,,,,,,,,Diano rerio transcriptome,gcgr 2 20190506 2,gcgr 2 20190506 2,RNA seq of Diano rerio with gcgr mutant,,,RNA-Seq,TRANSCRIPTOMIC,other,SINGLE,BGISEQ,BGISEQ-500,,SRP195685,,loader:fastq load.py,gcgr2.1.fq,fastq,1094410100.0,21888202.0,gcgr2.1.fq,0:50,A:290062779;C:256358687;G:264488431;T:282812212;N:687991,50,,,,290062779,256358687,264488431,282812212,687991,SRX5799150,SRS4730321,SRA883435,Xiamen University|School of Pharmaceutical Sciences,Xiamen University,1,0.94074,,0.09337,,0.67633,,0.46861,,50,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-01-18,Larval,Larval,Undetermined,Undetermined 52215,SRR9021063,SRX5799149,SRS4730319,SRP195685,PRJNA541367,Global transcriptomic analysis of zebrafish glucagon receptor mutant,PRJNA541367,Other,We performed RNA sequencing RNA seq analysis of whole fish to provide a comprehensive view of its global transcriptomic regulation in this study.,,,,,gcgr 3,,replicate:biological replicate 3|strain:AB|age:7 days|sex:not applicable|tissue:total|BioSampleModel:Model organism or animal,,,,,,,,,Diano rerio transcriptome,gcgr 3 20190506 3,gcgr 3 20190506 3,RNA seq of Diano rerio with gcgr mutant,,,RNA-Seq,TRANSCRIPTOMIC,other,SINGLE,BGISEQ,BGISEQ-500,,SRP195685,,loader:fastq load.py,gcgr3.1.fq,fastq,1094284800.0,21885696.0,gcgr3.1.fq,0:50,A:289313514;C:257096636;G:264011408;T:283143600;N:719642,50,,,,289313514,257096636,264011408,283143600,719642,SRX5799149,SRS4730319,SRA883435,Xiamen University|School of Pharmaceutical Sciences,Xiamen University,1,0.94222,,0.09557,,0.67521,,0.46664,,50,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-01-18,Larval,Larval,Undetermined,Undetermined 59503,SRR11924320,SRX8469993,SRS6770644,SRP265951,PRJNA637293,The shift from early to late types of ribosomes in zebrafish development involves changes at a subset of rRNA 2' O Me sites,GSE151797,Other,A sequencing based profiling method RiboMeth seq for ribose methylations was used to study methylation patterns during Zebrafish Danio rerio development Overall design: All samples were analyzed in biological triplicates except for adult tail trunk that was in duplicate.,,pubmed:32912962,,PM 3,GSM4591060,,source name:protruding mouth stage|tissue:protruding mouth stage|rna fraction:size fractionated 20 40 nt whole cell RNA,PM 3,Library strategy: RiboMeth seq Barcode separation using python script Adaptor trimming using Cutadapt v. 2.0 Mapping to rRNA reference sequence using Bowtie2 v. 2.3.4.1 Counting read ends and calculating RiboMeth seq scores using python scripts The output FASTA files from small RNA seq were merged and used as the basis of the SNORD search and rRNA interaction prediction. Initially SNORDs were identified by running the merged FASTA file through snoScan Schattner et al. 2005 against zebrafish early and late rRNA reference sequences Locati et al. 2017. Genome build: early and late zebrafish rRNA locati et al. The reference sequences are available in the FASTA file on the series record. Supplementary files format and content: MS Excel file contains five prime and three prime read count and calculated RiboMeth seq score at all positions in the rRNA sequence.,protruding mouth stage,,Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U Christensen Dalsgaard M Krogh N Sabarinathan R Gorodkin J Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description,,tissue:protruding mouth stage|rna fraction:size fractionated 20 40 nt whole cell RNA,GSM4591060,GSM4591060: PM 3; Danio rerio; OTHER,GSM4591060,,1,Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U Christensen Dalsgaard M Krogh N Sabarinathan R Gorodkin J Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description,GEO Accession:GSM4591060,OTHER,TRANSCRIPTOMIC,other,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP265951,,intentional duplicate,GSE151797_Reference_sequence.fa PM_3.bam,bam bam,215125332.0,6403488.0,GSM4591060 r1,0:33.60,A:50202267;C:65116674;G:52637331;T:47169060;N:0,33,,,,50202267,65116674,52637331,47169060,0,SRX8469993,SRS6770644,SRA1083099,GEO,"RNA Group - Prof. Henrik Nielsen, Department of Cellular and Molecular Medicine, University of Copenhagen",1,0.73594,,0.21617,,0.86251,,0.68892,,42,,B,,usable mapping rate,ion_torrent,ion_torrent,5prime,small_rna,unknown,bulk,unknown,unknown,,Denmark,2020-06-04,Larval,Larval,Undetermined,Undetermined 59504,SRR11924318,SRX8469992,SRS6770643,SRP265951,PRJNA637293,The shift from early to late types of ribosomes in zebrafish development involves changes at a subset of rRNA 2' O Me sites,GSE151797,Other,A sequencing based profiling method RiboMeth seq for ribose methylations was used to study methylation patterns during Zebrafish Danio rerio development Overall design: All samples were analyzed in biological triplicates except for adult tail trunk that was in duplicate.,,pubmed:32912962,,PM 2,GSM4591059,,source name:protruding mouth stage|tissue:protruding mouth stage|rna fraction:size fractionated 20 40 nt whole cell RNA,PM 2,Library strategy: RiboMeth seq Barcode separation using python script Adaptor trimming using Cutadapt v. 2.0 Mapping to rRNA reference sequence using Bowtie2 v. 2.3.4.1 Counting read ends and calculating RiboMeth seq scores using python scripts The output FASTA files from small RNA seq were merged and used as the basis of the SNORD search and rRNA interaction prediction. Initially SNORDs were identified by running the merged FASTA file through snoScan Schattner et al. 2005 against zebrafish early and late rRNA reference sequences Locati et al. 2017. Genome build: early and late zebrafish rRNA locati et al. The reference sequences are available in the FASTA file on the series record. Supplementary files format and content: MS Excel file contains five prime and three prime read count and calculated RiboMeth seq score at all positions in the rRNA sequence.,protruding mouth stage,,Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U Christensen Dalsgaard M Krogh N Sabarinathan R Gorodkin J Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description,,tissue:protruding mouth stage|rna fraction:size fractionated 20 40 nt whole cell RNA,GSM4591059,GSM4591059: PM 2; Danio rerio; OTHER,GSM4591059,,1,Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U Christensen Dalsgaard M Krogh N Sabarinathan R Gorodkin J Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description,GEO Accession:GSM4591059,OTHER,TRANSCRIPTOMIC,other,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP265951,,intentional duplicate,GSE151797_Reference_sequence.fa PM_2.bam,bam bam,426315355.0,12915702.0,GSM4591059 r1,0:33.01,A:92276988;C:141702085;G:104175159;T:88161123;N:0,33,,,,92276988,141702085,104175159,88161123,0,SRX8469992,SRS6770643,SRA1083099,GEO,"RNA Group - Prof. Henrik Nielsen, Department of Cellular and Molecular Medicine, University of Copenhagen",1,0.76385,,0.1921,,0.87207,,0.71495,,40,,B,,usable mapping rate,ion_torrent,ion_torrent,5prime,small_rna,unknown,bulk,unknown,unknown,,Denmark,2020-06-04,Larval,Larval,Undetermined,Undetermined 59505,SRR11924317,SRX8469990,SRS6770641,SRP265951,PRJNA637293,The shift from early to late types of ribosomes in zebrafish development involves changes at a subset of rRNA 2' O Me sites,GSE151797,Other,A sequencing based profiling method RiboMeth seq for ribose methylations was used to study methylation patterns during Zebrafish Danio rerio development Overall design: All samples were analyzed in biological triplicates except for adult tail trunk that was in duplicate.,,pubmed:32912962,,PM 1,GSM4591058,,source name:protruding mouth stage|tissue:protruding mouth stage|rna fraction:size fractionated 20 40 nt whole cell RNA,PM 1,Library strategy: RiboMeth seq Barcode separation using python script Adaptor trimming using Cutadapt v. 2.0 Mapping to rRNA reference sequence using Bowtie2 v. 2.3.4.1 Counting read ends and calculating RiboMeth seq scores using python scripts The output FASTA files from small RNA seq were merged and used as the basis of the SNORD search and rRNA interaction prediction. Initially SNORDs were identified by running the merged FASTA file through snoScan Schattner et al. 2005 against zebrafish early and late rRNA reference sequences Locati et al. 2017. Genome build: early and late zebrafish rRNA locati et al. The reference sequences are available in the FASTA file on the series record. Supplementary files format and content: MS Excel file contains five prime and three prime read count and calculated RiboMeth seq score at all positions in the rRNA sequence.,protruding mouth stage,,Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U Christensen Dalsgaard M Krogh N Sabarinathan R Gorodkin J Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description,,tissue:protruding mouth stage|rna fraction:size fractionated 20 40 nt whole cell RNA,GSM4591058,GSM4591058: PM 1; Danio rerio; OTHER,GSM4591058,,1,Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U Christensen Dalsgaard M Krogh N Sabarinathan R Gorodkin J Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description,GEO Accession:GSM4591058,OTHER,TRANSCRIPTOMIC,other,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP265951,,intentional duplicate,GSE151797_Reference_sequence.fa PM_1.bam,bam bam,130388595.0,5124384.0,GSM4591058 r1,0:25.44,A:27290253;C:42592303;G:31075292;T:29430747;N:0,25,,,,27290253,42592303,31075292,29430747,0,SRX8469990,SRS6770641,SRA1083099,GEO,"RNA Group - Prof. Henrik Nielsen, Department of Cellular and Molecular Medicine, University of Copenhagen",1,0.78884,,0.23004,,0.85113,,0.67571,,38,,B,,usable mapping rate,ion_torrent,ion_torrent,5prime,small_rna,unknown,bulk,unknown,unknown,,Denmark,2020-06-04,Larval,Larval,Undetermined,Undetermined