{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_layout = \"PAIRED\", experiment.library_selection = \"other\" and tissue_curation = \"Undetermined\"", "rows": [[9337, "ERR2865439", "ERX2871399", "ERS2871019", "ERP111778", "PRJEB29472", "RNAseq analysis of slbp mutants in Zebrafish", "ena-STUDY-Department of Cell and Developmental Biology-01-11-2018-15:10:58:144-14", "Other", "Through forward genetic screening for mutations affecting visual system development  we identified prominent coloboma and cell autonomous retinal neuron differentiation  lamination and retinal axon projection defects in eisspalte ele mutant zebrafish. Additional axonal deficits were present  most notably at midline axon commissures. Genetic mapping and cloning of the ele mutation showed that the affected gene is slbp  which encodes a conserved RNA stem loop binding protein involved in replication dependent histone mRNA metabolism. Cells throughout the central nervous system remained in the cell cycle in ele mutant embryos at stages when  and locations where  post mitotic cells have differentiated in wild type siblings. Indeed  RNAseq analysis showed down regulation of many genes associated with neuronal differentiation. This was coincident with changes in the levels and spatial localisation of expression of various genes implicated  for instance  in axon guidance  that likely underlie specific ele phenotypes. These results suggest that many of the cell and tissue specific phenotypes in ele mutant embryos are secondary to altered expression of modules of developmental regulatory genes that characterise  or promote transitions in  cell state and require the correct function of Slbp dependent histone and chromatin regulatory genes.", "ENA FIRST PUBLIC:2018 11 02|ENA LAST UPDATE:2018 11 01", null, null, "sibling 3", "SAMEA5059848", "Department of Cell and Developmental Biology", "ENA FIRST PUBLIC:2018 11 02T17:01:55Z|ENA LAST UPDATE:2018 11 01T15:11:02Z|External Id:SAMEA5059848|INSDC center name:Department of Cell and Developmental Biology|INSDC first public:2018 11 02T17:01:55Z|INSDC last update:2018 11 01T15:11:02Z|INSDC status:public|Submitter Id:ele sibling3|common name:zebrafish|sample name:ele sibling3|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq 3000 paired end sequencing", "ena EXPERIMENT Department of Cell and Developmental Biology 01 11 2018 15:10:57:717 6", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "ERP111778", "Illumina HiSeq 3000 paired end sequencing", "ENA FIRST PUBLIC:2018 11 02|ENA LAST UPDATE:2018 11 16", "ele_sib_F_CTTGTA_L004_R2_001.fastq.gz ele_sib_F_CTTGTA_L004_R1_001.fastq.gz", "fastq fastq", 2823621200.0, 14118106.0, "ena RUN Department of Cell and Developmental Biology 01 11 2018 15:10:57:717 6", "0:100 1:100", "A:752781583;C:663838191;G:656422705;T:750213027;N:365694", 100, 100, null, null, 752781583, 663838191, 656422705, 750213027, 365694, "ERX2871399", "ERS2871019", "ERA1643817", "Department of Cell and Developmental Biology|European Nucleotide Archive", "Department of Cell and Developmental Biology", 2, 0.95595, 0.95486, 0.09407, 0.09431, 0.67529, 0.67673, 0.45173, 0.44515, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2018-11-01", "Undetermined", "Embryo", "Undetermined", "Embryo Imprecise"], [9338, "ERR2865438", "ERX2871398", "ERS2871018", "ERP111778", "PRJEB29472", "RNAseq analysis of slbp mutants in Zebrafish", "ena-STUDY-Department of Cell and Developmental Biology-01-11-2018-15:10:58:144-14", "Other", "Through forward genetic screening for mutations affecting visual system development  we identified prominent coloboma and cell autonomous retinal neuron differentiation  lamination and retinal axon projection defects in eisspalte ele mutant zebrafish. Additional axonal deficits were present  most notably at midline axon commissures. Genetic mapping and cloning of the ele mutation showed that the affected gene is slbp  which encodes a conserved RNA stem loop binding protein involved in replication dependent histone mRNA metabolism. Cells throughout the central nervous system remained in the cell cycle in ele mutant embryos at stages when  and locations where  post mitotic cells have differentiated in wild type siblings. Indeed  RNAseq analysis showed down regulation of many genes associated with neuronal differentiation. This was coincident with changes in the levels and spatial localisation of expression of various genes implicated  for instance  in axon guidance  that likely underlie specific ele phenotypes. These results suggest that many of the cell and tissue specific phenotypes in ele mutant embryos are secondary to altered expression of modules of developmental regulatory genes that characterise  or promote transitions in  cell state and require the correct function of Slbp dependent histone and chromatin regulatory genes.", "ENA FIRST PUBLIC:2018 11 02|ENA LAST UPDATE:2018 11 01", null, null, "sibling 2", "SAMEA5059847", "Department of Cell and Developmental Biology", "ENA FIRST PUBLIC:2018 11 02T17:01:55Z|ENA LAST UPDATE:2018 11 01T15:11:02Z|External Id:SAMEA5059847|INSDC center name:Department of Cell and Developmental Biology|INSDC first public:2018 11 02T17:01:55Z|INSDC last update:2018 11 01T15:11:02Z|INSDC status:public|Submitter Id:ele sibling2|common name:zebrafish|sample name:ele sibling2|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq 3000 paired end sequencing", "ena EXPERIMENT Department of Cell and Developmental Biology 01 11 2018 15:10:57:717 5", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "ERP111778", "Illumina HiSeq 3000 paired end sequencing", "ENA FIRST PUBLIC:2018 11 02|ENA LAST UPDATE:2018 11 16", "ele_sib_D_GCCAAT_L004_R1_001.fastq.gz ele_sib_D_GCCAAT_L004_R2_001.fastq.gz", "fastq fastq", 4217962600.0, 21089813.0, "ena RUN Department of Cell and Developmental Biology 01 11 2018 15:10:57:717 5", "0:100 1:100", "A:1119324653;C:996982862;G:984906708;T:1116209552;N:538825", 100, 100, null, null, 1119324653, 996982862, 984906708, 1116209552, 538825, "ERX2871398", "ERS2871018", "ERA1643817", "Department of Cell and Developmental Biology|European Nucleotide Archive", "Department of Cell and Developmental Biology", 2, 0.95341, 0.95274, 0.09215, 0.09238, 0.67296, 0.67493, 0.46185, 0.4648, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2018-11-01", "Undetermined", "Embryo", "Undetermined", "Embryo Imprecise"], [9339, "ERR2865437", "ERX2871397", "ERS2871017", "ERP111778", "PRJEB29472", "RNAseq analysis of slbp mutants in Zebrafish", "ena-STUDY-Department of Cell and Developmental Biology-01-11-2018-15:10:58:144-14", "Other", "Through forward genetic screening for mutations affecting visual system development  we identified prominent coloboma and cell autonomous retinal neuron differentiation  lamination and retinal axon projection defects in eisspalte ele mutant zebrafish. Additional axonal deficits were present  most notably at midline axon commissures. Genetic mapping and cloning of the ele mutation showed that the affected gene is slbp  which encodes a conserved RNA stem loop binding protein involved in replication dependent histone mRNA metabolism. Cells throughout the central nervous system remained in the cell cycle in ele mutant embryos at stages when  and locations where  post mitotic cells have differentiated in wild type siblings. Indeed  RNAseq analysis showed down regulation of many genes associated with neuronal differentiation. This was coincident with changes in the levels and spatial localisation of expression of various genes implicated  for instance  in axon guidance  that likely underlie specific ele phenotypes. These results suggest that many of the cell and tissue specific phenotypes in ele mutant embryos are secondary to altered expression of modules of developmental regulatory genes that characterise  or promote transitions in  cell state and require the correct function of Slbp dependent histone and chromatin regulatory genes.", "ENA FIRST PUBLIC:2018 11 02|ENA LAST UPDATE:2018 11 01", null, null, "sibling 1", "SAMEA5059846", "Department of Cell and Developmental Biology", "ENA FIRST PUBLIC:2018 11 02T17:01:55Z|ENA LAST UPDATE:2018 11 01T15:11:02Z|External Id:SAMEA5059846|INSDC center name:Department of Cell and Developmental Biology|INSDC first public:2018 11 02T17:01:55Z|INSDC last update:2018 11 01T15:11:02Z|INSDC status:public|Submitter Id:ele sibling1|common name:zebrafish|sample name:ele sibling1|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq 3000 paired end sequencing", "ena EXPERIMENT Department of Cell and Developmental Biology 01 11 2018 15:10:57:717 4", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "ERP111778", "Illumina HiSeq 3000 paired end sequencing", "ENA FIRST PUBLIC:2018 11 02|ENA LAST UPDATE:2018 11 16", "ele_sib_B_TGACCA_L004_R1_001.fastq.gz ele_sib_B_TGACCA_L004_R2_001.fastq.gz", "fastq fastq", 5241628000.0, 26208140.0, "ena RUN Department of Cell and Developmental Biology 01 11 2018 15:10:57:717 4", "0:100 1:100", "A:1393802799;C:1235804455;G:1219328189;T:1392021956;N:670601", 100, 100, null, null, 1393802799, 1235804455, 1219328189, 1392021956, 670601, "ERX2871397", "ERS2871017", "ERA1643817", "Department of Cell and Developmental Biology|European Nucleotide Archive", "Department of Cell and Developmental Biology", 2, 0.95296, 0.95133, 0.10275, 0.1028, 0.67018, 0.67146, 0.46488, 0.46482, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2018-11-01", "Undetermined", "Embryo", "Undetermined", "Embryo Imprecise"], [9340, "ERR2865436", "ERX2871396", "ERS2871016", "ERP111778", "PRJEB29472", "RNAseq analysis of slbp mutants in Zebrafish", "ena-STUDY-Department of Cell and Developmental Biology-01-11-2018-15:10:58:144-14", "Other", "Through forward genetic screening for mutations affecting visual system development  we identified prominent coloboma and cell autonomous retinal neuron differentiation  lamination and retinal axon projection defects in eisspalte ele mutant zebrafish. Additional axonal deficits were present  most notably at midline axon commissures. Genetic mapping and cloning of the ele mutation showed that the affected gene is slbp  which encodes a conserved RNA stem loop binding protein involved in replication dependent histone mRNA metabolism. Cells throughout the central nervous system remained in the cell cycle in ele mutant embryos at stages when  and locations where  post mitotic cells have differentiated in wild type siblings. Indeed  RNAseq analysis showed down regulation of many genes associated with neuronal differentiation. This was coincident with changes in the levels and spatial localisation of expression of various genes implicated  for instance  in axon guidance  that likely underlie specific ele phenotypes. These results suggest that many of the cell and tissue specific phenotypes in ele mutant embryos are secondary to altered expression of modules of developmental regulatory genes that characterise  or promote transitions in  cell state and require the correct function of Slbp dependent histone and chromatin regulatory genes.", "ENA FIRST PUBLIC:2018 11 02|ENA LAST UPDATE:2018 11 01", null, null, "mutant3", "SAMEA5059845", "Department of Cell and Developmental Biology", "ENA FIRST PUBLIC:2018 11 02T17:01:55Z|ENA LAST UPDATE:2018 11 01T15:11:02Z|External Id:SAMEA5059845|INSDC center name:Department of Cell and Developmental Biology|INSDC first public:2018 11 02T17:01:55Z|INSDC last update:2018 11 01T15:11:02Z|INSDC status:public|Submitter Id:ele mutant3|common name:zebrafish|sample name:ele mutant3|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq 3000 paired end sequencing", "ena EXPERIMENT Department of Cell and Developmental Biology 01 11 2018 15:10:57:717 3", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "ERP111778", "Illumina HiSeq 3000 paired end sequencing", "ENA FIRST PUBLIC:2018 11 02|ENA LAST UPDATE:2018 11 16", "ele_E_CAGATC_L004_R1_001.fastq.gz ele_E_CAGATC_L004_R2_001.fastq.gz", "fastq fastq", 3529752000.0, 17648760.0, "ena RUN Department of Cell and Developmental Biology 01 11 2018 15:10:57:717 3", "0:100 1:100", "A:933354224;C:837396695;G:828677816;T:929860782;N:462483", 100, 100, null, null, 933354224, 837396695, 828677816, 929860782, 462483, "ERX2871396", "ERS2871016", "ERA1643817", "Department of Cell and Developmental Biology|European Nucleotide Archive", "Department of Cell and Developmental Biology", 2, 0.95621, 0.95302, 0.08584, 0.08536, 0.67048, 0.67146, 0.46615, 0.46682, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2018-11-01", "Undetermined", "Embryo", "Undetermined", "Embryo Imprecise"], [9341, "ERR2865435", "ERX2871395", "ERS2871015", "ERP111778", "PRJEB29472", "RNAseq analysis of slbp mutants in Zebrafish", "ena-STUDY-Department of Cell and Developmental Biology-01-11-2018-15:10:58:144-14", "Other", "Through forward genetic screening for mutations affecting visual system development  we identified prominent coloboma and cell autonomous retinal neuron differentiation  lamination and retinal axon projection defects in eisspalte ele mutant zebrafish. Additional axonal deficits were present  most notably at midline axon commissures. Genetic mapping and cloning of the ele mutation showed that the affected gene is slbp  which encodes a conserved RNA stem loop binding protein involved in replication dependent histone mRNA metabolism. Cells throughout the central nervous system remained in the cell cycle in ele mutant embryos at stages when  and locations where  post mitotic cells have differentiated in wild type siblings. Indeed  RNAseq analysis showed down regulation of many genes associated with neuronal differentiation. This was coincident with changes in the levels and spatial localisation of expression of various genes implicated  for instance  in axon guidance  that likely underlie specific ele phenotypes. These results suggest that many of the cell and tissue specific phenotypes in ele mutant embryos are secondary to altered expression of modules of developmental regulatory genes that characterise  or promote transitions in  cell state and require the correct function of Slbp dependent histone and chromatin regulatory genes.", "ENA FIRST PUBLIC:2018 11 02|ENA LAST UPDATE:2018 11 01", null, null, "mutant2", "SAMEA5059844", "Department of Cell and Developmental Biology", "ENA FIRST PUBLIC:2018 11 02T17:01:55Z|ENA LAST UPDATE:2018 11 01T15:11:02Z|External Id:SAMEA5059844|INSDC center name:Department of Cell and Developmental Biology|INSDC first public:2018 11 02T17:01:55Z|INSDC last update:2018 11 01T15:11:02Z|INSDC status:public|Submitter Id:ele mutant2|common name:zebrafish|sample name:ele mutant2|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq 3000 paired end sequencing", "ena EXPERIMENT Department of Cell and Developmental Biology 01 11 2018 15:10:57:717 2", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "ERP111778", "Illumina HiSeq 3000 paired end sequencing", "ENA FIRST PUBLIC:2018 11 02|ENA LAST UPDATE:2018 11 16", "ele_C_ACAGTG_L004_R1_001.fastq.gz ele_C_ACAGTG_L004_R2_001.fastq.gz", "fastq fastq", 3119723800.0, 15598619.0, "ena RUN Department of Cell and Developmental Biology 01 11 2018 15:10:57:717 2", "0:100 1:100", "A:828335602;C:736691663;G:727853394;T:826449133;N:394008", 100, 100, null, null, 828335602, 736691663, 727853394, 826449133, 394008, "ERX2871395", "ERS2871015", "ERA1643817", "Department of Cell and Developmental Biology|European Nucleotide Archive", "Department of Cell and Developmental Biology", 2, 0.94967, 0.94864, 0.0992, 0.09955, 0.65928, 0.66014, 0.47042, 0.46835, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2018-11-01", "Undetermined", "Embryo", "Undetermined", "Embryo Imprecise"], [9342, "ERR2865434", "ERX2871394", "ERS2871014", "ERP111778", "PRJEB29472", "RNAseq analysis of slbp mutants in Zebrafish", "ena-STUDY-Department of Cell and Developmental Biology-01-11-2018-15:10:58:144-14", "Other", "Through forward genetic screening for mutations affecting visual system development  we identified prominent coloboma and cell autonomous retinal neuron differentiation  lamination and retinal axon projection defects in eisspalte ele mutant zebrafish. Additional axonal deficits were present  most notably at midline axon commissures. Genetic mapping and cloning of the ele mutation showed that the affected gene is slbp  which encodes a conserved RNA stem loop binding protein involved in replication dependent histone mRNA metabolism. Cells throughout the central nervous system remained in the cell cycle in ele mutant embryos at stages when  and locations where  post mitotic cells have differentiated in wild type siblings. Indeed  RNAseq analysis showed down regulation of many genes associated with neuronal differentiation. This was coincident with changes in the levels and spatial localisation of expression of various genes implicated  for instance  in axon guidance  that likely underlie specific ele phenotypes. These results suggest that many of the cell and tissue specific phenotypes in ele mutant embryos are secondary to altered expression of modules of developmental regulatory genes that characterise  or promote transitions in  cell state and require the correct function of Slbp dependent histone and chromatin regulatory genes.", "ENA FIRST PUBLIC:2018 11 02|ENA LAST UPDATE:2018 11 01", null, null, "mutant1", "SAMEA5059843", "Department of Cell and Developmental Biology", "ENA FIRST PUBLIC:2018 11 02T17:01:55Z|ENA LAST UPDATE:2018 11 01T15:11:02Z|External Id:SAMEA5059843|INSDC center name:Department of Cell and Developmental Biology|INSDC first public:2018 11 02T17:01:55Z|INSDC last update:2018 11 01T15:11:02Z|INSDC status:public|Submitter Id:ele mutant1|common name:zebrafish|sample name:ele mutant1|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq 3000 paired end sequencing", "ena EXPERIMENT Department of Cell and Developmental Biology 01 11 2018 15:10:57:716 1", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "ERP111778", "Illumina HiSeq 3000 paired end sequencing", "ENA FIRST PUBLIC:2018 11 02|ENA LAST UPDATE:2018 11 16", "ele_A_CGATGT_L004_R1_001.fastq.gz ele_A_CGATGT_L004_R2_001.fastq.gz", "fastq fastq", 2181939600.0, 10909698.0, "ena RUN Department of Cell and Developmental Biology 01 11 2018 15:10:57:717 1", "0:100 1:100", "A:578028200;C:516249107;G:510965740;T:576417363;N:279190", 100, 100, null, null, 578028200, 516249107, 510965740, 576417363, 279190, "ERX2871394", "ERS2871014", "ERA1643817", "Department of Cell and Developmental Biology|European Nucleotide Archive", "Department of Cell and Developmental Biology", 2, 0.94968, 0.94939, 0.1131, 0.11293, 0.66245, 0.66251, 0.46654, 0.47475, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2018-11-01", "Undetermined", "Embryo", "Undetermined", "Embryo Imprecise"], [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.", null, null, null, null, "S21K1228", null, "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", null, null, null, null, null, null, null, null, "High 1", "H 1", "H 1", "missing", null, null, "RNA-Seq", "METATRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP491086", null, null, "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, null, null, 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", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "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.", null, null, null, null, "S21K1227", null, "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", null, null, null, null, null, null, null, null, "Medium 3", "M 3", "M 3", "missing", null, null, "RNA-Seq", "METATRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP491086", null, null, "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, null, null, 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", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "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.", null, null, null, null, "S21K1226", null, "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", null, null, null, null, null, null, null, null, "Medium 2", "M 2", "M 2", "missing", null, null, "RNA-Seq", "METATRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP491086", null, null, "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, null, null, 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", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "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.", null, null, null, null, "S21K1225", null, "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", null, null, null, null, null, null, null, null, "Medium 1", "M 1", "M 1", "missing", null, null, "RNA-Seq", "METATRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP491086", null, null, "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, null, null, 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", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "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.", null, null, null, null, "S21K1224", null, "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", null, null, null, null, null, null, null, null, "Low 3", "L 3", "L 3", "missing", null, null, "RNA-Seq", "METATRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP491086", null, null, "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, null, null, 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", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "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.", null, null, null, null, "S21K1223", null, "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", null, null, null, null, null, null, null, null, "Low 2", "L 2", "L 2", "missing", null, null, "RNA-Seq", "METATRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP491086", null, null, "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, null, null, 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", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "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.", null, null, null, null, "S21K1222", null, "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", null, null, null, null, null, null, null, null, "Low 1", "L 1", "L 1", "missing", null, null, "RNA-Seq", "METATRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP491086", null, null, "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, null, null, 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", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "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.", null, null, null, null, "S21K1221", null, "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", null, null, null, null, null, null, null, null, "Control 3", "C 3", "C 3", "missing", null, null, "RNA-Seq", "METATRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP491086", null, null, "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, null, null, 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", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "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.", null, null, null, null, "S21K1229", null, "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", null, null, null, null, null, null, null, null, "High 2", "H 2", "H 2", "missing", null, null, "RNA-Seq", "METATRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP491086", null, null, "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, null, null, 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", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "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.", null, null, null, null, "S21K1220", null, "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", null, null, null, null, null, null, null, null, "Control 2", "C 2", "C 2", "missing", null, null, "RNA-Seq", "METATRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP491086", null, null, "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, null, null, 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", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "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.", null, null, null, null, "S21K1219", null, "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", null, null, null, null, null, null, null, null, "Control 1", "C 1", "C 1", "missing", null, null, "RNA-Seq", "METATRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP491086", null, null, "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, null, null, 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", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "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.", null, null, null, "Zebrafish ac4C", "GSM8372406", null, "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", null, "Total RNA was extracted according to manufacturer\u2019s instruction. The stranded RNA sequencing library was constructed by KC DigitalTM Stranded mRNA Library Prep Kit for Illumina\u00ae Catalog NO. DR08502  Wuhan Seqhealth Co.  Ltd. China following the manufacturer\u2019s 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", null, "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\u00ae 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", null, "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP517393", null, null, "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, null, null, 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", null, "China", "2024-07-01", "Undetermined", "Undetermined", "Undetermined", "Undetermined"], [33886, "SRR30907854", "SRX26311176", "SRS22839346", "SRP537088", "PRJNA1167252", "Eukaryotic transcriptome sequencing of zebrafish", "PRJNA1167252", "Other", "To study the effects of TDCPP reports on protein expression and RNA transcription in zebrafish", null, null, null, "zebrafish", "E2 R1", null, "strain:zebrafish|isolate:missing|breed:AB|cultivar:missing|ecotype:missing|age:48hpf|dev stage:48hpf|collection date:2023 11 30|geo loc name:missing|sex:missing|tissue:missing|tmp:9|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "zebrafish", "9", "9", "Effects of TDCPP exposure on transcription in zebrafish", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina MiSeq", null, "SRP537088", null, null, "L1EFA241016_E2.R1.raw.fastq.gz L1EFA241016_E2.R2.raw.fastq.gz", "fastq fastq", 8244899282.0, 27300991.0, "L1EFA241016 E2.R1.raw.fastq.gz", "0:151 1:151", "A:2186915781;C:1920264424;G:1996130250;T:2141502974;N:85853", 151, 151, null, null, 2186915781, 1920264424, 1996130250, 2141502974, 85853, "SRX26311176", "SRS22839346", "SRA1987398", "Beijing Normal University|College of Water Sciences", "Beijing Normal University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "miseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-10-08", "Hatching", "Embryo", "Undetermined", "Embryo Imprecise"], [33887, "SRR30907855", "SRX26311175", "SRS22839344", "SRP537088", "PRJNA1167252", "Eukaryotic transcriptome sequencing of zebrafish", "PRJNA1167252", "Other", "To study the effects of TDCPP reports on protein expression and RNA transcription in zebrafish", null, null, null, "zebrafish", "E1 R1", null, "strain:zebrafish|isolate:missing|breed:AB|cultivar:missing|ecotype:missing|age:48hpf|dev stage:48hpf|collection date:2023 11 30|geo loc name:missing|sex:missing|tissue:missing|tmp:7|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "zebrafish", "7", "7", "Effects of TDCPP exposure on transcription in zebrafish", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina MiSeq", null, "SRP537088", null, null, "L1EFA241015_E1.R1.raw.fastq.gz L1EFA241015_E1.R2.raw.fastq.gz", "fastq fastq", 7083661566.0, 23455833.0, "L1EFA241015 E1.R1.raw.fastq.gz", "0:151 1:151", "A:1848193884;C:1679679234;G:1751186922;T:1804529897;N:71629", 151, 151, null, null, 1848193884, 1679679234, 1751186922, 1804529897, 71629, "SRX26311175", "SRS22839344", "SRA1987398", "Beijing Normal University|College of Water Sciences", "Beijing Normal University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "miseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-10-08", "Hatching", "Embryo", "Undetermined", "Embryo Imprecise"], [33888, "SRR30907856", "SRX26311174", "SRS22839345", "SRP537088", "PRJNA1167252", "Eukaryotic transcriptome sequencing of zebrafish", "PRJNA1167252", "Other", "To study the effects of TDCPP reports on protein expression and RNA transcription in zebrafish", null, null, null, "zebrafish", "A3 R1", null, "strain:zebrafish|isolate:missing|breed:AB|cultivar:missing|ecotype:missing|age:48hpf|dev stage:48hpf|collection date:2023 11 30|geo loc name:missing|sex:missing|tissue:missing|tmp:5|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "zebrafish", "5", "5", "Effects of TDCPP exposure on transcription in zebrafish", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina MiSeq", null, "SRP537088", null, null, "L1EFA241014_A3.R1.raw.fastq.gz L1EFA241014_A3.R2.raw.fastq.gz", "fastq fastq", 7926170898.0, 26245599.0, "L1EFA241014 A3.R1.raw.fastq.gz", "0:151 1:151", "A:2128209130;C:1819597773;G:1900902610;T:2077378388;N:82997", 151, 151, null, null, 2128209130, 1819597773, 1900902610, 2077378388, 82997, "SRX26311174", "SRS22839345", "SRA1987398", "Beijing Normal University|College of Water Sciences", "Beijing Normal University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "miseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-10-08", "Hatching", "Embryo", "Undetermined", "Embryo Imprecise"], [33889, "SRR30907857", "SRX26311173", "SRS22839343", "SRP537088", "PRJNA1167252", "Eukaryotic transcriptome sequencing of zebrafish", "PRJNA1167252", "Other", "To study the effects of TDCPP reports on protein expression and RNA transcription in zebrafish", null, null, null, "zebrafish", "A2 R1", null, "strain:zebrafish|isolate:missing|breed:AB|cultivar:missing|ecotype:missing|age:48hpf|dev stage:48hpf|collection date:2023 11 30|geo loc name:missing|sex:missing|tissue:missing|tmp:3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "zebrafish", "3", "3", "Effects of TDCPP exposure on transcription in zebrafish", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina MiSeq", null, "SRP537088", null, null, "L1EFA241013_A2.R1.raw.fastq.gz L1EFA241013_A2.R2.raw.fastq.gz", "fastq fastq", 7889851774.0, 26125337.0, "L1EFA241013 A2.R1.raw.fastq.gz", "0:151 1:151", "A:2121620438;C:1812268472;G:1879664190;T:2076216345;N:82329", 151, 151, null, null, 2121620438, 1812268472, 1879664190, 2076216345, 82329, "SRX26311173", "SRS22839343", "SRA1987398", "Beijing Normal University|College of Water Sciences", "Beijing Normal University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "miseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-10-08", "Hatching", "Embryo", "Undetermined", "Embryo Imprecise"], [33890, "SRR30907858", "SRX26311172", "SRS22839342", "SRP537088", "PRJNA1167252", "Eukaryotic transcriptome sequencing of zebrafish", "PRJNA1167252", "Other", "To study the effects of TDCPP reports on protein expression and RNA transcription in zebrafish", null, null, null, "zebrafish", "E3 R1", null, "strain:zebrafish|isolate:missing|breed:AB|cultivar:missing|ecotype:missing|age:48hpf|dev stage:48hpf|collection date:2023 11 30|geo loc name:missing|sex:missing|tissue:missing|tmp:11|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "zebrafish", "11", "11", "Effects of TDCPP exposure on transcription in zebrafish", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina MiSeq", null, "SRP537088", null, null, "L1EFA241017_E3.R1.raw.fastq.gz L1EFA241017_E3.R2.raw.fastq.gz", "fastq fastq", 7824546992.0, 25909096.0, "L1EFA241017 E3.R1.raw.fastq.gz", "0:151 1:151", "A:2082463940;C:1810596613;G:1891675714;T:2039730477;N:80248", 151, 151, null, null, 2082463940, 1810596613, 1891675714, 2039730477, 80248, "SRX26311172", "SRS22839342", "SRA1987398", "Beijing Normal University|College of Water Sciences", "Beijing Normal University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "miseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-10-08", "Hatching", "Embryo", "Undetermined", "Embryo Imprecise"], [33891, "SRR30907859", "SRX26311171", "SRS22839341", "SRP537088", "PRJNA1167252", "Eukaryotic transcriptome sequencing of zebrafish", "PRJNA1167252", "Other", "To study the effects of TDCPP reports on protein expression and RNA transcription in zebrafish", null, null, null, "zebrafish", "A1 R1", null, "strain:zebrafish|isolate:missing|breed:AB|cultivar:missing|ecotype:missing|age:48hpf|dev stage:48hpf|collection date:2023 11 30|geo loc name:missing|sex:missing|tissue:missing|tmp:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "zebrafish", "1", "1", "Effects of TDCPP exposure on transcription in zebrafish", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina MiSeq", null, "SRP537088", null, null, "L1EFA241012_A1.R1.raw.fastq.gz L1EFA241012_A1.R2.raw.fastq.gz", "fastq fastq", 8017250474.0, 26547187.0, "L1EFA241012 A1.R1.raw.fastq.gz", "0:151 1:151", "A:2139416119;C:1853218216;G:1930287523;T:2094246996;N:81620", 151, 151, null, null, 2139416119, 1853218216, 1930287523, 2094246996, 81620, "SRX26311171", "SRS22839341", "SRA1987398", "Beijing Normal University|College of Water Sciences", "Beijing Normal University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "miseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-10-08", "Hatching", "Embryo", "Undetermined", "Embryo Imprecise"], [50535, "SRR8134458", "SRX4955494", "SRS3996631", "SRP167225", "PRJNA501843", "Characterization of Transcriptomic Profile in Early Zebrafish PGCs by Single Cell Sequencing", "PRJNA501843", "Other", "Single cell RNA seq was applied for studying the transcriptomic profile in early zebrafish PGCsprimordial germ cells by choosing three time points during zebrafish embryonic development. The three time points were 6hpfhpf  also called shield stage  11hpfalso called 3 somite stage and 24hpfalso called prim 5 stage.", null, null, null, null, "H24 3", null, "strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|dev stage:24hpf biological replicate 3|sex:missing|tissue:PGC|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio: PGC", "H24 3", "H24 3", "smart2", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP167225", null, null, "H24_3_R1.fastq H24_3_R2.fastq", "fastq fastq", 1303220750.0, 5212883.0, "H24 3 R1.fastq", "0:125 1:125", "A:353042196;C:298548859;G:299882991;T:351742904;N:3800", 125, 125, null, null, 353042196, 298548859, 299882991, 351742904, 3800, "SRX4955494", "SRS3996631", "SRA800727", "Shanghai Institute of Biochemistry and Cell Biology, CAS|State Key Laboratory of cell Biology", "Shanghai Institute of Biochemistry and Cell Biology, CAS", 2, 0.95284, 0.94903, 0.03485, 0.03522, 0.8606, 0.86168, 0.49556, 0.49795, 125, 125, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "other", "unknown", "sc_generic", "single_cell_generic", "generic-scrnaseq-only", null, "China", "2019-02-01", "Pharyngula", "Embryo", "Undetermined", "Embryo Imprecise"], [50536, "SRR8134459", "SRX4955493", "SRS3996630", "SRP167225", "PRJNA501843", "Characterization of Transcriptomic Profile in Early Zebrafish PGCs by Single Cell Sequencing", "PRJNA501843", "Other", "Single cell RNA seq was applied for studying the transcriptomic profile in early zebrafish PGCsprimordial germ cells by choosing three time points during zebrafish embryonic development. The three time points were 6hpfhpf  also called shield stage  11hpfalso called 3 somite stage and 24hpfalso called prim 5 stage.", null, null, null, null, "H24 1", null, "strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|dev stage:24hpf biological replicate 1|sex:missing|tissue:PGC|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio: PGC", "H24 1", "H24 1", "smart2", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP167225", null, null, "H24_1_R1.fastq H24_1_R2.fastq", "fastq fastq", 1040367750.0, 4161471.0, "H24 1 R1.fastq", "0:125 1:125", "A:285190807;C:235796611;G:237165817;T:282211556;N:2959", 125, 125, null, null, 285190807, 235796611, 237165817, 282211556, 2959, "SRX4955493", "SRS3996630", "SRA800727", "Shanghai Institute of Biochemistry and Cell Biology, CAS|State Key Laboratory of cell Biology", "Shanghai Institute of Biochemistry and Cell Biology, CAS", 2, 0.94648, 0.94488, 0.0507, 0.05253, 0.87353, 0.87513, 0.52936, 0.52764, 125, 125, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "other", "unknown", "sc_generic", "single_cell_generic", "generic-scrnaseq-only", null, "China", "2019-02-01", "Pharyngula", "Embryo", "Undetermined", "Embryo Imprecise"], [50537, "SRR8134460", "SRX4955492", "SRS3996629", "SRP167225", "PRJNA501843", "Characterization of Transcriptomic Profile in Early Zebrafish PGCs by Single Cell Sequencing", "PRJNA501843", "Other", "Single cell RNA seq was applied for studying the transcriptomic profile in early zebrafish PGCsprimordial germ cells by choosing three time points during zebrafish embryonic development. The three time points were 6hpfhpf  also called shield stage  11hpfalso called 3 somite stage and 24hpfalso called prim 5 stage.", null, null, null, null, "H24 2", null, "strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|dev stage:24hpf biological replicate 2|sex:missing|tissue:PGC|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio: PGC", "H24 2", "H24 2", "smart2", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP167225", null, null, "H24_2_R1.fastq H24_2_R2.fastq", "fastq fastq", 1003243000.0, 4012972.0, "H24 2 R1.fastq", "0:125 1:125", "A:275192369;C:227024454;G:228346661;T:272676506;N:3010", 125, 125, null, null, 275192369, 227024454, 228346661, 272676506, 3010, "SRX4955492", "SRS3996629", "SRA800727", "Shanghai Institute of Biochemistry and Cell Biology, CAS|State Key Laboratory of cell Biology", "Shanghai Institute of Biochemistry and Cell Biology, CAS", 2, 0.94467, 0.94348, 0.06361, 0.06541, 0.8423, 0.84478, 0.51257, 0.51745, 125, 125, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "other", "unknown", "sc_generic", "single_cell_generic", "generic-scrnaseq-only", null, "China", "2019-02-01", "Pharyngula", "Embryo", "Undetermined", "Embryo Imprecise"], [50538, "SRR8134461", "SRX4955491", "SRS3996628", "SRP167225", "PRJNA501843", "Characterization of Transcriptomic Profile in Early Zebrafish PGCs by Single Cell Sequencing", "PRJNA501843", "Other", "Single cell RNA seq was applied for studying the transcriptomic profile in early zebrafish PGCsprimordial germ cells by choosing three time points during zebrafish embryonic development. The three time points were 6hpfhpf  also called shield stage  11hpfalso called 3 somite stage and 24hpfalso called prim 5 stage.", null, null, null, null, "H11 2", null, "strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|dev stage:11hpf biological replicate 2|sex:missing|tissue:PGC|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio: PGC", "H11 2", "H11 2", "smart2", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP167225", null, null, "H11_2_R1.fastq H11_2_R2.fastq", "fastq fastq", 1034277500.0, 4137110.0, "H11 2 R1.fastq", "0:125 1:125", "A:286346530;C:232910512;G:234755237;T:280262966;N:2255", 125, 125, null, null, 286346530, 232910512, 234755237, 280262966, 2255, "SRX4955491", "SRS3996628", "SRA800727", "Shanghai Institute of Biochemistry and Cell Biology, CAS|State Key Laboratory of cell Biology", "Shanghai Institute of Biochemistry and Cell Biology, CAS", 2, 0.94693, 0.94598, 0.03067, 0.03082, 0.8562, 0.85774, 0.51961, 0.51451, 125, 125, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "other", "unknown", "sc_generic", "single_cell_generic", "generic-scrnaseq-only", null, "China", "2019-02-01", "Segmentation", "Embryo", "Undetermined", "Embryo Imprecise"], [50539, "SRR8134462", "SRX4955490", "SRS3996627", "SRP167225", "PRJNA501843", "Characterization of Transcriptomic Profile in Early Zebrafish PGCs by Single Cell Sequencing", "PRJNA501843", "Other", "Single cell RNA seq was applied for studying the transcriptomic profile in early zebrafish PGCsprimordial germ cells by choosing three time points during zebrafish embryonic development. 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