metadata: run_metadata: 12 rows where experiment.library_layout = "PAIRED", experiment.library_selection = "other" and tissue_curation

12 rows where experiment.library_layout = "PAIRED", experiment.library_selection = "other" and tissue_curation_coarse = "Undetermined"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	sample.title	sample.alias	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.extractprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.study_ref	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.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	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
30650	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	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	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	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	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	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	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	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
30659	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	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	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	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

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