metadata: run_metadata: 34 rows where devstage_curation_coarse = "Multi-stage" and experiment.library

34 rows where devstage_curation_coarse = "Multi-stage" and experiment.library_selection = "other"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.PMIDs	sample.title	sample.alias	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.treatmentprotocol	GEOsample.extractprotocol	GEOsample.growthprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.study_ref	run.attributes	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.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
30658	30658	SRR28054753	SRX23704452	SRS20534448	SRP491086	PRJNA1078753	Integrated mRNA and miRNA sequencing analyses unveil the underlying mechanism of tobacco pollutant induced developmental toxicity in zebrafish embryos	PRJNA1078753	Other	Tobacco pollutants are prevalent in the environment leading to inadvertent exposure of pregnant females. Studies of these pollutants' toxic effects on development have not fully elucidated the potential underlying mechanisms. Therefore in this study we aim at investigate the developmental toxicity induced by cigarette smoke extract CSE at concentrations of 0.25% 1% and 2.5% using a zebrafish embryo toxicity test and integrated transcriptomic analysis of microRNA miRNA and messenger RNA mRNA. The findings revealed that CSE caused developmental toxicity including increased mortality and decreased incubation rate in a dose dependent manner. Moreover CSE induced malformations and apoptosis specifically in the head and heart of zebrafish larvae. We used mRNA and miRNA sequencing analyses to compare changes in the expression of genes and miRNAs in zebrafish larvae. The bioinformatics analysis indicates that the mechanism underlying CSE induced developmental toxicity was associated with genetic repair impairment apoptosis disorder and lipid metabolism disturbance. The enrichment analysis and RT qPCR show that the ctsba gene plays a crucial function in embryo developmental apoptosis and the fads2 gene mainly regulates lipid metabolic toxicity. The results of this study improve the understanding of CSE induced developmental toxicity in zebrafish embryos and contribute insights into the formulation of novel preventive strategies against tobacco pollutants during early embryonic development.			S21K1230	library ID:H 3\|title:High 3\|library strategy:OTHER\|library source:METATRANSCRIPTIOMIC\|library selection:other\|library layout:paired\|platform:ILLUMINA\|instrument model:RNA seq\|filetype:fastq\|filename:S21K1230 rep1 1 URNA S74 L003 R1 001.fastq\|filename2:S21K1230 rep1 1 URNA S74 L003 R2 001.fastq\|host:missing\|isolation source:missing\|collection date:missing\|geographic location:missing\|latitude and longitude:missing\|age:missing\|breed:missing\|cultivar:missing\|dev stage:missing\|ecotype:missing\|isolate:missing\|sex:missing\|strain:missing\|tissue:missing\|BioSampleModel:Model organism or animal									High 3	H 3	H 3	missing		RNA-Seq	METATRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP491086		S21K1230_rep1_1_URNA_S74_L003_R1_001.fastq.gz S21K1230_rep1_1_URNA_S74_L003_R2_001.fastq.gz	fastq fastq	6117817800.0	20392726.0	S21K1230 rep1 1 URNA S74 L003 R1 001.fastq.gz	0:150 1:150	A:1635728688;C:1405168032;G:1464072107;T:1612834762;N:14211	150	150	1635728688	1405168032	1464072107	1612834762	14211	SRX23704452	SRS20534448	SRA1806456	The Second Affiliated Hospital of Shantou University Medical College\|Department of Burns and Plastic Surgery	The Second Affiliated Hospital of Shantou University Medical College												B	B	biological fallback assumption	illumina	novaseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	China	2024-02-22	Undetermined	Multi-stage	Undetermined	Undetermined
30659	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
68556	68556	SRR18028171	SRX14182301	SRS12005942	SRP359829	PRJNA807002	samll RNA seq of zebrafish gonads of wildtype and pld6 / at 22 dpf	PRJNA807002	Other	In this study we generated zebrafish pld6 knockouts and found that the pld6 null mutants developed as infertile males with testes containing no germ cells. Pld6 is considered to be a candidate ribonuclease participating in primary piRNA biogenesis which is essential for the survival of germ cells. We deep sequenced 20 33 nt total small RNAs obtained from 22 dpf wildtype and pld6 / gonad with three repetition. In pld6 / gonad small RNAs mapped to the known piRNA clusters were almost absent. Moreover piRNA clusters in pld6 / gonad lost the enrichment for uridine at the first position or for adenine at the 10th position. our results unequivocally demonstrate a conserved role for MitoPLD in the piRNA biogenesis pathway.			6WT 3	strain:AB\|isolate:replicate3\|ecotype:wt\|age:post fertilization day 22\|dev stage:juvenile\|sex:missing\|tissue:Gonad\|BioSampleModel:Model organism or animal									wt 3 S11 L001 R1	011	011	Zebrafish larvae were anesthetized in 0.2 mg/mL MS 222 and disected to isolate gonads under a microscope. Three wildtype or mutant gonads were mixed into one repeat and three repeats were performed for samll RNA sequencing.		ncRNA-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	HiSeq X Ten	SRP359829		wt-3_S11_L001_R1_001.fastq.gz wt-3_S11_L001_R2_001.fastq.gz	fastq fastq	3576981600.0	11923272.0	wt 3 S11 L001 R1 001.fastq.gz	0:150 1:150	A:689001630;C:496844981;G:1779990511;T:610974133;N:170345	150	150	689001630	496844981	1779990511	610974133	170345	SRX14182301	SRS12005942	SRA1372890	Huazhong agricultural university\|School of Life Science and Technology	Huazhong agricultural university	2	0.8179	0.81697	0.60905	0.60864	0.82692	0.82915	0.52425	0.52623	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	China	2022-02-14	Multi-stage	Multi-stage	Gonad	Reproductive System
68557	68557	SRR18028172	SRX14182300	SRS12005941	SRP359829	PRJNA807002	samll RNA seq of zebrafish gonads of wildtype and pld6 / at 22 dpf	PRJNA807002	Other	In this study we generated zebrafish pld6 knockouts and found that the pld6 null mutants developed as infertile males with testes containing no germ cells. Pld6 is considered to be a candidate ribonuclease participating in primary piRNA biogenesis which is essential for the survival of germ cells. We deep sequenced 20 33 nt total small RNAs obtained from 22 dpf wildtype and pld6 / gonad with three repetition. In pld6 / gonad small RNAs mapped to the known piRNA clusters were almost absent. Moreover piRNA clusters in pld6 / gonad lost the enrichment for uridine at the first position or for adenine at the 10th position. our results unequivocally demonstrate a conserved role for MitoPLD in the piRNA biogenesis pathway.			5WT 2	strain:AB\|isolate:replicate2\|ecotype:wt\|age:post fertilization day 22\|dev stage:juvenile\|sex:missing\|tissue:Gonad\|BioSampleModel:Model organism or animal									wt 2 S10 L001 R1	009	009	Zebrafish larvae were anesthetized in 0.2 mg/mL MS 222 and disected to isolate gonads under a microscope. Three wildtype or mutant gonads were mixed into one repeat and three repeats were performed for samll RNA sequencing.		ncRNA-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	HiSeq X Ten	SRP359829		wt-2_S10_L001_R1_001.fastq.gz wt-2_S10_L001_R2_001.fastq.gz	fastq fastq	4200013800.0	14000046.0	wt 2 S10 L001 R1 001.fastq.gz	0:150 1:150	A:781057232;C:617020885;G:2110010128;T:691723797;N:201758	150	150	781057232	617020885	2110010128	691723797	201758	SRX14182300	SRS12005941	SRA1372890	Huazhong agricultural university\|School of Life Science and Technology	Huazhong agricultural university	2	0.8213	0.82216	0.59414	0.59507	0.81089	0.81306	0.53839	0.52755	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	China	2022-02-14	Multi-stage	Multi-stage	Gonad	Reproductive System
68558	68558	SRR18028173	SRX14182299	SRS12005940	SRP359829	PRJNA807002	samll RNA seq of zebrafish gonads of wildtype and pld6 / at 22 dpf	PRJNA807002	Other	In this study we generated zebrafish pld6 knockouts and found that the pld6 null mutants developed as infertile males with testes containing no germ cells. Pld6 is considered to be a candidate ribonuclease participating in primary piRNA biogenesis which is essential for the survival of germ cells. We deep sequenced 20 33 nt total small RNAs obtained from 22 dpf wildtype and pld6 / gonad with three repetition. In pld6 / gonad small RNAs mapped to the known piRNA clusters were almost absent. Moreover piRNA clusters in pld6 / gonad lost the enrichment for uridine at the first position or for adenine at the 10th position. our results unequivocally demonstrate a conserved role for MitoPLD in the piRNA biogenesis pathway.			4WT 1	strain:AB\|isolate:replicate1\|ecotype:wt\|age:post fertilization day 22\|dev stage:juvenile\|sex:missing\|tissue:Gonad\|BioSampleModel:Model organism or animal									wt 1 S9 L001 R1	007	007	Zebrafish larvae were anesthetized in 0.2 mg/mL MS 222 and disected to isolate gonads under a microscope. Three wildtype or mutant gonads were mixed into one repeat and three repeats were performed for samll RNA sequencing.		ncRNA-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	HiSeq X Ten	SRP359829		wt-1_S9_L001_R1_001.fastq.gz wt-1_S9_L001_R2_001.fastq.gz	fastq fastq	4820063700.0	16066879.0	wt 1 S9 L001 R1 001.fastq.gz	0:150 1:150	A:996304548;C:657334691;G:2379519106;T:786675131;N:230224	150	150	996304548	657334691	2379519106	786675131	230224	SRX14182299	SRS12005940	SRA1372890	Huazhong agricultural university\|School of Life Science and Technology	Huazhong agricultural university	2	0.80219	0.80319	0.60906	0.60878	0.83238	0.83303	0.52559	0.51852	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	China	2022-02-14	Multi-stage	Multi-stage	Gonad	Reproductive System
68559	68559	SRR18028174	SRX14182298	SRS12005939	SRP359829	PRJNA807002	samll RNA seq of zebrafish gonads of wildtype and pld6 / at 22 dpf	PRJNA807002	Other	In this study we generated zebrafish pld6 knockouts and found that the pld6 null mutants developed as infertile males with testes containing no germ cells. Pld6 is considered to be a candidate ribonuclease participating in primary piRNA biogenesis which is essential for the survival of germ cells. We deep sequenced 20 33 nt total small RNAs obtained from 22 dpf wildtype and pld6 / gonad with three repetition. In pld6 / gonad small RNAs mapped to the known piRNA clusters were almost absent. Moreover piRNA clusters in pld6 / gonad lost the enrichment for uridine at the first position or for adenine at the 10th position. our results unequivocally demonstrate a conserved role for MitoPLD in the piRNA biogenesis pathway.			3PLD6 3	strain:AB\|isolate:replicate3\|ecotype:pld6 / \|age:post fertilization day 22\|dev stage:juvenile\|sex:missing\|tissue:Gonad\|BioSampleModel:Model organism or animal									pld6 3 S3 L003 R1	005	005	Zebrafish larvae were anesthetized in 0.2 mg/mL MS 222 and disected to isolate gonads under a microscope. Three wildtype or mutant gonads were mixed into one repeat and three repeats were performed for samll RNA sequencing.		ncRNA-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	HiSeq X Ten	SRP359829		pld6-3_S3_L003_R1_001.fastq.gz pld6-3_S3_L003_R2_001.fastq.gz	fastq fastq	816686700.0	2722289.0	pld6 3 S3 L003 R1 001.fastq.gz	0:150 1:150	A:145681738;C:137123477;G:401610833;T:132256312;N:14340	150	150	145681738	137123477	401610833	132256312	14340	SRX14182298	SRS12005939	SRA1372890	Huazhong agricultural university\|School of Life Science and Technology	Huazhong agricultural university	2	0.78314	0.73942	0.07641	0.09097	0.91603	0.91545	0.6312	0.64467	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	China	2022-02-14	Multi-stage	Multi-stage	Gonad	Reproductive System
68560	68560	SRR18028175	SRX14182297	SRS12005938	SRP359829	PRJNA807002	samll RNA seq of zebrafish gonads of wildtype and pld6 / at 22 dpf	PRJNA807002	Other	In this study we generated zebrafish pld6 knockouts and found that the pld6 null mutants developed as infertile males with testes containing no germ cells. Pld6 is considered to be a candidate ribonuclease participating in primary piRNA biogenesis which is essential for the survival of germ cells. We deep sequenced 20 33 nt total small RNAs obtained from 22 dpf wildtype and pld6 / gonad with three repetition. In pld6 / gonad small RNAs mapped to the known piRNA clusters were almost absent. Moreover piRNA clusters in pld6 / gonad lost the enrichment for uridine at the first position or for adenine at the 10th position. our results unequivocally demonstrate a conserved role for MitoPLD in the piRNA biogenesis pathway.			2PLD6 2	strain:AB\|isolate:replicate2\|ecotype:pld6 / \|age:post fertilization day 22\|dev stage:juvenile\|sex:missing\|tissue:Gonad\|BioSampleModel:Model organism or animal									pld6 2 S2 L003 R1	003	003	Zebrafish larvae were anesthetized in 0.2 mg/mL MS 222 and disected to isolate gonads under a microscope. Three wildtype or mutant gonads were mixed into one repeat and three repeats were performed for samll RNA sequencing.		ncRNA-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	HiSeq X Ten	SRP359829		pld6-2_S2_L003_R1_001.fastq.gz pld6-2_S2_L003_R2_001.fastq.gz	fastq fastq	6546276900.0	21820923.0	pld6 2 S2 L003 R1 001.fastq.gz	0:150 1:150	A:1161502458;C:1095580994;G:3226725392;T:1062358099;N:109957	150	150	1161502458	1095580994	3226725392	1062358099	109957	SRX14182297	SRS12005938	SRA1372890	Huazhong agricultural university\|School of Life Science and Technology	Huazhong agricultural university	2	0.6471	0.593	0.07935	0.09168	0.92058	0.92005	0.53626	0.65284	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	China	2022-02-14	Multi-stage	Multi-stage	Gonad	Reproductive System
68561	68561	SRR18028176	SRX14182296	SRS12005937	SRP359829	PRJNA807002	samll RNA seq of zebrafish gonads of wildtype and pld6 / at 22 dpf	PRJNA807002	Other	In this study we generated zebrafish pld6 knockouts and found that the pld6 null mutants developed as infertile males with testes containing no germ cells. Pld6 is considered to be a candidate ribonuclease participating in primary piRNA biogenesis which is essential for the survival of germ cells. We deep sequenced 20 33 nt total small RNAs obtained from 22 dpf wildtype and pld6 / gonad with three repetition. In pld6 / gonad small RNAs mapped to the known piRNA clusters were almost absent. Moreover piRNA clusters in pld6 / gonad lost the enrichment for uridine at the first position or for adenine at the 10th position. our results unequivocally demonstrate a conserved role for MitoPLD in the piRNA biogenesis pathway.			1PLD6 1	strain:AB\|isolate:replicate1\|ecotype:pld6 / \|age:post fertilization day 22\|dev stage:juvenile\|sex:missing\|tissue:Gonad\|BioSampleModel:Model organism or animal									pld6 1 S1 L003 R1	001	001	Zebrafish larvae were anesthetized in 0.2 mg/mL MS 222 and disected to isolate gonads under a microscope. Three wildtype or mutant gonads were mixed into one repeat and three repeats were performed for samll RNA sequencing.		ncRNA-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	HiSeq X Ten	SRP359829		pld6-1_S1_L003_R1_001.fastq.gz pld6-1_S1_L003_R2_001.fastq.gz	fastq fastq	5535130200.0	18450434.0	pld6 1 S1 L003 R1 001.fastq.gz	0:150 1:150	A:1014761790;C:833992394;G:2813863824;T:872418512;N:93680	150	150	1014761790	833992394	2813863824	872418512	93680	SRX14182296	SRS12005937	SRA1372890	Huazhong agricultural university\|School of Life Science and Technology	Huazhong agricultural university	2	0.70358	0.73288	0.08649	0.09366	0.91066	0.90914	0.6197	0.6207	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	China	2022-02-14	Multi-stage	Multi-stage	Gonad	Reproductive System
71064	71064	SRR21218373	SRX17229104	SRS14795570	SRP394145	PRJNA872137	The Translation Initiation Factor Homolog eif4e1c Regulates Cardiomyocyte Metabolism and Proliferation During Heart Regeneration.	GSE211793	Other	The?eIF4E family of translation initiation factors bind five prime methylated caps and act as the limiting step for mRNA translation. The canonical eIF4E1A is required for cell viability yet other related families exist and are all utilized in specific contexts or tissues. Here we describe a new family called Eif4e1c that is ancestral to the canonical eIF4E1A in vertebrates and for which we find roles during heart development and regeneration in zebrafish.?The Eif4e1c family is present in all aquatic vertebrates but has been lost in all terrestrial species. A core group of amino acids shared over 500 million yrs of evolution from?ray finned fish to sharks?forms an evolutionarily conserved binding interface along the surface of the protein suggesting Eif4e1c functions in a novel pathway.? Deletion of eif4e1c?in zebrafish caused growth deficits and impaired survival in juveniles.?Mutants surviving to maturity had fewer cardiomyocytes while also showing reduced proliferative responses to cardiac injury. Ribosome profiling of mutant hearts demonstrated changes in translation efficiency of mRNA for genes known to regulate cardiomyocyte proliferation. Although?eif4e1c?is expressed in many tissues and is the predominant cap binding initiation homolog in embryos its disruption had most notable impact on the heart and at juvenile stages. ?Our findings reveal context dependent requirements for translation initiation regulators during heart regeneration. Overall design: Ribosome profiling of adult uninjured eif4e1c zebrafish mutant hearts and adult uninjured EK zebrafish wildtype hearts.	pubmed:37306388	zebrafish Ribo seq Eif4e1c / rep2 [r mR2]	GSM6502516	source name:heart\|tissue:heart\|cell line:Mutant\|genotype:Eif4e1c /	zebrafish Ribo seq Eif4e1c / rep2 [r mR2]	Fastq files were processed using FastQC v0.11.8; RRID:SCR 014583 for quality control QC analysis. Pre processing of sequencing reads was based on the QC report using the FASTQ Quality Filter module in the FASTX Toolkit RRID:SCR 019035. This was used to filter the bases with 99% accuracy based on Q Score. Reads were removed that showed less than 70% of nucleotides with an accuracy of at least 99%. The sequences were collapsed according to their by Unique Molecular Identifiers UMIs. Cutadapt RRID:SCR 011841 was used to trim 21 nt adaptor before the first nt and the last 4 nt from the reads to remove the UMI. The processed reads were aligned to GRCz11/danRer11 assembly of the zebrafish genome; Genome Reference Consortium using STAR v2.5.3a RRID:SCR 004463. Generated bam files were processed with RiboProfiling package v1.2.2. Coverage counts on the coding regions CDS were obtained for each sample based on RiboProfiling function modules TxDb.Drerio.UCSC.danRer11.refGene v3.4.6; Annotation package for TxDb objects; Team BC 2019 and GenomicFeatures package v1.46.1. Differential expression analysis was performed using the DESeq2 pipeline version 1.26.0 based on the expressed raw reads. Assembly: GRCz11/danRer11 Library strategy: Ribo seq	heart		The hearts were lysed on ice with 100ul of lysis buffer with 53 mg/ml cycloheximide using mechanical homogenization with a pestle for thirty seconds. Cells were lysed further by trituration of the sample using a 27.5 gauge needle syringe 20x on ice. Cell extracts average OD 7 were treated with MNase NEB CaCl2 5mM final concentration and Turbo DNAse I Invitrogen at 25°C for 30 minutes. MNase digestion was stopped with SUPERase inhibitor incubation on ice. 80S ribosomes were isolated using SH400 spin columns Cytiva. Columns were prepared according to the manufacturer’s instructions. 100 µls of MNase treated sample was loaded per column and centrifuged for 2 min at 600 RCF. The flow through was isolated and incubated for 5 min. with 3x volume of Trizol LS Ambion. 200 µl of chloroform was added and incubated for 2 min. Samples were centrifuged for 15 min. at 12 000 rpm 4°C. The aqueous phase was extracted and precipitated overnight at 20°C using glycoblue ThermoFisher and isopropanol followed by centrifugation for 30 minutes at 4C at 10 000 RPM. Pellets were washed with 75% Ethanol and resuspended into RNase free water. Next Flex smRNA seq kit v3	Zebrafish used for ribosome profiling were grown together under normal conditions and were genotyped upon reaching maturity.	tissue:heart\|cell line:Mutant\|genotype:Eif4e1c /	GSM6502516	GSM6502516: zebrafish Ribo seq Eif4e1c / rep2 [r mR2]; Danio rerio; OTHER	GSM6502516 r1	GSM6502516	1	The hearts were lysed on ice with 100ul of lysis buffer with 53 mg/ml cycloheximide using mechanical homogenization with a pestle for thirty seconds. Cells were lysed further by trituration of the sample using a 27.5 gauge needle syringe 20x on ice. Cell extracts average OD 7 were treated with MNase NEB CaCl2 5mM final concentration and Turbo DNAse I Invitrogen at 25°C for 30 minutes. MNase digestion was stopped with SUPERase inhibitor incubation on ice. 80S ribosomes were isolated using SH400 spin columns Cytiva. Columns were prepared according to the manufacturer's instructions. 100 µls of MNase treated sample was loaded per column and centrifuged for 2 min at 600 RCF. The flow through was isolated and incubated for 5 min. with 3x volume of Trizol LS Ambion. 200 µl of chloroform was added and incubated for 2 min. Samples were centrifuged for 15 min. at 12 000 rpm 4°C. The aqueous phase was extracted and precipitated overnight at 20°C using glycoblue ThermoFisher and isopropanol followed by centrifugation for 30 minutes at 4C at 10 000 RPM. Pellets were washed with 75% Ethanol and resuspended into RNase free water. Next Flex smRNA seq kit v3	OTHER	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	NextSeq 550	SRP394145		rS4_mR2.fastq.gz	fastq	6611131472.0	86988572.0	GSM6502516 r1	0:76 1:0	A:1748359123;C:1658689534;G:1706027528;T:1497702781;N:352506	76	0	1748359123	1658689534	1706027528	1497702781	352506	SRX17229104	SRS14795570	SRA1485233	Biological Chemistry and Pharmacology, The Ohio State University	Biological Chemistry and Pharmacology, The Ohio State University	1	0.0		0.0		1.0				76		T		under 1.2% mapping rate	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	United States	2022-08-22	Undetermined	Multi-stage	Heart	Cardiovascular System
71065	71065	SRR21218374	SRX17229103	SRS14795569	SRP394145	PRJNA872137	The Translation Initiation Factor Homolog eif4e1c Regulates Cardiomyocyte Metabolism and Proliferation During Heart Regeneration.	GSE211793	Other	The?eIF4E family of translation initiation factors bind five prime methylated caps and act as the limiting step for mRNA translation. The canonical eIF4E1A is required for cell viability yet other related families exist and are all utilized in specific contexts or tissues. Here we describe a new family called Eif4e1c that is ancestral to the canonical eIF4E1A in vertebrates and for which we find roles during heart development and regeneration in zebrafish.?The Eif4e1c family is present in all aquatic vertebrates but has been lost in all terrestrial species. A core group of amino acids shared over 500 million yrs of evolution from?ray finned fish to sharks?forms an evolutionarily conserved binding interface along the surface of the protein suggesting Eif4e1c functions in a novel pathway.? Deletion of eif4e1c?in zebrafish caused growth deficits and impaired survival in juveniles.?Mutants surviving to maturity had fewer cardiomyocytes while also showing reduced proliferative responses to cardiac injury. Ribosome profiling of mutant hearts demonstrated changes in translation efficiency of mRNA for genes known to regulate cardiomyocyte proliferation. Although?eif4e1c?is expressed in many tissues and is the predominant cap binding initiation homolog in embryos its disruption had most notable impact on the heart and at juvenile stages. ?Our findings reveal context dependent requirements for translation initiation regulators during heart regeneration. Overall design: Ribosome profiling of adult uninjured eif4e1c zebrafish mutant hearts and adult uninjured EK zebrafish wildtype hearts.	pubmed:37306388	zebrafish Ribo seq Eif4e1c / rep 1 [r mR1]	GSM6502515	source name:heart\|tissue:heart\|cell line:Mutant\|genotype:Eif4e1c /	zebrafish Ribo seq Eif4e1c / rep 1 [r mR1]	Fastq files were processed using FastQC v0.11.8; RRID:SCR 014583 for quality control QC analysis. Pre processing of sequencing reads was based on the QC report using the FASTQ Quality Filter module in the FASTX Toolkit RRID:SCR 019035. This was used to filter the bases with 99% accuracy based on Q Score. Reads were removed that showed less than 70% of nucleotides with an accuracy of at least 99%. The sequences were collapsed according to their by Unique Molecular Identifiers UMIs. Cutadapt RRID:SCR 011841 was used to trim 21 nt adaptor before the first nt and the last 4 nt from the reads to remove the UMI. The processed reads were aligned to GRCz11/danRer11 assembly of the zebrafish genome; Genome Reference Consortium using STAR v2.5.3a RRID:SCR 004463. Generated bam files were processed with RiboProfiling package v1.2.2. Coverage counts on the coding regions CDS were obtained for each sample based on RiboProfiling function modules TxDb.Drerio.UCSC.danRer11.refGene v3.4.6; Annotation package for TxDb objects; Team BC 2019 and GenomicFeatures package v1.46.1. Differential expression analysis was performed using the DESeq2 pipeline version 1.26.0 based on the expressed raw reads. Assembly: GRCz11/danRer11 Library strategy: Ribo seq	heart		The hearts were lysed on ice with 100ul of lysis buffer with 53 mg/ml cycloheximide using mechanical homogenization with a pestle for thirty seconds. Cells were lysed further by trituration of the sample using a 27.5 gauge needle syringe 20x on ice. Cell extracts average OD 7 were treated with MNase NEB CaCl2 5mM final concentration and Turbo DNAse I Invitrogen at 25°C for 30 minutes. MNase digestion was stopped with SUPERase inhibitor incubation on ice. 80S ribosomes were isolated using SH400 spin columns Cytiva. Columns were prepared according to the manufacturer’s instructions. 100 µls of MNase treated sample was loaded per column and centrifuged for 2 min at 600 RCF. The flow through was isolated and incubated for 5 min. with 3x volume of Trizol LS Ambion. 200 µl of chloroform was added and incubated for 2 min. Samples were centrifuged for 15 min. at 12 000 rpm 4°C. The aqueous phase was extracted and precipitated overnight at 20°C using glycoblue ThermoFisher and isopropanol followed by centrifugation for 30 minutes at 4C at 10 000 RPM. Pellets were washed with 75% Ethanol and resuspended into RNase free water. Next Flex smRNA seq kit v3	Zebrafish used for ribosome profiling were grown together under normal conditions and were genotyped upon reaching maturity.	tissue:heart\|cell line:Mutant\|genotype:Eif4e1c /	GSM6502515	GSM6502515: zebrafish Ribo seq Eif4e1c / rep 1 [r mR1]; Danio rerio; OTHER	GSM6502515 r1	GSM6502515	1	The hearts were lysed on ice with 100ul of lysis buffer with 53 mg/ml cycloheximide using mechanical homogenization with a pestle for thirty seconds. Cells were lysed further by trituration of the sample using a 27.5 gauge needle syringe 20x on ice. Cell extracts average OD 7 were treated with MNase NEB CaCl2 5mM final concentration and Turbo DNAse I Invitrogen at 25°C for 30 minutes. MNase digestion was stopped with SUPERase inhibitor incubation on ice. 80S ribosomes were isolated using SH400 spin columns Cytiva. Columns were prepared according to the manufacturer's instructions. 100 µls of MNase treated sample was loaded per column and centrifuged for 2 min at 600 RCF. The flow through was isolated and incubated for 5 min. with 3x volume of Trizol LS Ambion. 200 µl of chloroform was added and incubated for 2 min. Samples were centrifuged for 15 min. at 12 000 rpm 4°C. The aqueous phase was extracted and precipitated overnight at 20°C using glycoblue ThermoFisher and isopropanol followed by centrifugation for 30 minutes at 4C at 10 000 RPM. Pellets were washed with 75% Ethanol and resuspended into RNase free water. Next Flex smRNA seq kit v3	OTHER	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	NextSeq 550	SRP394145		rS3_mR1.fastq.gz	fastq	13677356644.0	179965219.0	GSM6502515 r1	0:76 1:0	A:3346749848;C:3412648254;G:3629003006;T:3288222747;N:732789	76	0	3346749848	3412648254	3629003006	3288222747	732789	SRX17229103	SRS14795569	SRA1485233	Biological Chemistry and Pharmacology, The Ohio State University	Biological Chemistry and Pharmacology, The Ohio State University	1	0.0		0.0		1.0				76		T		under 1.2% mapping rate	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	United States	2022-08-22	Undetermined	Multi-stage	Heart	Cardiovascular System
71066	71066	SRR21218377	SRX17229102	SRS14795568	SRP394145	PRJNA872137	The Translation Initiation Factor Homolog eif4e1c Regulates Cardiomyocyte Metabolism and Proliferation During Heart Regeneration.	GSE211793	Other	The?eIF4E family of translation initiation factors bind five prime methylated caps and act as the limiting step for mRNA translation. The canonical eIF4E1A is required for cell viability yet other related families exist and are all utilized in specific contexts or tissues. Here we describe a new family called Eif4e1c that is ancestral to the canonical eIF4E1A in vertebrates and for which we find roles during heart development and regeneration in zebrafish.?The Eif4e1c family is present in all aquatic vertebrates but has been lost in all terrestrial species. A core group of amino acids shared over 500 million yrs of evolution from?ray finned fish to sharks?forms an evolutionarily conserved binding interface along the surface of the protein suggesting Eif4e1c functions in a novel pathway.? Deletion of eif4e1c?in zebrafish caused growth deficits and impaired survival in juveniles.?Mutants surviving to maturity had fewer cardiomyocytes while also showing reduced proliferative responses to cardiac injury. Ribosome profiling of mutant hearts demonstrated changes in translation efficiency of mRNA for genes known to regulate cardiomyocyte proliferation. Although?eif4e1c?is expressed in many tissues and is the predominant cap binding initiation homolog in embryos its disruption had most notable impact on the heart and at juvenile stages. ?Our findings reveal context dependent requirements for translation initiation regulators during heart regeneration. Overall design: Ribosome profiling of adult uninjured eif4e1c zebrafish mutant hearts and adult uninjured EK zebrafish wildtype hearts.	pubmed:37306388	zebrafish Ribo seq Eif4e1c +/+ rep 2 [r pR2]	GSM6502514	source name:heart\|tissue:heart\|cell line:Wt\|genotype:Eif4e1c +/+	zebrafish Ribo seq Eif4e1c +/+ rep 2 [r pR2]	Fastq files were processed using FastQC v0.11.8; RRID:SCR 014583 for quality control QC analysis. Pre processing of sequencing reads was based on the QC report using the FASTQ Quality Filter module in the FASTX Toolkit RRID:SCR 019035. This was used to filter the bases with 99% accuracy based on Q Score. Reads were removed that showed less than 70% of nucleotides with an accuracy of at least 99%. The sequences were collapsed according to their by Unique Molecular Identifiers UMIs. Cutadapt RRID:SCR 011841 was used to trim 21 nt adaptor before the first nt and the last 4 nt from the reads to remove the UMI. The processed reads were aligned to GRCz11/danRer11 assembly of the zebrafish genome; Genome Reference Consortium using STAR v2.5.3a RRID:SCR 004463. Generated bam files were processed with RiboProfiling package v1.2.2. Coverage counts on the coding regions CDS were obtained for each sample based on RiboProfiling function modules TxDb.Drerio.UCSC.danRer11.refGene v3.4.6; Annotation package for TxDb objects; Team BC 2019 and GenomicFeatures package v1.46.1. Differential expression analysis was performed using the DESeq2 pipeline version 1.26.0 based on the expressed raw reads. Assembly: GRCz11/danRer11 Library strategy: Ribo seq	heart		The hearts were lysed on ice with 100ul of lysis buffer with 53 mg/ml cycloheximide using mechanical homogenization with a pestle for thirty seconds. Cells were lysed further by trituration of the sample using a 27.5 gauge needle syringe 20x on ice. Cell extracts average OD 7 were treated with MNase NEB CaCl2 5mM final concentration and Turbo DNAse I Invitrogen at 25°C for 30 minutes. MNase digestion was stopped with SUPERase inhibitor incubation on ice. 80S ribosomes were isolated using SH400 spin columns Cytiva. Columns were prepared according to the manufacturer’s instructions. 100 µls of MNase treated sample was loaded per column and centrifuged for 2 min at 600 RCF. The flow through was isolated and incubated for 5 min. with 3x volume of Trizol LS Ambion. 200 µl of chloroform was added and incubated for 2 min. Samples were centrifuged for 15 min. at 12 000 rpm 4°C. The aqueous phase was extracted and precipitated overnight at 20°C using glycoblue ThermoFisher and isopropanol followed by centrifugation for 30 minutes at 4C at 10 000 RPM. Pellets were washed with 75% Ethanol and resuspended into RNase free water. Next Flex smRNA seq kit v3	Zebrafish used for ribosome profiling were grown together under normal conditions and were genotyped upon reaching maturity.	tissue:heart\|cell line:Wt\|genotype:Eif4e1c +/+	GSM6502514	GSM6502514: zebrafish Ribo seq Eif4e1c +/+ rep 2 [r pR2]; Danio rerio; OTHER	GSM6502514 r1	GSM6502514	1	The hearts were lysed on ice with 100ul of lysis buffer with 53 mg/ml cycloheximide using mechanical homogenization with a pestle for thirty seconds. Cells were lysed further by trituration of the sample using a 27.5 gauge needle syringe 20x on ice. Cell extracts average OD 7 were treated with MNase NEB CaCl2 5mM final concentration and Turbo DNAse I Invitrogen at 25°C for 30 minutes. MNase digestion was stopped with SUPERase inhibitor incubation on ice. 80S ribosomes were isolated using SH400 spin columns Cytiva. Columns were prepared according to the manufacturer's instructions. 100 µls of MNase treated sample was loaded per column and centrifuged for 2 min at 600 RCF. The flow through was isolated and incubated for 5 min. with 3x volume of Trizol LS Ambion. 200 µl of chloroform was added and incubated for 2 min. Samples were centrifuged for 15 min. at 12 000 rpm 4°C. The aqueous phase was extracted and precipitated overnight at 20°C using glycoblue ThermoFisher and isopropanol followed by centrifugation for 30 minutes at 4C at 10 000 RPM. Pellets were washed with 75% Ethanol and resuspended into RNase free water. Next Flex smRNA seq kit v3	OTHER	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	NextSeq 550	SRP394145		rS2_pR2.fastq.gz	fastq	8919983048.0	117368198.0	GSM6502514 r1	0:76 1:0	A:2208663451;C:2257902067;G:2371468879;T:2081476473;N:472178	76	0	2208663451	2257902067	2371468879	2081476473	472178	SRX17229102	SRS14795568	SRA1485233	Biological Chemistry and Pharmacology, The Ohio State University	Biological Chemistry and Pharmacology, The Ohio State University	1	1e-05		0.0		0.99997		1.0		76		T		under 1.2% mapping rate	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	United States	2022-08-22	Undetermined	Multi-stage	Heart	Cardiovascular System
71067	71067	SRR21218378	SRX17229101	SRS14795567	SRP394145	PRJNA872137	The Translation Initiation Factor Homolog eif4e1c Regulates Cardiomyocyte Metabolism and Proliferation During Heart Regeneration.	GSE211793	Other	The?eIF4E family of translation initiation factors bind five prime methylated caps and act as the limiting step for mRNA translation. The canonical eIF4E1A is required for cell viability yet other related families exist and are all utilized in specific contexts or tissues. Here we describe a new family called Eif4e1c that is ancestral to the canonical eIF4E1A in vertebrates and for which we find roles during heart development and regeneration in zebrafish.?The Eif4e1c family is present in all aquatic vertebrates but has been lost in all terrestrial species. A core group of amino acids shared over 500 million yrs of evolution from?ray finned fish to sharks?forms an evolutionarily conserved binding interface along the surface of the protein suggesting Eif4e1c functions in a novel pathway.? Deletion of eif4e1c?in zebrafish caused growth deficits and impaired survival in juveniles.?Mutants surviving to maturity had fewer cardiomyocytes while also showing reduced proliferative responses to cardiac injury. Ribosome profiling of mutant hearts demonstrated changes in translation efficiency of mRNA for genes known to regulate cardiomyocyte proliferation. Although?eif4e1c?is expressed in many tissues and is the predominant cap binding initiation homolog in embryos its disruption had most notable impact on the heart and at juvenile stages. ?Our findings reveal context dependent requirements for translation initiation regulators during heart regeneration. Overall design: Ribosome profiling of adult uninjured eif4e1c zebrafish mutant hearts and adult uninjured EK zebrafish wildtype hearts.	pubmed:37306388	zebrafish Ribo seq Eif4e1c +/+ rep 1 [r pR1]	GSM6502513	source name:heart\|tissue:heart\|cell line:Wt\|genotype:Eif4e1c +/+	zebrafish Ribo seq Eif4e1c +/+ rep 1 [r pR1]	Fastq files were processed using FastQC v0.11.8; RRID:SCR 014583 for quality control QC analysis. Pre processing of sequencing reads was based on the QC report using the FASTQ Quality Filter module in the FASTX Toolkit RRID:SCR 019035. This was used to filter the bases with 99% accuracy based on Q Score. Reads were removed that showed less than 70% of nucleotides with an accuracy of at least 99%. The sequences were collapsed according to their by Unique Molecular Identifiers UMIs. Cutadapt RRID:SCR 011841 was used to trim 21 nt adaptor before the first nt and the last 4 nt from the reads to remove the UMI. The processed reads were aligned to GRCz11/danRer11 assembly of the zebrafish genome; Genome Reference Consortium using STAR v2.5.3a RRID:SCR 004463. Generated bam files were processed with RiboProfiling package v1.2.2. Coverage counts on the coding regions CDS were obtained for each sample based on RiboProfiling function modules TxDb.Drerio.UCSC.danRer11.refGene v3.4.6; Annotation package for TxDb objects; Team BC 2019 and GenomicFeatures package v1.46.1. Differential expression analysis was performed using the DESeq2 pipeline version 1.26.0 based on the expressed raw reads. Assembly: GRCz11/danRer11 Library strategy: Ribo seq	heart		The hearts were lysed on ice with 100ul of lysis buffer with 53 mg/ml cycloheximide using mechanical homogenization with a pestle for thirty seconds. Cells were lysed further by trituration of the sample using a 27.5 gauge needle syringe 20x on ice. Cell extracts average OD 7 were treated with MNase NEB CaCl2 5mM final concentration and Turbo DNAse I Invitrogen at 25°C for 30 minutes. MNase digestion was stopped with SUPERase inhibitor incubation on ice. 80S ribosomes were isolated using SH400 spin columns Cytiva. Columns were prepared according to the manufacturer’s instructions. 100 µls of MNase treated sample was loaded per column and centrifuged for 2 min at 600 RCF. The flow through was isolated and incubated for 5 min. with 3x volume of Trizol LS Ambion. 200 µl of chloroform was added and incubated for 2 min. Samples were centrifuged for 15 min. at 12 000 rpm 4°C. The aqueous phase was extracted and precipitated overnight at 20°C using glycoblue ThermoFisher and isopropanol followed by centrifugation for 30 minutes at 4C at 10 000 RPM. Pellets were washed with 75% Ethanol and resuspended into RNase free water. Next Flex smRNA seq kit v3	Zebrafish used for ribosome profiling were grown together under normal conditions and were genotyped upon reaching maturity.	tissue:heart\|cell line:Wt\|genotype:Eif4e1c +/+	GSM6502513	GSM6502513: zebrafish Ribo seq Eif4e1c +/+ rep 1 [r pR1]; Danio rerio; OTHER	GSM6502513 r1	GSM6502513	1	The hearts were lysed on ice with 100ul of lysis buffer with 53 mg/ml cycloheximide using mechanical homogenization with a pestle for thirty seconds. Cells were lysed further by trituration of the sample using a 27.5 gauge needle syringe 20x on ice. Cell extracts average OD 7 were treated with MNase NEB CaCl2 5mM final concentration and Turbo DNAse I Invitrogen at 25°C for 30 minutes. MNase digestion was stopped with SUPERase inhibitor incubation on ice. 80S ribosomes were isolated using SH400 spin columns Cytiva. Columns were prepared according to the manufacturer's instructions. 100 µls of MNase treated sample was loaded per column and centrifuged for 2 min at 600 RCF. The flow through was isolated and incubated for 5 min. with 3x volume of Trizol LS Ambion. 200 µl of chloroform was added and incubated for 2 min. Samples were centrifuged for 15 min. at 12 000 rpm 4°C. The aqueous phase was extracted and precipitated overnight at 20°C using glycoblue ThermoFisher and isopropanol followed by centrifugation for 30 minutes at 4C at 10 000 RPM. Pellets were washed with 75% Ethanol and resuspended into RNase free water. Next Flex smRNA seq kit v3	OTHER	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	NextSeq 550	SRP394145		rS1_pR1.fastq.gz	fastq	8551941876.0	112525551.0	GSM6502513 r1	0:76 1:0	A:2015417703;C:2191682962;G:2364697448;T:1979683824;N:459939	76	0	2015417703	2191682962	2364697448	1979683824	459939	SRX17229101	SRS14795567	SRA1485233	Biological Chemistry and Pharmacology, The Ohio State University	Biological Chemistry and Pharmacology, The Ohio State University	1	1e-05		0.0		0.99997		0.0		76		T		under 1.2% mapping rate	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	United States	2022-08-22	Undetermined	Multi-stage	Heart	Cardiovascular System
72695	72695	SRR23071963	SRX19025119	SRS16444168	SRP417272	PRJNA923391	MBD5 a m5C RNA reader regulates histone ubiquitylation in development and function	GSE222803	Other	Methyl CpG binding domain MBD containing proteins are readers of epigenetic information. The founding member MeCP2 mutated in the Rett Syndrome binds to methylated CpG DNAs. MBD5 is an evolutionarily conserved MBD family member associated with epilepsy autism spectrum disorders ASD and early onset dementia. The mechanism of action of MBD5 remains unclear. Here we report that mbd5 regulates embryonic development erythrocyte differentiation iron metabolism and behavior in zebrafish. MBD5 is essential to activate the expression of erythrocyte differentiation genes e.g. hbae3 iron regulated genes e.g. fth1 and ASD related genes e.g. gabbr2 by binding to 5 methylcytosine m5C modified mRNAs interacting with and stabilizing Additional Sex Combs Like 1 ASXL1 a component of the Polycomb Repressive Deubiquinase PR DUB complex to facilitate removal of the repressive monoubiquitin mark at histone H2A H2A K119Ub thereby facilitating gene activation. Together these findings reveal MBD5 as a m5C RNA reader that links RNA methylation to histone modification in vivo. Overall design: [Dataset 1] 6 samples. Triplicates for ribo minus RNA Seq from 78 hpf zebrafish embryos treated with control or mbd5 morpholino [Dataset 2] 16 samples. Duplicates for CLIP seq experiments from 48 hpf 78 hpf zebrafish embryos treated with 0.5 mM DFO or 1 mM FAC	pubmed:38366571	fac input rep2	GSM6932553	source name:whole embryo\|tissue:whole embryo\|genotype:Tg[zhsp70l:FLAGmbd5iso2 E2AGFP]\|treatment:1 mM FAC from 48 hpf to 78 hpf\|geo loc name:missing\|collection date:missing	fac input rep2	Adapter trimming by Cutadapt Reads mapping by STAR to the transcriptome peak calling with pureCLIP or differential gene expression with DESeq2 Assembly: dr10 Supplementary files format and content: For [Dataset 1] excel xlsx files with differential expression by DESeq2. For [Dataset 2] excel xlsx files with CLIP seq peaks identified by pureCLIP algorithm	whole embryo	For [Dataset 1] morpholino oligonucleotides are applied by microinjection. For [Dataset 2] FAC F5879 Sigma Aldrich was dissolved in E3 medium at 50 mM and stored at 4°C. zebrafish were treated with 1 mM fresh FAC from 3 dpf 6 dpf every day prior to behavior analysis. DFO D9533 Sigma Aldrich was dissolved in E3 medium at 150 mM and stored at 20°C. Zebrafish were treated with 0.5 mM DFO from 3 dpf 6 dpf replenished every day prior to behavior analysis.	For [Dataset 1] total RNAs were extracted with standard TRIzol protocol. For [Dataset 2] 76 hpf larval zebrafish were UV crosslinked and flash frozen in liquid nitrogen. Pellets were thawed on ice and resuspended in 3 volume of ice cold CLIP lysis buffer 50 mM HEPES pH 7.5 150 mM KCl 2 mM EDTA 0.5% v/v NP 40 0.5 mM DTT 1 × Halt™ Protease and Phosphatase Inhibitor Cocktail 1 × RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 °C for 15 minutes post passing through a 26 G needle BD Biosciences. Embryo suspensions were sonicated on a bioruptor Diagenode with 30 s on/30 s off for 5 cycles. Lysates were cleared by centrifugation at 21 000 g for 15 minutes at 4 °C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 °C on an end to end rotor. Beads were washed extensively with 1 ml wash buffer 50 mM HEPES pH 7.5 300 mM KCl 0.05% v/v NP 40 1 × Halt™ Protease and Phosphatase Inhibitor Cocktail 1 × RNaseOUT Recombinant Ribonuclease Inhibitor at 4 °C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/μL RNase T1 Thermo Scientific at 22 °C for 10 minutes with shaking. Input samples are digested in parallel. Then input and IP samples were separated on an SDS PAGE gel and gel slices at corresponding size ranges were treated by proteinase K Invitrogen elution. RNA was recovered with TRIZol reagent Invitrogen. Then T4 PNK Thermo Scientific end repair was performed with purified RNA before library constructions. For [Dataset 1] RNA libraries for input samples were constructed by SMARTer Stranded Total RNA Seq Kit v2 TaKaRa 634417 with ribo minus RNA as input. For [Dataset 2] RNA libraries were constructed with NEB small RNA kit NEB. Libraries were pooled and sequenced on a NovaSeq 6000 sequencer with paired end mode 50 bp setting.	Zebrafish embryos were treated with 0.003% 1 phenyl 2 thiourea PTU in E3 medium to prevent pigment formation. 3 month 9 month aged wild type or mbd5 mutant lines generated in this study were used for breeding or adult behavior analyses. Developmental stages were determined according to their morphology.	tissue:whole embryo\|genotype:Tg[zhsp70l:FLAGmbd5iso2 E2AGFP]\|treatment:1 mM FAC from 48 hpf to 78 hpf	GSM6932553	GSM6932553: fac input rep2; Danio rerio; RIP Seq	GSM6932553 r1	GSM6932553	1	For [Dataset 1] total RNAs were extracted with standard TRIzol protocol. For [Dataset 2] 76 hpf larval zebrafish were UV crosslinked and flash frozen in liquid nitrogen. Pellets were thawed on ice and resuspended in 3 volume of ice cold CLIP lysis buffer 50 mM HEPES pH 7.5 150 mM KCl 2 mM EDTA 0.5% v/v NP 40 0.5 mM DTT 1 × Halt™ Protease and Phosphatase Inhibitor Cocktail 1 × RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 °C for 15 minutes post passing through a 26 G needle BD Biosciences. Embryo suspensions were sonicated on a bioruptor Diagenode with 30 s on/30 s off for 5 cycles. Lysates were cleared by centrifugation at 21 000 g for 15 minutes at 4 °C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 °C on an end to end rotor. Beads were washed extensively with 1 ml wash buffer 50 mM HEPES pH 7.5 300 mM KCl 0.05% v/v NP 40 1 × Halt™ Protease and Phosphatase Inhibitor Cocktail 1 × RNaseOUT Recombinant Ribonuclease Inhibitor at 4 °C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/μL RNase T1 Thermo Scientific at 22 °C for 10 minutes with shaking. Input samples are digested in parallel. Then input and IP samples were separated on an SDS PAGE gel and gel slices at corresponding size ranges were treated by proteinase K Invitrogen elution. RNA was recovered with TRIZol reagent Invitrogen. Then T4 PNK Thermo Scientific end repair was performed with purified RNA before library constructions. For [Dataset 1] RNA libraries for input samples were constructed by SMARTer Stranded Total RNA Seq Kit v2 TaKaRa 634417 with ribo minus RNA as input. For [Dataset 2] RNA libraries were constructed with NEB small RNA kit NEB. Libraries were pooled and sequenced on a NovaSeq 6000 sequencer with paired end mode 50 bp setting.	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP417272	loader:fastq load.py	fac_input_rep2.r1.fastq.gz fac_input_rep2.r2.fastq.gz	fastq fastq	2715443520.0	22628696.0	GSM6932553 r1	0:60 1:60	A:568252635;C:811004878;G:879629678;T:456548654;N:7675	60	60	568252635	811004878	879629678	456548654	7675	SRX19025119	SRS16444168	SRA1573941	University of Chicago	University of Chicago	2	0.76709	0.75848	0.06636	0.06594	0.96465	0.96617	0.79957	0.75254	60	60	B	B	biological fallback assumption	illumina	novaseq_era	full_length	small_rna	smarter	bulk	unknown	unknown	United States	2023-01-12	Multi-stage	Multi-stage	Whole Organism	All anatomical structures
72696	72696	SRR23071964	SRX19025118	SRS16444167	SRP417272	PRJNA923391	MBD5 a m5C RNA reader regulates histone ubiquitylation in development and function	GSE222803	Other	Methyl CpG binding domain MBD containing proteins are readers of epigenetic information. The founding member MeCP2 mutated in the Rett Syndrome binds to methylated CpG DNAs. MBD5 is an evolutionarily conserved MBD family member associated with epilepsy autism spectrum disorders ASD and early onset dementia. The mechanism of action of MBD5 remains unclear. Here we report that mbd5 regulates embryonic development erythrocyte differentiation iron metabolism and behavior in zebrafish. MBD5 is essential to activate the expression of erythrocyte differentiation genes e.g. hbae3 iron regulated genes e.g. fth1 and ASD related genes e.g. gabbr2 by binding to 5 methylcytosine m5C modified mRNAs interacting with and stabilizing Additional Sex Combs Like 1 ASXL1 a component of the Polycomb Repressive Deubiquinase PR DUB complex to facilitate removal of the repressive monoubiquitin mark at histone H2A H2A K119Ub thereby facilitating gene activation. Together these findings reveal MBD5 as a m5C RNA reader that links RNA methylation to histone modification in vivo. Overall design: [Dataset 1] 6 samples. Triplicates for ribo minus RNA Seq from 78 hpf zebrafish embryos treated with control or mbd5 morpholino [Dataset 2] 16 samples. Duplicates for CLIP seq experiments from 48 hpf 78 hpf zebrafish embryos treated with 0.5 mM DFO or 1 mM FAC	pubmed:38366571	fac input rep1	GSM6932552	source name:whole embryo\|tissue:whole embryo\|genotype:Tg[zhsp70l:FLAGmbd5iso2 E2AGFP]\|treatment:1 mM FAC from 48 hpf to 78 hpf\|geo loc name:missing\|collection date:missing	fac input rep1	Adapter trimming by Cutadapt Reads mapping by STAR to the transcriptome peak calling with pureCLIP or differential gene expression with DESeq2 Assembly: dr10 Supplementary files format and content: For [Dataset 1] excel xlsx files with differential expression by DESeq2. For [Dataset 2] excel xlsx files with CLIP seq peaks identified by pureCLIP algorithm	whole embryo	For [Dataset 1] morpholino oligonucleotides are applied by microinjection. For [Dataset 2] FAC F5879 Sigma Aldrich was dissolved in E3 medium at 50 mM and stored at 4°C. zebrafish were treated with 1 mM fresh FAC from 3 dpf 6 dpf every day prior to behavior analysis. DFO D9533 Sigma Aldrich was dissolved in E3 medium at 150 mM and stored at 20°C. Zebrafish were treated with 0.5 mM DFO from 3 dpf 6 dpf replenished every day prior to behavior analysis.	For [Dataset 1] total RNAs were extracted with standard TRIzol protocol. For [Dataset 2] 76 hpf larval zebrafish were UV crosslinked and flash frozen in liquid nitrogen. Pellets were thawed on ice and resuspended in 3 volume of ice cold CLIP lysis buffer 50 mM HEPES pH 7.5 150 mM KCl 2 mM EDTA 0.5% v/v NP 40 0.5 mM DTT 1 × Halt™ Protease and Phosphatase Inhibitor Cocktail 1 × RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 °C for 15 minutes post passing through a 26 G needle BD Biosciences. Embryo suspensions were sonicated on a bioruptor Diagenode with 30 s on/30 s off for 5 cycles. Lysates were cleared by centrifugation at 21 000 g for 15 minutes at 4 °C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 °C on an end to end rotor. Beads were washed extensively with 1 ml wash buffer 50 mM HEPES pH 7.5 300 mM KCl 0.05% v/v NP 40 1 × Halt™ Protease and Phosphatase Inhibitor Cocktail 1 × RNaseOUT Recombinant Ribonuclease Inhibitor at 4 °C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/μL RNase T1 Thermo Scientific at 22 °C for 10 minutes with shaking. Input samples are digested in parallel. Then input and IP samples were separated on an SDS PAGE gel and gel slices at corresponding size ranges were treated by proteinase K Invitrogen elution. RNA was recovered with TRIZol reagent Invitrogen. Then T4 PNK Thermo Scientific end repair was performed with purified RNA before library constructions. For [Dataset 1] RNA libraries for input samples were constructed by SMARTer Stranded Total RNA Seq Kit v2 TaKaRa 634417 with ribo minus RNA as input. For [Dataset 2] RNA libraries were constructed with NEB small RNA kit NEB. Libraries were pooled and sequenced on a NovaSeq 6000 sequencer with paired end mode 50 bp setting.	Zebrafish embryos were treated with 0.003% 1 phenyl 2 thiourea PTU in E3 medium to prevent pigment formation. 3 month 9 month aged wild type or mbd5 mutant lines generated in this study were used for breeding or adult behavior analyses. Developmental stages were determined according to their morphology.	tissue:whole embryo\|genotype:Tg[zhsp70l:FLAGmbd5iso2 E2AGFP]\|treatment:1 mM FAC from 48 hpf to 78 hpf	GSM6932552	GSM6932552: fac input rep1; Danio rerio; RIP Seq	GSM6932552 r1	GSM6932552	1	For [Dataset 1] total RNAs were extracted with standard TRIzol protocol. For [Dataset 2] 76 hpf larval zebrafish were UV crosslinked and flash frozen in liquid nitrogen. Pellets were thawed on ice and resuspended in 3 volume of ice cold CLIP lysis buffer 50 mM HEPES pH 7.5 150 mM KCl 2 mM EDTA 0.5% v/v NP 40 0.5 mM DTT 1 × Halt™ Protease and Phosphatase Inhibitor Cocktail 1 × RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 °C for 15 minutes post passing through a 26 G needle BD Biosciences. Embryo suspensions were sonicated on a bioruptor Diagenode with 30 s on/30 s off for 5 cycles. Lysates were cleared by centrifugation at 21 000 g for 15 minutes at 4 °C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 °C on an end to end rotor. Beads were washed extensively with 1 ml wash buffer 50 mM HEPES pH 7.5 300 mM KCl 0.05% v/v NP 40 1 × Halt™ Protease and Phosphatase Inhibitor Cocktail 1 × RNaseOUT Recombinant Ribonuclease Inhibitor at 4 °C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/μL RNase T1 Thermo Scientific at 22 °C for 10 minutes with shaking. Input samples are digested in parallel. Then input and IP samples were separated on an SDS PAGE gel and gel slices at corresponding size ranges were treated by proteinase K Invitrogen elution. RNA was recovered with TRIZol reagent Invitrogen. Then T4 PNK Thermo Scientific end repair was performed with purified RNA before library constructions. For [Dataset 1] RNA libraries for input samples were constructed by SMARTer Stranded Total RNA Seq Kit v2 TaKaRa 634417 with ribo minus RNA as input. For [Dataset 2] RNA libraries were constructed with NEB small RNA kit NEB. Libraries were pooled and sequenced on a NovaSeq 6000 sequencer with paired end mode 50 bp setting.	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP417272	loader:fastq load.py	fac_input_rep1.r1.fastq.gz fac_input_rep1.r2.fastq.gz	fastq fastq	2788666560.0	23238888.0	GSM6932552 r1	0:60 1:60	A:597611112;C:824776004;G:894293861;T:471977509;N:8074	60	60	597611112	824776004	894293861	471977509	8074	SRX19025118	SRS16444167	SRA1573941	University of Chicago	University of Chicago	2	0.75557	0.74928	0.06802	0.06744	0.96364	0.96508	0.80265	0.73963	60	60	B	B	biological fallback assumption	illumina	novaseq_era	full_length	small_rna	smarter	bulk	unknown	unknown	United States	2023-01-12	Multi-stage	Multi-stage	Whole Organism	All anatomical structures
72697	72697	SRR23071965	SRX19025117	SRS16444166	SRP417272	PRJNA923391	MBD5 a m5C RNA reader regulates histone ubiquitylation in development and function	GSE222803	Other	Methyl CpG binding domain MBD containing proteins are readers of epigenetic information. The founding member MeCP2 mutated in the Rett Syndrome binds to methylated CpG DNAs. MBD5 is an evolutionarily conserved MBD family member associated with epilepsy autism spectrum disorders ASD and early onset dementia. The mechanism of action of MBD5 remains unclear. Here we report that mbd5 regulates embryonic development erythrocyte differentiation iron metabolism and behavior in zebrafish. MBD5 is essential to activate the expression of erythrocyte differentiation genes e.g. hbae3 iron regulated genes e.g. fth1 and ASD related genes e.g. gabbr2 by binding to 5 methylcytosine m5C modified mRNAs interacting with and stabilizing Additional Sex Combs Like 1 ASXL1 a component of the Polycomb Repressive Deubiquinase PR DUB complex to facilitate removal of the repressive monoubiquitin mark at histone H2A H2A K119Ub thereby facilitating gene activation. Together these findings reveal MBD5 as a m5C RNA reader that links RNA methylation to histone modification in vivo. Overall design: [Dataset 1] 6 samples. Triplicates for ribo minus RNA Seq from 78 hpf zebrafish embryos treated with control or mbd5 morpholino [Dataset 2] 16 samples. Duplicates for CLIP seq experiments from 48 hpf 78 hpf zebrafish embryos treated with 0.5 mM DFO or 1 mM FAC	pubmed:38366571	fac clip rep2	GSM6932551	source name:whole embryo\|tissue:whole embryo\|genotype:Tg[zhsp70l:FLAGmbd5iso2 E2AGFP]\|treatment:1 mM FAC from 48 hpf to 78 hpf\|geo loc name:missing\|collection date:missing	fac clip rep2	Adapter trimming by Cutadapt Reads mapping by STAR to the transcriptome peak calling with pureCLIP or differential gene expression with DESeq2 Assembly: dr10 Supplementary files format and content: For [Dataset 1] excel xlsx files with differential expression by DESeq2. For [Dataset 2] excel xlsx files with CLIP seq peaks identified by pureCLIP algorithm	whole embryo	For [Dataset 1] morpholino oligonucleotides are applied by microinjection. For [Dataset 2] FAC F5879 Sigma Aldrich was dissolved in E3 medium at 50 mM and stored at 4°C. zebrafish were treated with 1 mM fresh FAC from 3 dpf 6 dpf every day prior to behavior analysis. DFO D9533 Sigma Aldrich was dissolved in E3 medium at 150 mM and stored at 20°C. Zebrafish were treated with 0.5 mM DFO from 3 dpf 6 dpf replenished every day prior to behavior analysis.	For [Dataset 1] total RNAs were extracted with standard TRIzol protocol. For [Dataset 2] 76 hpf larval zebrafish were UV crosslinked and flash frozen in liquid nitrogen. Pellets were thawed on ice and resuspended in 3 volume of ice cold CLIP lysis buffer 50 mM HEPES pH 7.5 150 mM KCl 2 mM EDTA 0.5% v/v NP 40 0.5 mM DTT 1 × Halt™ Protease and Phosphatase Inhibitor Cocktail 1 × RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 °C for 15 minutes post passing through a 26 G needle BD Biosciences. Embryo suspensions were sonicated on a bioruptor Diagenode with 30 s on/30 s off for 5 cycles. Lysates were cleared by centrifugation at 21 000 g for 15 minutes at 4 °C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 °C on an end to end rotor. Beads were washed extensively with 1 ml wash buffer 50 mM HEPES pH 7.5 300 mM KCl 0.05% v/v NP 40 1 × Halt™ Protease and Phosphatase Inhibitor Cocktail 1 × RNaseOUT Recombinant Ribonuclease Inhibitor at 4 °C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/μL RNase T1 Thermo Scientific at 22 °C for 10 minutes with shaking. Input samples are digested in parallel. Then input and IP samples were separated on an SDS PAGE gel and gel slices at corresponding size ranges were treated by proteinase K Invitrogen elution. RNA was recovered with TRIZol reagent Invitrogen. Then T4 PNK Thermo Scientific end repair was performed with purified RNA before library constructions. For [Dataset 1] RNA libraries for input samples were constructed by SMARTer Stranded Total RNA Seq Kit v2 TaKaRa 634417 with ribo minus RNA as input. For [Dataset 2] RNA libraries were constructed with NEB small RNA kit NEB. Libraries were pooled and sequenced on a NovaSeq 6000 sequencer with paired end mode 50 bp setting.	Zebrafish embryos were treated with 0.003% 1 phenyl 2 thiourea PTU in E3 medium to prevent pigment formation. 3 month 9 month aged wild type or mbd5 mutant lines generated in this study were used for breeding or adult behavior analyses. Developmental stages were determined according to their morphology.	tissue:whole embryo\|genotype:Tg[zhsp70l:FLAGmbd5iso2 E2AGFP]\|treatment:1 mM FAC from 48 hpf to 78 hpf	GSM6932551	GSM6932551: fac clip rep2; Danio rerio; RIP Seq	GSM6932551 r1	GSM6932551	1	For [Dataset 1] total RNAs were extracted with standard TRIzol protocol. For [Dataset 2] 76 hpf larval zebrafish were UV crosslinked and flash frozen in liquid nitrogen. Pellets were thawed on ice and resuspended in 3 volume of ice cold CLIP lysis buffer 50 mM HEPES pH 7.5 150 mM KCl 2 mM EDTA 0.5% v/v NP 40 0.5 mM DTT 1 × Halt™ Protease and Phosphatase Inhibitor Cocktail 1 × RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 °C for 15 minutes post passing through a 26 G needle BD Biosciences. Embryo suspensions were sonicated on a bioruptor Diagenode with 30 s on/30 s off for 5 cycles. Lysates were cleared by centrifugation at 21 000 g for 15 minutes at 4 °C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 °C on an end to end rotor. Beads were washed extensively with 1 ml wash buffer 50 mM HEPES pH 7.5 300 mM KCl 0.05% v/v NP 40 1 × Halt™ Protease and Phosphatase Inhibitor Cocktail 1 × RNaseOUT Recombinant Ribonuclease Inhibitor at 4 °C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/μL RNase T1 Thermo Scientific at 22 °C for 10 minutes with shaking. Input samples are digested in parallel. Then input and IP samples were separated on an SDS PAGE gel and gel slices at corresponding size ranges were treated by proteinase K Invitrogen elution. RNA was recovered with TRIZol reagent Invitrogen. Then T4 PNK Thermo Scientific end repair was performed with purified RNA before library constructions. For [Dataset 1] RNA libraries for input samples were constructed by SMARTer Stranded Total RNA Seq Kit v2 TaKaRa 634417 with ribo minus RNA as input. For [Dataset 2] RNA libraries were constructed with NEB small RNA kit NEB. Libraries were pooled and sequenced on a NovaSeq 6000 sequencer with paired end mode 50 bp setting.	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP417272	loader:fastq load.py	fac_clip_rep2.r1.fastq.gz fac_clip_rep2.r2.fastq.gz	fastq fastq	3636207480.0	30301729.0	GSM6932551 r1	0:60 1:60	A:856114407;C:984704325;G:1019721588;T:775657296;N:9864	60	60	856114407	984704325	1019721588	775657296	9864	SRX19025117	SRS16444166	SRA1573941	University of Chicago	University of Chicago	2	0.95337	0.93978	0.20127	0.22016	0.90295	0.90893	0.69108	0.66666	60	60	B	B	biological fallback assumption	illumina	novaseq_era	full_length	small_rna	smarter	bulk	unknown	unknown	United States	2023-01-12	Multi-stage	Multi-stage	Whole Organism	All anatomical structures
72698	72698	SRR23071966	SRX19025116	SRS16444165	SRP417272	PRJNA923391	MBD5 a m5C RNA reader regulates histone ubiquitylation in development and function	GSE222803	Other	Methyl CpG binding domain MBD containing proteins are readers of epigenetic information. The founding member MeCP2 mutated in the Rett Syndrome binds to methylated CpG DNAs. MBD5 is an evolutionarily conserved MBD family member associated with epilepsy autism spectrum disorders ASD and early onset dementia. The mechanism of action of MBD5 remains unclear. Here we report that mbd5 regulates embryonic development erythrocyte differentiation iron metabolism and behavior in zebrafish. MBD5 is essential to activate the expression of erythrocyte differentiation genes e.g. hbae3 iron regulated genes e.g. fth1 and ASD related genes e.g. gabbr2 by binding to 5 methylcytosine m5C modified mRNAs interacting with and stabilizing Additional Sex Combs Like 1 ASXL1 a component of the Polycomb Repressive Deubiquinase PR DUB complex to facilitate removal of the repressive monoubiquitin mark at histone H2A H2A K119Ub thereby facilitating gene activation. Together these findings reveal MBD5 as a m5C RNA reader that links RNA methylation to histone modification in vivo. Overall design: [Dataset 1] 6 samples. Triplicates for ribo minus RNA Seq from 78 hpf zebrafish embryos treated with control or mbd5 morpholino [Dataset 2] 16 samples. Duplicates for CLIP seq experiments from 48 hpf 78 hpf zebrafish embryos treated with 0.5 mM DFO or 1 mM FAC	pubmed:38366571	fac clip rep1	GSM6932550	source name:whole embryo\|tissue:whole embryo\|genotype:Tg[zhsp70l:FLAGmbd5iso2 E2AGFP]\|treatment:1 mM FAC from 48 hpf to 78 hpf\|geo loc name:missing\|collection date:missing	fac clip rep1	Adapter trimming by Cutadapt Reads mapping by STAR to the transcriptome peak calling with pureCLIP or differential gene expression with DESeq2 Assembly: dr10 Supplementary files format and content: For [Dataset 1] excel xlsx files with differential expression by DESeq2. For [Dataset 2] excel xlsx files with CLIP seq peaks identified by pureCLIP algorithm	whole embryo	For [Dataset 1] morpholino oligonucleotides are applied by microinjection. For [Dataset 2] FAC F5879 Sigma Aldrich was dissolved in E3 medium at 50 mM and stored at 4°C. zebrafish were treated with 1 mM fresh FAC from 3 dpf 6 dpf every day prior to behavior analysis. DFO D9533 Sigma Aldrich was dissolved in E3 medium at 150 mM and stored at 20°C. Zebrafish were treated with 0.5 mM DFO from 3 dpf 6 dpf replenished every day prior to behavior analysis.	For [Dataset 1] total RNAs were extracted with standard TRIzol protocol. For [Dataset 2] 76 hpf larval zebrafish were UV crosslinked and flash frozen in liquid nitrogen. Pellets were thawed on ice and resuspended in 3 volume of ice cold CLIP lysis buffer 50 mM HEPES pH 7.5 150 mM KCl 2 mM EDTA 0.5% v/v NP 40 0.5 mM DTT 1 × Halt™ Protease and Phosphatase Inhibitor Cocktail 1 × RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 °C for 15 minutes post passing through a 26 G needle BD Biosciences. Embryo suspensions were sonicated on a bioruptor Diagenode with 30 s on/30 s off for 5 cycles. Lysates were cleared by centrifugation at 21 000 g for 15 minutes at 4 °C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 °C on an end to end rotor. Beads were washed extensively with 1 ml wash buffer 50 mM HEPES pH 7.5 300 mM KCl 0.05% v/v NP 40 1 × Halt™ Protease and Phosphatase Inhibitor Cocktail 1 × RNaseOUT Recombinant Ribonuclease Inhibitor at 4 °C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/μL RNase T1 Thermo Scientific at 22 °C for 10 minutes with shaking. Input samples are digested in parallel. Then input and IP samples were separated on an SDS PAGE gel and gel slices at corresponding size ranges were treated by proteinase K Invitrogen elution. RNA was recovered with TRIZol reagent Invitrogen. Then T4 PNK Thermo Scientific end repair was performed with purified RNA before library constructions. For [Dataset 1] RNA libraries for input samples were constructed by SMARTer Stranded Total RNA Seq Kit v2 TaKaRa 634417 with ribo minus RNA as input. For [Dataset 2] RNA libraries were constructed with NEB small RNA kit NEB. Libraries were pooled and sequenced on a NovaSeq 6000 sequencer with paired end mode 50 bp setting.	Zebrafish embryos were treated with 0.003% 1 phenyl 2 thiourea PTU in E3 medium to prevent pigment formation. 3 month 9 month aged wild type or mbd5 mutant lines generated in this study were used for breeding or adult behavior analyses. Developmental stages were determined according to their morphology.	tissue:whole embryo\|genotype:Tg[zhsp70l:FLAGmbd5iso2 E2AGFP]\|treatment:1 mM FAC from 48 hpf to 78 hpf	GSM6932550	GSM6932550: fac clip rep1; Danio rerio; RIP Seq	GSM6932550 r1	GSM6932550	1	For [Dataset 1] total RNAs were extracted with standard TRIzol protocol. For [Dataset 2] 76 hpf larval zebrafish were UV crosslinked and flash frozen in liquid nitrogen. Pellets were thawed on ice and resuspended in 3 volume of ice cold CLIP lysis buffer 50 mM HEPES pH 7.5 150 mM KCl 2 mM EDTA 0.5% v/v NP 40 0.5 mM DTT 1 × Halt™ Protease and Phosphatase Inhibitor Cocktail 1 × RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 °C for 15 minutes post passing through a 26 G needle BD Biosciences. Embryo suspensions were sonicated on a bioruptor Diagenode with 30 s on/30 s off for 5 cycles. Lysates were cleared by centrifugation at 21 000 g for 15 minutes at 4 °C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 °C on an end to end rotor. Beads were washed extensively with 1 ml wash buffer 50 mM HEPES pH 7.5 300 mM KCl 0.05% v/v NP 40 1 × Halt™ Protease and Phosphatase Inhibitor Cocktail 1 × RNaseOUT Recombinant Ribonuclease Inhibitor at 4 °C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/μL RNase T1 Thermo Scientific at 22 °C for 10 minutes with shaking. Input samples are digested in parallel. Then input and IP samples were separated on an SDS PAGE gel and gel slices at corresponding size ranges were treated by proteinase K Invitrogen elution. RNA was recovered with TRIZol reagent Invitrogen. Then T4 PNK Thermo Scientific end repair was performed with purified RNA before library constructions. For [Dataset 1] RNA libraries for input samples were constructed by SMARTer Stranded Total RNA Seq Kit v2 TaKaRa 634417 with ribo minus RNA as input. For [Dataset 2] RNA libraries were constructed with NEB small RNA kit NEB. Libraries were pooled and sequenced on a NovaSeq 6000 sequencer with paired end mode 50 bp setting.	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP417272	loader:fastq load.py	fac_clip_rep1.r1.fastq.gz fac_clip_rep1.r2.fastq.gz	fastq fastq	4241534520.0	35346121.0	GSM6932550 r1	0:60 1:60	A:1001822053;C:1148816744;G:1187189848;T:903693863;N:12012	60	60	1001822053	1148816744	1187189848	903693863	12012	SRX19025116	SRS16444165	SRA1573941	University of Chicago	University of Chicago	2	0.9489	0.9407	0.19979	0.22138	0.90161	0.90741	0.67794	0.66231	60	60	B	B	biological fallback assumption	illumina	novaseq_era	full_length	small_rna	smarter	bulk	unknown	unknown	United States	2023-01-12	Multi-stage	Multi-stage	Whole Organism	All anatomical structures
72699	72699	SRR23071967	SRX19025115	SRS16444164	SRP417272	PRJNA923391	MBD5 a m5C RNA reader regulates histone ubiquitylation in development and function	GSE222803	Other	Methyl CpG binding domain MBD containing proteins are readers of epigenetic information. The founding member MeCP2 mutated in the Rett Syndrome binds to methylated CpG DNAs. MBD5 is an evolutionarily conserved MBD family member associated with epilepsy autism spectrum disorders ASD and early onset dementia. The mechanism of action of MBD5 remains unclear. Here we report that mbd5 regulates embryonic development erythrocyte differentiation iron metabolism and behavior in zebrafish. MBD5 is essential to activate the expression of erythrocyte differentiation genes e.g. hbae3 iron regulated genes e.g. fth1 and ASD related genes e.g. gabbr2 by binding to 5 methylcytosine m5C modified mRNAs interacting with and stabilizing Additional Sex Combs Like 1 ASXL1 a component of the Polycomb Repressive Deubiquinase PR DUB complex to facilitate removal of the repressive monoubiquitin mark at histone H2A H2A K119Ub thereby facilitating gene activation. Together these findings reveal MBD5 as a m5C RNA reader that links RNA methylation to histone modification in vivo. Overall design: [Dataset 1] 6 samples. Triplicates for ribo minus RNA Seq from 78 hpf zebrafish embryos treated with control or mbd5 morpholino [Dataset 2] 16 samples. Duplicates for CLIP seq experiments from 48 hpf 78 hpf zebrafish embryos treated with 0.5 mM DFO or 1 mM FAC	pubmed:38366571	dfo input rep2	GSM6932549	source name:whole embryo\|tissue:whole embryo\|genotype:Tg[zhsp70l:FLAGmbd5iso2 E2AGFP]\|treatment:0.5 mM DFO from 48 hpf to 78 hpf\|geo loc name:missing\|collection date:missing	dfo input rep2	Adapter trimming by Cutadapt Reads mapping by STAR to the transcriptome peak calling with pureCLIP or differential gene expression with DESeq2 Assembly: dr10 Supplementary files format and content: For [Dataset 1] excel xlsx files with differential expression by DESeq2. For [Dataset 2] excel xlsx files with CLIP seq peaks identified by pureCLIP algorithm	whole embryo	For [Dataset 1] morpholino oligonucleotides are applied by microinjection. For [Dataset 2] FAC F5879 Sigma Aldrich was dissolved in E3 medium at 50 mM and stored at 4°C. zebrafish were treated with 1 mM fresh FAC from 3 dpf 6 dpf every day prior to behavior analysis. DFO D9533 Sigma Aldrich was dissolved in E3 medium at 150 mM and stored at 20°C. Zebrafish were treated with 0.5 mM DFO from 3 dpf 6 dpf replenished every day prior to behavior analysis.	For [Dataset 1] total RNAs were extracted with standard TRIzol protocol. For [Dataset 2] 76 hpf larval zebrafish were UV crosslinked and flash frozen in liquid nitrogen. Pellets were thawed on ice and resuspended in 3 volume of ice cold CLIP lysis buffer 50 mM HEPES pH 7.5 150 mM KCl 2 mM EDTA 0.5% v/v NP 40 0.5 mM DTT 1 × Halt™ Protease and Phosphatase Inhibitor Cocktail 1 × RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 °C for 15 minutes post passing through a 26 G needle BD Biosciences. Embryo suspensions were sonicated on a bioruptor Diagenode with 30 s on/30 s off for 5 cycles. Lysates were cleared by centrifugation at 21 000 g for 15 minutes at 4 °C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 °C on an end to end rotor. Beads were washed extensively with 1 ml wash buffer 50 mM HEPES pH 7.5 300 mM KCl 0.05% v/v NP 40 1 × Halt™ Protease and Phosphatase Inhibitor Cocktail 1 × RNaseOUT Recombinant Ribonuclease Inhibitor at 4 °C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/μL RNase T1 Thermo Scientific at 22 °C for 10 minutes with shaking. Input samples are digested in parallel. Then input and IP samples were separated on an SDS PAGE gel and gel slices at corresponding size ranges were treated by proteinase K Invitrogen elution. RNA was recovered with TRIZol reagent Invitrogen. Then T4 PNK Thermo Scientific end repair was performed with purified RNA before library constructions. For [Dataset 1] RNA libraries for input samples were constructed by SMARTer Stranded Total RNA Seq Kit v2 TaKaRa 634417 with ribo minus RNA as input. For [Dataset 2] RNA libraries were constructed with NEB small RNA kit NEB. Libraries were pooled and sequenced on a NovaSeq 6000 sequencer with paired end mode 50 bp setting.	Zebrafish embryos were treated with 0.003% 1 phenyl 2 thiourea PTU in E3 medium to prevent pigment formation. 3 month 9 month aged wild type or mbd5 mutant lines generated in this study were used for breeding or adult behavior analyses. Developmental stages were determined according to their morphology.	tissue:whole embryo\|genotype:Tg[zhsp70l:FLAGmbd5iso2 E2AGFP]\|treatment:0.5 mM DFO from 48 hpf to 78 hpf	GSM6932549	GSM6932549: dfo input rep2; Danio rerio; RIP Seq	GSM6932549 r1	GSM6932549	1	For [Dataset 1] total RNAs were extracted with standard TRIzol protocol. For [Dataset 2] 76 hpf larval zebrafish were UV crosslinked and flash frozen in liquid nitrogen. Pellets were thawed on ice and resuspended in 3 volume of ice cold CLIP lysis buffer 50 mM HEPES pH 7.5 150 mM KCl 2 mM EDTA 0.5% v/v NP 40 0.5 mM DTT 1 × Halt™ Protease and Phosphatase Inhibitor Cocktail 1 × RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 °C for 15 minutes post passing through a 26 G needle BD Biosciences. Embryo suspensions were sonicated on a bioruptor Diagenode with 30 s on/30 s off for 5 cycles. Lysates were cleared by centrifugation at 21 000 g for 15 minutes at 4 °C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 °C on an end to end rotor. Beads were washed extensively with 1 ml wash buffer 50 mM HEPES pH 7.5 300 mM KCl 0.05% v/v NP 40 1 × Halt™ Protease and Phosphatase Inhibitor Cocktail 1 × RNaseOUT Recombinant Ribonuclease Inhibitor at 4 °C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/μL RNase T1 Thermo Scientific at 22 °C for 10 minutes with shaking. Input samples are digested in parallel. Then input and IP samples were separated on an SDS PAGE gel and gel slices at corresponding size ranges were treated by proteinase K Invitrogen elution. RNA was recovered with TRIZol reagent Invitrogen. Then T4 PNK Thermo Scientific end repair was performed with purified RNA before library constructions. For [Dataset 1] RNA libraries for input samples were constructed by SMARTer Stranded Total RNA Seq Kit v2 TaKaRa 634417 with ribo minus RNA as input. For [Dataset 2] RNA libraries were constructed with NEB small RNA kit NEB. Libraries were pooled and sequenced on a NovaSeq 6000 sequencer with paired end mode 50 bp setting.	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP417272	loader:fastq load.py	dfo_input_rep2.r1.fastq.gz dfo_input_rep2.r2.fastq.gz	fastq fastq	2472387240.0	20603227.0	GSM6932549 r1	0:60 1:60	A:522247513;C:735343841;G:798068271;T:416720603;N:7012	60	60	522247513	735343841	798068271	416720603	7012	SRX19025115	SRS16444164	SRA1573941	University of Chicago	University of Chicago	2	0.7577	0.75837	0.06797	0.06744	0.96437	0.96627	0.80292	0.74592	60	60	B	B	biological fallback assumption	illumina	novaseq_era	full_length	small_rna	smarter	bulk	unknown	unknown	United States	2023-01-12	Multi-stage	Multi-stage	Whole Organism	All anatomical structures
72700	72700	SRR23071968	SRX19025114	SRS16444163	SRP417272	PRJNA923391	MBD5 a m5C RNA reader regulates histone ubiquitylation in development and function	GSE222803	Other	Methyl CpG binding domain MBD containing proteins are readers of epigenetic information. The founding member MeCP2 mutated in the Rett Syndrome binds to methylated CpG DNAs. MBD5 is an evolutionarily conserved MBD family member associated with epilepsy autism spectrum disorders ASD and early onset dementia. The mechanism of action of MBD5 remains unclear. Here we report that mbd5 regulates embryonic development erythrocyte differentiation iron metabolism and behavior in zebrafish. MBD5 is essential to activate the expression of erythrocyte differentiation genes e.g. hbae3 iron regulated genes e.g. fth1 and ASD related genes e.g. gabbr2 by binding to 5 methylcytosine m5C modified mRNAs interacting with and stabilizing Additional Sex Combs Like 1 ASXL1 a component of the Polycomb Repressive Deubiquinase PR DUB complex to facilitate removal of the repressive monoubiquitin mark at histone H2A H2A K119Ub thereby facilitating gene activation. Together these findings reveal MBD5 as a m5C RNA reader that links RNA methylation to histone modification in vivo. Overall design: [Dataset 1] 6 samples. Triplicates for ribo minus RNA Seq from 78 hpf zebrafish embryos treated with control or mbd5 morpholino [Dataset 2] 16 samples. Duplicates for CLIP seq experiments from 48 hpf 78 hpf zebrafish embryos treated with 0.5 mM DFO or 1 mM FAC	pubmed:38366571	dfo input rep1	GSM6932548	source name:whole embryo\|tissue:whole embryo\|genotype:Tg[zhsp70l:FLAGmbd5iso2 E2AGFP]\|treatment:0.5 mM DFO from 48 hpf to 78 hpf\|geo loc name:missing\|collection date:missing	dfo input rep1	Adapter trimming by Cutadapt Reads mapping by STAR to the transcriptome peak calling with pureCLIP or differential gene expression with DESeq2 Assembly: dr10 Supplementary files format and content: For [Dataset 1] excel xlsx files with differential expression by DESeq2. For [Dataset 2] excel xlsx files with CLIP seq peaks identified by pureCLIP algorithm	whole embryo	For [Dataset 1] morpholino oligonucleotides are applied by microinjection. For [Dataset 2] FAC F5879 Sigma Aldrich was dissolved in E3 medium at 50 mM and stored at 4°C. zebrafish were treated with 1 mM fresh FAC from 3 dpf 6 dpf every day prior to behavior analysis. DFO D9533 Sigma Aldrich was dissolved in E3 medium at 150 mM and stored at 20°C. Zebrafish were treated with 0.5 mM DFO from 3 dpf 6 dpf replenished every day prior to behavior analysis.	For [Dataset 1] total RNAs were extracted with standard TRIzol protocol. For [Dataset 2] 76 hpf larval zebrafish were UV crosslinked and flash frozen in liquid nitrogen. Pellets were thawed on ice and resuspended in 3 volume of ice cold CLIP lysis buffer 50 mM HEPES pH 7.5 150 mM KCl 2 mM EDTA 0.5% v/v NP 40 0.5 mM DTT 1 × Halt™ Protease and Phosphatase Inhibitor Cocktail 1 × RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 °C for 15 minutes post passing through a 26 G needle BD Biosciences. Embryo suspensions were sonicated on a bioruptor Diagenode with 30 s on/30 s off for 5 cycles. Lysates were cleared by centrifugation at 21 000 g for 15 minutes at 4 °C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 °C on an end to end rotor. Beads were washed extensively with 1 ml wash buffer 50 mM HEPES pH 7.5 300 mM KCl 0.05% v/v NP 40 1 × Halt™ Protease and Phosphatase Inhibitor Cocktail 1 × RNaseOUT Recombinant Ribonuclease Inhibitor at 4 °C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/μL RNase T1 Thermo Scientific at 22 °C for 10 minutes with shaking. Input samples are digested in parallel. Then input and IP samples were separated on an SDS PAGE gel and gel slices at corresponding size ranges were treated by proteinase K Invitrogen elution. RNA was recovered with TRIZol reagent Invitrogen. Then T4 PNK Thermo Scientific end repair was performed with purified RNA before library constructions. For [Dataset 1] RNA libraries for input samples were constructed by SMARTer Stranded Total RNA Seq Kit v2 TaKaRa 634417 with ribo minus RNA as input. For [Dataset 2] RNA libraries were constructed with NEB small RNA kit NEB. Libraries were pooled and sequenced on a NovaSeq 6000 sequencer with paired end mode 50 bp setting.	Zebrafish embryos were treated with 0.003% 1 phenyl 2 thiourea PTU in E3 medium to prevent pigment formation. 3 month 9 month aged wild type or mbd5 mutant lines generated in this study were used for breeding or adult behavior analyses. Developmental stages were determined according to their morphology.	tissue:whole embryo\|genotype:Tg[zhsp70l:FLAGmbd5iso2 E2AGFP]\|treatment:0.5 mM DFO from 48 hpf to 78 hpf	GSM6932548	GSM6932548: dfo input rep1; Danio rerio; RIP Seq	GSM6932548 r1	GSM6932548	1	For [Dataset 1] total RNAs were extracted with standard TRIzol protocol. For [Dataset 2] 76 hpf larval zebrafish were UV crosslinked and flash frozen in liquid nitrogen. Pellets were thawed on ice and resuspended in 3 volume of ice cold CLIP lysis buffer 50 mM HEPES pH 7.5 150 mM KCl 2 mM EDTA 0.5% v/v NP 40 0.5 mM DTT 1 × Halt™ Protease and Phosphatase Inhibitor Cocktail 1 × RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 °C for 15 minutes post passing through a 26 G needle BD Biosciences. Embryo suspensions were sonicated on a bioruptor Diagenode with 30 s on/30 s off for 5 cycles. Lysates were cleared by centrifugation at 21 000 g for 15 minutes at 4 °C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 °C on an end to end rotor. Beads were washed extensively with 1 ml wash buffer 50 mM HEPES pH 7.5 300 mM KCl 0.05% v/v NP 40 1 × Halt™ Protease and Phosphatase Inhibitor Cocktail 1 × RNaseOUT Recombinant Ribonuclease Inhibitor at 4 °C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/μL RNase T1 Thermo Scientific at 22 °C for 10 minutes with shaking. Input samples are digested in parallel. Then input and IP samples were separated on an SDS PAGE gel and gel slices at corresponding size ranges were treated by proteinase K Invitrogen elution. RNA was recovered with TRIZol reagent Invitrogen. Then T4 PNK Thermo Scientific end repair was performed with purified RNA before library constructions. For [Dataset 1] RNA libraries for input samples were constructed by SMARTer Stranded Total RNA Seq Kit v2 TaKaRa 634417 with ribo minus RNA as input. For [Dataset 2] RNA libraries were constructed with NEB small RNA kit NEB. Libraries were pooled and sequenced on a NovaSeq 6000 sequencer with paired end mode 50 bp setting.	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP417272	loader:fastq load.py	dfo_input_rep1.fastq.gz dfo_input_rep1.r2.fastq.gz	fastq fastq	2546588760.0	21221573.0	GSM6932548 r1	0:60 1:60	A:536450815;C:753080253;G:819027741;T:438022880;N:7071	60	60	536450815	753080253	819027741	438022880	7071	SRX19025114	SRS16444163	SRA1573941	University of Chicago	University of Chicago	2	0.75957	0.75514	0.06963	0.06896	0.96345	0.96526	0.80322	0.73584	60	60	B	B	biological fallback assumption	illumina	novaseq_era	full_length	small_rna	smarter	bulk	unknown	unknown	United States	2023-01-12	Multi-stage	Multi-stage	Whole Organism	All anatomical structures
72701	72701	SRR23071969	SRX19025113	SRS16444162	SRP417272	PRJNA923391	MBD5 a m5C RNA reader regulates histone ubiquitylation in development and function	GSE222803	Other	Methyl CpG binding domain MBD containing proteins are readers of epigenetic information. The founding member MeCP2 mutated in the Rett Syndrome binds to methylated CpG DNAs. MBD5 is an evolutionarily conserved MBD family member associated with epilepsy autism spectrum disorders ASD and early onset dementia. The mechanism of action of MBD5 remains unclear. Here we report that mbd5 regulates embryonic development erythrocyte differentiation iron metabolism and behavior in zebrafish. MBD5 is essential to activate the expression of erythrocyte differentiation genes e.g. hbae3 iron regulated genes e.g. fth1 and ASD related genes e.g. gabbr2 by binding to 5 methylcytosine m5C modified mRNAs interacting with and stabilizing Additional Sex Combs Like 1 ASXL1 a component of the Polycomb Repressive Deubiquinase PR DUB complex to facilitate removal of the repressive monoubiquitin mark at histone H2A H2A K119Ub thereby facilitating gene activation. Together these findings reveal MBD5 as a m5C RNA reader that links RNA methylation to histone modification in vivo. Overall design: [Dataset 1] 6 samples. Triplicates for ribo minus RNA Seq from 78 hpf zebrafish embryos treated with control or mbd5 morpholino [Dataset 2] 16 samples. Duplicates for CLIP seq experiments from 48 hpf 78 hpf zebrafish embryos treated with 0.5 mM DFO or 1 mM FAC	pubmed:38366571	dfo clip rep2	GSM6932547	source name:whole embryo\|tissue:whole embryo\|genotype:Tg[zhsp70l:FLAGmbd5iso2 E2AGFP]\|treatment:0.5 mM DFO from 48 hpf to 78 hpf\|geo loc name:missing\|collection date:missing	dfo clip rep2	Adapter trimming by Cutadapt Reads mapping by STAR to the transcriptome peak calling with pureCLIP or differential gene expression with DESeq2 Assembly: dr10 Supplementary files format and content: For [Dataset 1] excel xlsx files with differential expression by DESeq2. For [Dataset 2] excel xlsx files with CLIP seq peaks identified by pureCLIP algorithm	whole embryo	For [Dataset 1] morpholino oligonucleotides are applied by microinjection. For [Dataset 2] FAC F5879 Sigma Aldrich was dissolved in E3 medium at 50 mM and stored at 4°C. zebrafish were treated with 1 mM fresh FAC from 3 dpf 6 dpf every day prior to behavior analysis. DFO D9533 Sigma Aldrich was dissolved in E3 medium at 150 mM and stored at 20°C. Zebrafish were treated with 0.5 mM DFO from 3 dpf 6 dpf replenished every day prior to behavior analysis.	For [Dataset 1] total RNAs were extracted with standard TRIzol protocol. For [Dataset 2] 76 hpf larval zebrafish were UV crosslinked and flash frozen in liquid nitrogen. Pellets were thawed on ice and resuspended in 3 volume of ice cold CLIP lysis buffer 50 mM HEPES pH 7.5 150 mM KCl 2 mM EDTA 0.5% v/v NP 40 0.5 mM DTT 1 × Halt™ Protease and Phosphatase Inhibitor Cocktail 1 × RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 °C for 15 minutes post passing through a 26 G needle BD Biosciences. Embryo suspensions were sonicated on a bioruptor Diagenode with 30 s on/30 s off for 5 cycles. Lysates were cleared by centrifugation at 21 000 g for 15 minutes at 4 °C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 °C on an end to end rotor. Beads were washed extensively with 1 ml wash buffer 50 mM HEPES pH 7.5 300 mM KCl 0.05% v/v NP 40 1 × Halt™ Protease and Phosphatase Inhibitor Cocktail 1 × RNaseOUT Recombinant Ribonuclease Inhibitor at 4 °C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/μL RNase T1 Thermo Scientific at 22 °C for 10 minutes with shaking. Input samples are digested in parallel. Then input and IP samples were separated on an SDS PAGE gel and gel slices at corresponding size ranges were treated by proteinase K Invitrogen elution. RNA was recovered with TRIZol reagent Invitrogen. Then T4 PNK Thermo Scientific end repair was performed with purified RNA before library constructions. For [Dataset 1] RNA libraries for input samples were constructed by SMARTer Stranded Total RNA Seq Kit v2 TaKaRa 634417 with ribo minus RNA as input. For [Dataset 2] RNA libraries were constructed with NEB small RNA kit NEB. Libraries were pooled and sequenced on a NovaSeq 6000 sequencer with paired end mode 50 bp setting.	Zebrafish embryos were treated with 0.003% 1 phenyl 2 thiourea PTU in E3 medium to prevent pigment formation. 3 month 9 month aged wild type or mbd5 mutant lines generated in this study were used for breeding or adult behavior analyses. Developmental stages were determined according to their morphology.	tissue:whole embryo\|genotype:Tg[zhsp70l:FLAGmbd5iso2 E2AGFP]\|treatment:0.5 mM DFO from 48 hpf to 78 hpf	GSM6932547	GSM6932547: dfo clip rep2; Danio rerio; RIP Seq	GSM6932547 r1	GSM6932547	1	For [Dataset 1] total RNAs were extracted with standard TRIzol protocol. For [Dataset 2] 76 hpf larval zebrafish were UV crosslinked and flash frozen in liquid nitrogen. Pellets were thawed on ice and resuspended in 3 volume of ice cold CLIP lysis buffer 50 mM HEPES pH 7.5 150 mM KCl 2 mM EDTA 0.5% v/v NP 40 0.5 mM DTT 1 × Halt™ Protease and Phosphatase Inhibitor Cocktail 1 × RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 °C for 15 minutes post passing through a 26 G needle BD Biosciences. Embryo suspensions were sonicated on a bioruptor Diagenode with 30 s on/30 s off for 5 cycles. Lysates were cleared by centrifugation at 21 000 g for 15 minutes at 4 °C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 °C on an end to end rotor. Beads were washed extensively with 1 ml wash buffer 50 mM HEPES pH 7.5 300 mM KCl 0.05% v/v NP 40 1 × Halt™ Protease and Phosphatase Inhibitor Cocktail 1 × RNaseOUT Recombinant Ribonuclease Inhibitor at 4 °C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/μL RNase T1 Thermo Scientific at 22 °C for 10 minutes with shaking. Input samples are digested in parallel. Then input and IP samples were separated on an SDS PAGE gel and gel slices at corresponding size ranges were treated by proteinase K Invitrogen elution. RNA was recovered with TRIZol reagent Invitrogen. Then T4 PNK Thermo Scientific end repair was performed with purified RNA before library constructions. For [Dataset 1] RNA libraries for input samples were constructed by SMARTer Stranded Total RNA Seq Kit v2 TaKaRa 634417 with ribo minus RNA as input. For [Dataset 2] RNA libraries were constructed with NEB small RNA kit NEB. Libraries were pooled and sequenced on a NovaSeq 6000 sequencer with paired end mode 50 bp setting.	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP417272	loader:fastq load.py	dfo_clip_rep2.r1.fastq.gz dfo_clip_rep2.r2.fastq.gz	fastq fastq	4151061480.0	34592179.0	GSM6932547 r1	0:60 1:60	A:968004394;C:1130874104;G:1164829960;T:887341478;N:11544	60	60	968004394	1130874104	1164829960	887341478	11544	SRX19025113	SRS16444162	SRA1573941	University of Chicago	University of Chicago	2	0.92425	0.93056	0.20043	0.2242	0.8966	0.901	0.68964	0.62588	60	60	B	B	biological fallback assumption	illumina	novaseq_era	full_length	small_rna	smarter	bulk	unknown	unknown	United States	2023-01-12	Multi-stage	Multi-stage	Whole Organism	All anatomical structures
72702	72702	SRR23071970	SRX19025112	SRS16444161	SRP417272	PRJNA923391	MBD5 a m5C RNA reader regulates histone ubiquitylation in development and function	GSE222803	Other	Methyl CpG binding domain MBD containing proteins are readers of epigenetic information. The founding member MeCP2 mutated in the Rett Syndrome binds to methylated CpG DNAs. MBD5 is an evolutionarily conserved MBD family member associated with epilepsy autism spectrum disorders ASD and early onset dementia. The mechanism of action of MBD5 remains unclear. Here we report that mbd5 regulates embryonic development erythrocyte differentiation iron metabolism and behavior in zebrafish. MBD5 is essential to activate the expression of erythrocyte differentiation genes e.g. hbae3 iron regulated genes e.g. fth1 and ASD related genes e.g. gabbr2 by binding to 5 methylcytosine m5C modified mRNAs interacting with and stabilizing Additional Sex Combs Like 1 ASXL1 a component of the Polycomb Repressive Deubiquinase PR DUB complex to facilitate removal of the repressive monoubiquitin mark at histone H2A H2A K119Ub thereby facilitating gene activation. Together these findings reveal MBD5 as a m5C RNA reader that links RNA methylation to histone modification in vivo. Overall design: [Dataset 1] 6 samples. Triplicates for ribo minus RNA Seq from 78 hpf zebrafish embryos treated with control or mbd5 morpholino [Dataset 2] 16 samples. Duplicates for CLIP seq experiments from 48 hpf 78 hpf zebrafish embryos treated with 0.5 mM DFO or 1 mM FAC	pubmed:38366571	dfo clip rep1	GSM6932546	source name:whole embryo\|tissue:whole embryo\|genotype:Tg[zhsp70l:FLAGmbd5iso2 E2AGFP]\|treatment:0.5 mM DFO from 48 hpf to 78 hpf\|geo loc name:missing\|collection date:missing	dfo clip rep1	Adapter trimming by Cutadapt Reads mapping by STAR to the transcriptome peak calling with pureCLIP or differential gene expression with DESeq2 Assembly: dr10 Supplementary files format and content: For [Dataset 1] excel xlsx files with differential expression by DESeq2. For [Dataset 2] excel xlsx files with CLIP seq peaks identified by pureCLIP algorithm	whole embryo	For [Dataset 1] morpholino oligonucleotides are applied by microinjection. For [Dataset 2] FAC F5879 Sigma Aldrich was dissolved in E3 medium at 50 mM and stored at 4°C. zebrafish were treated with 1 mM fresh FAC from 3 dpf 6 dpf every day prior to behavior analysis. DFO D9533 Sigma Aldrich was dissolved in E3 medium at 150 mM and stored at 20°C. Zebrafish were treated with 0.5 mM DFO from 3 dpf 6 dpf replenished every day prior to behavior analysis.	For [Dataset 1] total RNAs were extracted with standard TRIzol protocol. For [Dataset 2] 76 hpf larval zebrafish were UV crosslinked and flash frozen in liquid nitrogen. Pellets were thawed on ice and resuspended in 3 volume of ice cold CLIP lysis buffer 50 mM HEPES pH 7.5 150 mM KCl 2 mM EDTA 0.5% v/v NP 40 0.5 mM DTT 1 × Halt™ Protease and Phosphatase Inhibitor Cocktail 1 × RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 °C for 15 minutes post passing through a 26 G needle BD Biosciences. Embryo suspensions were sonicated on a bioruptor Diagenode with 30 s on/30 s off for 5 cycles. Lysates were cleared by centrifugation at 21 000 g for 15 minutes at 4 °C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 °C on an end to end rotor. Beads were washed extensively with 1 ml wash buffer 50 mM HEPES pH 7.5 300 mM KCl 0.05% v/v NP 40 1 × Halt™ Protease and Phosphatase Inhibitor Cocktail 1 × RNaseOUT Recombinant Ribonuclease Inhibitor at 4 °C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/μL RNase T1 Thermo Scientific at 22 °C for 10 minutes with shaking. Input samples are digested in parallel. Then input and IP samples were separated on an SDS PAGE gel and gel slices at corresponding size ranges were treated by proteinase K Invitrogen elution. RNA was recovered with TRIZol reagent Invitrogen. Then T4 PNK Thermo Scientific end repair was performed with purified RNA before library constructions. For [Dataset 1] RNA libraries for input samples were constructed by SMARTer Stranded Total RNA Seq Kit v2 TaKaRa 634417 with ribo minus RNA as input. For [Dataset 2] RNA libraries were constructed with NEB small RNA kit NEB. Libraries were pooled and sequenced on a NovaSeq 6000 sequencer with paired end mode 50 bp setting.	Zebrafish embryos were treated with 0.003% 1 phenyl 2 thiourea PTU in E3 medium to prevent pigment formation. 3 month 9 month aged wild type or mbd5 mutant lines generated in this study were used for breeding or adult behavior analyses. Developmental stages were determined according to their morphology.	tissue:whole embryo\|genotype:Tg[zhsp70l:FLAGmbd5iso2 E2AGFP]\|treatment:0.5 mM DFO from 48 hpf to 78 hpf	GSM6932546	GSM6932546: dfo clip rep1; Danio rerio; RIP Seq	GSM6932546 r1	GSM6932546	1	For [Dataset 1] total RNAs were extracted with standard TRIzol protocol. For [Dataset 2] 76 hpf larval zebrafish were UV crosslinked and flash frozen in liquid nitrogen. Pellets were thawed on ice and resuspended in 3 volume of ice cold CLIP lysis buffer 50 mM HEPES pH 7.5 150 mM KCl 2 mM EDTA 0.5% v/v NP 40 0.5 mM DTT 1 × Halt™ Protease and Phosphatase Inhibitor Cocktail 1 × RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 °C for 15 minutes post passing through a 26 G needle BD Biosciences. Embryo suspensions were sonicated on a bioruptor Diagenode with 30 s on/30 s off for 5 cycles. Lysates were cleared by centrifugation at 21 000 g for 15 minutes at 4 °C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 °C on an end to end rotor. Beads were washed extensively with 1 ml wash buffer 50 mM HEPES pH 7.5 300 mM KCl 0.05% v/v NP 40 1 × Halt™ Protease and Phosphatase Inhibitor Cocktail 1 × RNaseOUT Recombinant Ribonuclease Inhibitor at 4 °C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/μL RNase T1 Thermo Scientific at 22 °C for 10 minutes with shaking. Input samples are digested in parallel. Then input and IP samples were separated on an SDS PAGE gel and gel slices at corresponding size ranges were treated by proteinase K Invitrogen elution. RNA was recovered with TRIZol reagent Invitrogen. Then T4 PNK Thermo Scientific end repair was performed with purified RNA before library constructions. For [Dataset 1] RNA libraries for input samples were constructed by SMARTer Stranded Total RNA Seq Kit v2 TaKaRa 634417 with ribo minus RNA as input. For [Dataset 2] RNA libraries were constructed with NEB small RNA kit NEB. Libraries were pooled and sequenced on a NovaSeq 6000 sequencer with paired end mode 50 bp setting.	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP417272	loader:fastq load.py	dfo_clip_rep1.r1.fastq.gz dfo_clip_rep1.r2.fastq.gz	fastq fastq	3549376560.0	29578138.0	GSM6932546 r1	0:60 1:60	A:829453498;C:966398146;G:998787767;T:754727094;N:10055	60	60	829453498	966398146	998787767	754727094	10055	SRX19025112	SRS16444161	SRA1573941	University of Chicago	University of Chicago	2	0.94985	0.93128	0.20616	0.22409	0.89548	0.90055	0.67094	0.65117	60	60	B	B	biological fallback assumption	illumina	novaseq_era	full_length	small_rna	smarter	bulk	unknown	unknown	United States	2023-01-12	Multi-stage	Multi-stage	Whole Organism	All anatomical structures
72703	72703	SRR23071971	SRX19025111	SRS16444160	SRP417272	PRJNA923391	MBD5 a m5C RNA reader regulates histone ubiquitylation in development and function	GSE222803	Other	Methyl CpG binding domain MBD containing proteins are readers of epigenetic information. The founding member MeCP2 mutated in the Rett Syndrome binds to methylated CpG DNAs. MBD5 is an evolutionarily conserved MBD family member associated with epilepsy autism spectrum disorders ASD and early onset dementia. The mechanism of action of MBD5 remains unclear. Here we report that mbd5 regulates embryonic development erythrocyte differentiation iron metabolism and behavior in zebrafish. MBD5 is essential to activate the expression of erythrocyte differentiation genes e.g. hbae3 iron regulated genes e.g. fth1 and ASD related genes e.g. gabbr2 by binding to 5 methylcytosine m5C modified mRNAs interacting with and stabilizing Additional Sex Combs Like 1 ASXL1 a component of the Polycomb Repressive Deubiquinase PR DUB complex to facilitate removal of the repressive monoubiquitin mark at histone H2A H2A K119Ub thereby facilitating gene activation. Together these findings reveal MBD5 as a m5C RNA reader that links RNA methylation to histone modification in vivo. Overall design: [Dataset 1] 6 samples. Triplicates for ribo minus RNA Seq from 78 hpf zebrafish embryos treated with control or mbd5 morpholino [Dataset 2] 16 samples. Duplicates for CLIP seq experiments from 48 hpf 78 hpf zebrafish embryos treated with 0.5 mM DFO or 1 mM FAC	pubmed:38366571	ctrl input rep2	GSM6932545	source name:whole embryo\|tissue:whole embryo\|genotype:Tg[zhsp70l:FLAGmbd5iso2 E2AGFP]\|treatment:No treatment\|geo loc name:missing\|collection date:missing	ctrl input rep2	Adapter trimming by Cutadapt Reads mapping by STAR to the transcriptome peak calling with pureCLIP or differential gene expression with DESeq2 Assembly: dr10 Supplementary files format and content: For [Dataset 1] excel xlsx files with differential expression by DESeq2. For [Dataset 2] excel xlsx files with CLIP seq peaks identified by pureCLIP algorithm	whole embryo	For [Dataset 1] morpholino oligonucleotides are applied by microinjection. For [Dataset 2] FAC F5879 Sigma Aldrich was dissolved in E3 medium at 50 mM and stored at 4°C. zebrafish were treated with 1 mM fresh FAC from 3 dpf 6 dpf every day prior to behavior analysis. DFO D9533 Sigma Aldrich was dissolved in E3 medium at 150 mM and stored at 20°C. Zebrafish were treated with 0.5 mM DFO from 3 dpf 6 dpf replenished every day prior to behavior analysis.	For [Dataset 1] total RNAs were extracted with standard TRIzol protocol. For [Dataset 2] 76 hpf larval zebrafish were UV crosslinked and flash frozen in liquid nitrogen. Pellets were thawed on ice and resuspended in 3 volume of ice cold CLIP lysis buffer 50 mM HEPES pH 7.5 150 mM KCl 2 mM EDTA 0.5% v/v NP 40 0.5 mM DTT 1 × Halt™ Protease and Phosphatase Inhibitor Cocktail 1 × RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 °C for 15 minutes post passing through a 26 G needle BD Biosciences. Embryo suspensions were sonicated on a bioruptor Diagenode with 30 s on/30 s off for 5 cycles. Lysates were cleared by centrifugation at 21 000 g for 15 minutes at 4 °C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 °C on an end to end rotor. Beads were washed extensively with 1 ml wash buffer 50 mM HEPES pH 7.5 300 mM KCl 0.05% v/v NP 40 1 × Halt™ Protease and Phosphatase Inhibitor Cocktail 1 × RNaseOUT Recombinant Ribonuclease Inhibitor at 4 °C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/μL RNase T1 Thermo Scientific at 22 °C for 10 minutes with shaking. Input samples are digested in parallel. Then input and IP samples were separated on an SDS PAGE gel and gel slices at corresponding size ranges were treated by proteinase K Invitrogen elution. RNA was recovered with TRIZol reagent Invitrogen. Then T4 PNK Thermo Scientific end repair was performed with purified RNA before library constructions. For [Dataset 1] RNA libraries for input samples were constructed by SMARTer Stranded Total RNA Seq Kit v2 TaKaRa 634417 with ribo minus RNA as input. For [Dataset 2] RNA libraries were constructed with NEB small RNA kit NEB. Libraries were pooled and sequenced on a NovaSeq 6000 sequencer with paired end mode 50 bp setting.	Zebrafish embryos were treated with 0.003% 1 phenyl 2 thiourea PTU in E3 medium to prevent pigment formation. 3 month 9 month aged wild type or mbd5 mutant lines generated in this study were used for breeding or adult behavior analyses. Developmental stages were determined according to their morphology.	tissue:whole embryo\|genotype:Tg[zhsp70l:FLAGmbd5iso2 E2AGFP]\|treatment:No treatment	GSM6932545	GSM6932545: ctrl input rep2; Danio rerio; RIP Seq	GSM6932545 r1	GSM6932545	1	For [Dataset 1] total RNAs were extracted with standard TRIzol protocol. For [Dataset 2] 76 hpf larval zebrafish were UV crosslinked and flash frozen in liquid nitrogen. Pellets were thawed on ice and resuspended in 3 volume of ice cold CLIP lysis buffer 50 mM HEPES pH 7.5 150 mM KCl 2 mM EDTA 0.5% v/v NP 40 0.5 mM DTT 1 × Halt™ Protease and Phosphatase Inhibitor Cocktail 1 × RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 °C for 15 minutes post passing through a 26 G needle BD Biosciences. Embryo suspensions were sonicated on a bioruptor Diagenode with 30 s on/30 s off for 5 cycles. Lysates were cleared by centrifugation at 21 000 g for 15 minutes at 4 °C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 °C on an end to end rotor. Beads were washed extensively with 1 ml wash buffer 50 mM HEPES pH 7.5 300 mM KCl 0.05% v/v NP 40 1 × Halt™ Protease and Phosphatase Inhibitor Cocktail 1 × RNaseOUT Recombinant Ribonuclease Inhibitor at 4 °C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/μL RNase T1 Thermo Scientific at 22 °C for 10 minutes with shaking. Input samples are digested in parallel. Then input and IP samples were separated on an SDS PAGE gel and gel slices at corresponding size ranges were treated by proteinase K Invitrogen elution. RNA was recovered with TRIZol reagent Invitrogen. Then T4 PNK Thermo Scientific end repair was performed with purified RNA before library constructions. For [Dataset 1] RNA libraries for input samples were constructed by SMARTer Stranded Total RNA Seq Kit v2 TaKaRa 634417 with ribo minus RNA as input. For [Dataset 2] RNA libraries were constructed with NEB small RNA kit NEB. Libraries were pooled and sequenced on a NovaSeq 6000 sequencer with paired end mode 50 bp setting.	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP417272	loader:fastq load.py	ctrl_input_rep2.r1.fastq.gz ctrl_input_rep2.r2.fastq.gz	fastq fastq	2305351440.0	19211262.0	GSM6932545 r1	0:60 1:60	A:494731676;C:683635423;G:735706555;T:391271420;N:6366	60	60	494731676	683635423	735706555	391271420	6366	SRX19025111	SRS16444160	SRA1573941	University of Chicago	University of Chicago	2	0.75012	0.76494	0.06496	0.06503	0.9696	0.97023	0.80848	0.76006	60	60	B	B	biological fallback assumption	illumina	novaseq_era	full_length	small_rna	smarter	bulk	unknown	unknown	United States	2023-01-12	Multi-stage	Multi-stage	Whole Organism	All anatomical structures
72704	72704	SRR23071972	SRX19025110	SRS16444159	SRP417272	PRJNA923391	MBD5 a m5C RNA reader regulates histone ubiquitylation in development and function	GSE222803	Other	Methyl CpG binding domain MBD containing proteins are readers of epigenetic information. The founding member MeCP2 mutated in the Rett Syndrome binds to methylated CpG DNAs. MBD5 is an evolutionarily conserved MBD family member associated with epilepsy autism spectrum disorders ASD and early onset dementia. The mechanism of action of MBD5 remains unclear. Here we report that mbd5 regulates embryonic development erythrocyte differentiation iron metabolism and behavior in zebrafish. MBD5 is essential to activate the expression of erythrocyte differentiation genes e.g. hbae3 iron regulated genes e.g. fth1 and ASD related genes e.g. gabbr2 by binding to 5 methylcytosine m5C modified mRNAs interacting with and stabilizing Additional Sex Combs Like 1 ASXL1 a component of the Polycomb Repressive Deubiquinase PR DUB complex to facilitate removal of the repressive monoubiquitin mark at histone H2A H2A K119Ub thereby facilitating gene activation. Together these findings reveal MBD5 as a m5C RNA reader that links RNA methylation to histone modification in vivo. Overall design: [Dataset 1] 6 samples. Triplicates for ribo minus RNA Seq from 78 hpf zebrafish embryos treated with control or mbd5 morpholino [Dataset 2] 16 samples. Duplicates for CLIP seq experiments from 48 hpf 78 hpf zebrafish embryos treated with 0.5 mM DFO or 1 mM FAC	pubmed:38366571	ctrl input rep1	GSM6932544	source name:whole embryo\|tissue:whole embryo\|genotype:Tg[zhsp70l:FLAGmbd5iso2 E2AGFP]\|treatment:No treatment\|geo loc name:missing\|collection date:missing	ctrl input rep1	Adapter trimming by Cutadapt Reads mapping by STAR to the transcriptome peak calling with pureCLIP or differential gene expression with DESeq2 Assembly: dr10 Supplementary files format and content: For [Dataset 1] excel xlsx files with differential expression by DESeq2. For [Dataset 2] excel xlsx files with CLIP seq peaks identified by pureCLIP algorithm	whole embryo	For [Dataset 1] morpholino oligonucleotides are applied by microinjection. For [Dataset 2] FAC F5879 Sigma Aldrich was dissolved in E3 medium at 50 mM and stored at 4°C. zebrafish were treated with 1 mM fresh FAC from 3 dpf 6 dpf every day prior to behavior analysis. DFO D9533 Sigma Aldrich was dissolved in E3 medium at 150 mM and stored at 20°C. Zebrafish were treated with 0.5 mM DFO from 3 dpf 6 dpf replenished every day prior to behavior analysis.	For [Dataset 1] total RNAs were extracted with standard TRIzol protocol. For [Dataset 2] 76 hpf larval zebrafish were UV crosslinked and flash frozen in liquid nitrogen. Pellets were thawed on ice and resuspended in 3 volume of ice cold CLIP lysis buffer 50 mM HEPES pH 7.5 150 mM KCl 2 mM EDTA 0.5% v/v NP 40 0.5 mM DTT 1 × Halt™ Protease and Phosphatase Inhibitor Cocktail 1 × RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 °C for 15 minutes post passing through a 26 G needle BD Biosciences. Embryo suspensions were sonicated on a bioruptor Diagenode with 30 s on/30 s off for 5 cycles. Lysates were cleared by centrifugation at 21 000 g for 15 minutes at 4 °C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 °C on an end to end rotor. Beads were washed extensively with 1 ml wash buffer 50 mM HEPES pH 7.5 300 mM KCl 0.05% v/v NP 40 1 × Halt™ Protease and Phosphatase Inhibitor Cocktail 1 × RNaseOUT Recombinant Ribonuclease Inhibitor at 4 °C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/μL RNase T1 Thermo Scientific at 22 °C for 10 minutes with shaking. Input samples are digested in parallel. Then input and IP samples were separated on an SDS PAGE gel and gel slices at corresponding size ranges were treated by proteinase K Invitrogen elution. RNA was recovered with TRIZol reagent Invitrogen. Then T4 PNK Thermo Scientific end repair was performed with purified RNA before library constructions. For [Dataset 1] RNA libraries for input samples were constructed by SMARTer Stranded Total RNA Seq Kit v2 TaKaRa 634417 with ribo minus RNA as input. For [Dataset 2] RNA libraries were constructed with NEB small RNA kit NEB. Libraries were pooled and sequenced on a NovaSeq 6000 sequencer with paired end mode 50 bp setting.	Zebrafish embryos were treated with 0.003% 1 phenyl 2 thiourea PTU in E3 medium to prevent pigment formation. 3 month 9 month aged wild type or mbd5 mutant lines generated in this study were used for breeding or adult behavior analyses. Developmental stages were determined according to their morphology.	tissue:whole embryo\|genotype:Tg[zhsp70l:FLAGmbd5iso2 E2AGFP]\|treatment:No treatment	GSM6932544	GSM6932544: ctrl input rep1; Danio rerio; RIP Seq	GSM6932544 r1	GSM6932544	1	For [Dataset 1] total RNAs were extracted with standard TRIzol protocol. For [Dataset 2] 76 hpf larval zebrafish were UV crosslinked and flash frozen in liquid nitrogen. Pellets were thawed on ice and resuspended in 3 volume of ice cold CLIP lysis buffer 50 mM HEPES pH 7.5 150 mM KCl 2 mM EDTA 0.5% v/v NP 40 0.5 mM DTT 1 × Halt™ Protease and Phosphatase Inhibitor Cocktail 1 × RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 °C for 15 minutes post passing through a 26 G needle BD Biosciences. Embryo suspensions were sonicated on a bioruptor Diagenode with 30 s on/30 s off for 5 cycles. Lysates were cleared by centrifugation at 21 000 g for 15 minutes at 4 °C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 °C on an end to end rotor. Beads were washed extensively with 1 ml wash buffer 50 mM HEPES pH 7.5 300 mM KCl 0.05% v/v NP 40 1 × Halt™ Protease and Phosphatase Inhibitor Cocktail 1 × RNaseOUT Recombinant Ribonuclease Inhibitor at 4 °C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/μL RNase T1 Thermo Scientific at 22 °C for 10 minutes with shaking. Input samples are digested in parallel. Then input and IP samples were separated on an SDS PAGE gel and gel slices at corresponding size ranges were treated by proteinase K Invitrogen elution. RNA was recovered with TRIZol reagent Invitrogen. Then T4 PNK Thermo Scientific end repair was performed with purified RNA before library constructions. For [Dataset 1] RNA libraries for input samples were constructed by SMARTer Stranded Total RNA Seq Kit v2 TaKaRa 634417 with ribo minus RNA as input. For [Dataset 2] RNA libraries were constructed with NEB small RNA kit NEB. Libraries were pooled and sequenced on a NovaSeq 6000 sequencer with paired end mode 50 bp setting.	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP417272	loader:fastq load.py	ctrl_input_rep1.r1.fastq.gz ctrl_input_rep1.r2.fastq.gz	fastq fastq	2870115000.0	23917625.0	GSM6932544 r1	0:60 1:60	A:616586993;C:849261640;G:916690149;T:487568187;N:8031	60	60	616586993	849261640	916690149	487568187	8031	SRX19025110	SRS16444159	SRA1573941	University of Chicago	University of Chicago	2	0.76321	0.76237	0.06602	0.06566	0.97064	0.96903	0.68553	0.75314	60	60	B	B	biological fallback assumption	illumina	novaseq_era	full_length	small_rna	smarter	bulk	unknown	unknown	United States	2023-01-12	Multi-stage	Multi-stage	Whole Organism	All anatomical structures
72705	72705	SRR23071973	SRX19025109	SRS16444158	SRP417272	PRJNA923391	MBD5 a m5C RNA reader regulates histone ubiquitylation in development and function	GSE222803	Other	Methyl CpG binding domain MBD containing proteins are readers of epigenetic information. The founding member MeCP2 mutated in the Rett Syndrome binds to methylated CpG DNAs. MBD5 is an evolutionarily conserved MBD family member associated with epilepsy autism spectrum disorders ASD and early onset dementia. The mechanism of action of MBD5 remains unclear. Here we report that mbd5 regulates embryonic development erythrocyte differentiation iron metabolism and behavior in zebrafish. MBD5 is essential to activate the expression of erythrocyte differentiation genes e.g. hbae3 iron regulated genes e.g. fth1 and ASD related genes e.g. gabbr2 by binding to 5 methylcytosine m5C modified mRNAs interacting with and stabilizing Additional Sex Combs Like 1 ASXL1 a component of the Polycomb Repressive Deubiquinase PR DUB complex to facilitate removal of the repressive monoubiquitin mark at histone H2A H2A K119Ub thereby facilitating gene activation. Together these findings reveal MBD5 as a m5C RNA reader that links RNA methylation to histone modification in vivo. Overall design: [Dataset 1] 6 samples. Triplicates for ribo minus RNA Seq from 78 hpf zebrafish embryos treated with control or mbd5 morpholino [Dataset 2] 16 samples. Duplicates for CLIP seq experiments from 48 hpf 78 hpf zebrafish embryos treated with 0.5 mM DFO or 1 mM FAC	pubmed:38366571	ctrl clip rep2	GSM6932543	source name:whole embryo\|tissue:whole embryo\|genotype:Tg[zhsp70l:FLAGmbd5iso2 E2AGFP]\|treatment:No treatment\|geo loc name:missing\|collection date:missing	ctrl clip rep2	Adapter trimming by Cutadapt Reads mapping by STAR to the transcriptome peak calling with pureCLIP or differential gene expression with DESeq2 Assembly: dr10 Supplementary files format and content: For [Dataset 1] excel xlsx files with differential expression by DESeq2. For [Dataset 2] excel xlsx files with CLIP seq peaks identified by pureCLIP algorithm	whole embryo	For [Dataset 1] morpholino oligonucleotides are applied by microinjection. For [Dataset 2] FAC F5879 Sigma Aldrich was dissolved in E3 medium at 50 mM and stored at 4°C. zebrafish were treated with 1 mM fresh FAC from 3 dpf 6 dpf every day prior to behavior analysis. DFO D9533 Sigma Aldrich was dissolved in E3 medium at 150 mM and stored at 20°C. Zebrafish were treated with 0.5 mM DFO from 3 dpf 6 dpf replenished every day prior to behavior analysis.	For [Dataset 1] total RNAs were extracted with standard TRIzol protocol. For [Dataset 2] 76 hpf larval zebrafish were UV crosslinked and flash frozen in liquid nitrogen. Pellets were thawed on ice and resuspended in 3 volume of ice cold CLIP lysis buffer 50 mM HEPES pH 7.5 150 mM KCl 2 mM EDTA 0.5% v/v NP 40 0.5 mM DTT 1 × Halt™ Protease and Phosphatase Inhibitor Cocktail 1 × RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 °C for 15 minutes post passing through a 26 G needle BD Biosciences. Embryo suspensions were sonicated on a bioruptor Diagenode with 30 s on/30 s off for 5 cycles. Lysates were cleared by centrifugation at 21 000 g for 15 minutes at 4 °C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 °C on an end to end rotor. Beads were washed extensively with 1 ml wash buffer 50 mM HEPES pH 7.5 300 mM KCl 0.05% v/v NP 40 1 × Halt™ Protease and Phosphatase Inhibitor Cocktail 1 × RNaseOUT Recombinant Ribonuclease Inhibitor at 4 °C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/μL RNase T1 Thermo Scientific at 22 °C for 10 minutes with shaking. Input samples are digested in parallel. Then input and IP samples were separated on an SDS PAGE gel and gel slices at corresponding size ranges were treated by proteinase K Invitrogen elution. RNA was recovered with TRIZol reagent Invitrogen. Then T4 PNK Thermo Scientific end repair was performed with purified RNA before library constructions. For [Dataset 1] RNA libraries for input samples were constructed by SMARTer Stranded Total RNA Seq Kit v2 TaKaRa 634417 with ribo minus RNA as input. For [Dataset 2] RNA libraries were constructed with NEB small RNA kit NEB. Libraries were pooled and sequenced on a NovaSeq 6000 sequencer with paired end mode 50 bp setting.	Zebrafish embryos were treated with 0.003% 1 phenyl 2 thiourea PTU in E3 medium to prevent pigment formation. 3 month 9 month aged wild type or mbd5 mutant lines generated in this study were used for breeding or adult behavior analyses. Developmental stages were determined according to their morphology.	tissue:whole embryo\|genotype:Tg[zhsp70l:FLAGmbd5iso2 E2AGFP]\|treatment:No treatment	GSM6932543	GSM6932543: ctrl clip rep2; Danio rerio; RIP Seq	GSM6932543 r1	GSM6932543	1	For [Dataset 1] total RNAs were extracted with standard TRIzol protocol. For [Dataset 2] 76 hpf larval zebrafish were UV crosslinked and flash frozen in liquid nitrogen. Pellets were thawed on ice and resuspended in 3 volume of ice cold CLIP lysis buffer 50 mM HEPES pH 7.5 150 mM KCl 2 mM EDTA 0.5% v/v NP 40 0.5 mM DTT 1 × Halt™ Protease and Phosphatase Inhibitor Cocktail 1 × RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 °C for 15 minutes post passing through a 26 G needle BD Biosciences. Embryo suspensions were sonicated on a bioruptor Diagenode with 30 s on/30 s off for 5 cycles. Lysates were cleared by centrifugation at 21 000 g for 15 minutes at 4 °C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 °C on an end to end rotor. Beads were washed extensively with 1 ml wash buffer 50 mM HEPES pH 7.5 300 mM KCl 0.05% v/v NP 40 1 × Halt™ Protease and Phosphatase Inhibitor Cocktail 1 × RNaseOUT Recombinant Ribonuclease Inhibitor at 4 °C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/μL RNase T1 Thermo Scientific at 22 °C for 10 minutes with shaking. Input samples are digested in parallel. Then input and IP samples were separated on an SDS PAGE gel and gel slices at corresponding size ranges were treated by proteinase K Invitrogen elution. RNA was recovered with TRIZol reagent Invitrogen. Then T4 PNK Thermo Scientific end repair was performed with purified RNA before library constructions. For [Dataset 1] RNA libraries for input samples were constructed by SMARTer Stranded Total RNA Seq Kit v2 TaKaRa 634417 with ribo minus RNA as input. For [Dataset 2] RNA libraries were constructed with NEB small RNA kit NEB. Libraries were pooled and sequenced on a NovaSeq 6000 sequencer with paired end mode 50 bp setting.	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP417272	loader:fastq load.py	ctrl_clip_rep2.r1.fastq.gz ctrl_clip_rep2.r2.fastq.gz	fastq fastq	3309978960.0	27583158.0	GSM6932543 r1	0:60 1:60	A:774105538;C:895792317;G:931799487;T:708272623;N:8995	60	60	774105538	895792317	931799487	708272623	8995	SRX19025109	SRS16444158	SRA1573941	University of Chicago	University of Chicago	2	0.94553	0.92262	0.21092	0.22735	0.90985	0.91407	0.67372	0.67171	60	60	B	B	biological fallback assumption	illumina	novaseq_era	full_length	small_rna	smarter	bulk	unknown	unknown	United States	2023-01-12	Multi-stage	Multi-stage	Whole Organism	All anatomical structures
72706	72706	SRR23071974	SRX19025108	SRS16444157	SRP417272	PRJNA923391	MBD5 a m5C RNA reader regulates histone ubiquitylation in development and function	GSE222803	Other	Methyl CpG binding domain MBD containing proteins are readers of epigenetic information. The founding member MeCP2 mutated in the Rett Syndrome binds to methylated CpG DNAs. MBD5 is an evolutionarily conserved MBD family member associated with epilepsy autism spectrum disorders ASD and early onset dementia. The mechanism of action of MBD5 remains unclear. Here we report that mbd5 regulates embryonic development erythrocyte differentiation iron metabolism and behavior in zebrafish. MBD5 is essential to activate the expression of erythrocyte differentiation genes e.g. hbae3 iron regulated genes e.g. fth1 and ASD related genes e.g. gabbr2 by binding to 5 methylcytosine m5C modified mRNAs interacting with and stabilizing Additional Sex Combs Like 1 ASXL1 a component of the Polycomb Repressive Deubiquinase PR DUB complex to facilitate removal of the repressive monoubiquitin mark at histone H2A H2A K119Ub thereby facilitating gene activation. Together these findings reveal MBD5 as a m5C RNA reader that links RNA methylation to histone modification in vivo. Overall design: [Dataset 1] 6 samples. Triplicates for ribo minus RNA Seq from 78 hpf zebrafish embryos treated with control or mbd5 morpholino [Dataset 2] 16 samples. Duplicates for CLIP seq experiments from 48 hpf 78 hpf zebrafish embryos treated with 0.5 mM DFO or 1 mM FAC	pubmed:38366571	ctrl clip rep1	GSM6932542	source name:whole embryo\|tissue:whole embryo\|genotype:Tg[zhsp70l:FLAGmbd5iso2 E2AGFP]\|treatment:No treatment\|geo loc name:missing\|collection date:missing	ctrl clip rep1	Adapter trimming by Cutadapt Reads mapping by STAR to the transcriptome peak calling with pureCLIP or differential gene expression with DESeq2 Assembly: dr10 Supplementary files format and content: For [Dataset 1] excel xlsx files with differential expression by DESeq2. For [Dataset 2] excel xlsx files with CLIP seq peaks identified by pureCLIP algorithm	whole embryo	For [Dataset 1] morpholino oligonucleotides are applied by microinjection. For [Dataset 2] FAC F5879 Sigma Aldrich was dissolved in E3 medium at 50 mM and stored at 4°C. zebrafish were treated with 1 mM fresh FAC from 3 dpf 6 dpf every day prior to behavior analysis. DFO D9533 Sigma Aldrich was dissolved in E3 medium at 150 mM and stored at 20°C. Zebrafish were treated with 0.5 mM DFO from 3 dpf 6 dpf replenished every day prior to behavior analysis.	For [Dataset 1] total RNAs were extracted with standard TRIzol protocol. For [Dataset 2] 76 hpf larval zebrafish were UV crosslinked and flash frozen in liquid nitrogen. Pellets were thawed on ice and resuspended in 3 volume of ice cold CLIP lysis buffer 50 mM HEPES pH 7.5 150 mM KCl 2 mM EDTA 0.5% v/v NP 40 0.5 mM DTT 1 × Halt™ Protease and Phosphatase Inhibitor Cocktail 1 × RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 °C for 15 minutes post passing through a 26 G needle BD Biosciences. Embryo suspensions were sonicated on a bioruptor Diagenode with 30 s on/30 s off for 5 cycles. Lysates were cleared by centrifugation at 21 000 g for 15 minutes at 4 °C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 °C on an end to end rotor. Beads were washed extensively with 1 ml wash buffer 50 mM HEPES pH 7.5 300 mM KCl 0.05% v/v NP 40 1 × Halt™ Protease and Phosphatase Inhibitor Cocktail 1 × RNaseOUT Recombinant Ribonuclease Inhibitor at 4 °C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/μL RNase T1 Thermo Scientific at 22 °C for 10 minutes with shaking. Input samples are digested in parallel. Then input and IP samples were separated on an SDS PAGE gel and gel slices at corresponding size ranges were treated by proteinase K Invitrogen elution. RNA was recovered with TRIZol reagent Invitrogen. Then T4 PNK Thermo Scientific end repair was performed with purified RNA before library constructions. For [Dataset 1] RNA libraries for input samples were constructed by SMARTer Stranded Total RNA Seq Kit v2 TaKaRa 634417 with ribo minus RNA as input. For [Dataset 2] RNA libraries were constructed with NEB small RNA kit NEB. Libraries were pooled and sequenced on a NovaSeq 6000 sequencer with paired end mode 50 bp setting.	Zebrafish embryos were treated with 0.003% 1 phenyl 2 thiourea PTU in E3 medium to prevent pigment formation. 3 month 9 month aged wild type or mbd5 mutant lines generated in this study were used for breeding or adult behavior analyses. Developmental stages were determined according to their morphology.	tissue:whole embryo\|genotype:Tg[zhsp70l:FLAGmbd5iso2 E2AGFP]\|treatment:No treatment	GSM6932542	GSM6932542: ctrl clip rep1; Danio rerio; RIP Seq	GSM6932542 r1	GSM6932542	1	For [Dataset 1] total RNAs were extracted with standard TRIzol protocol. For [Dataset 2] 76 hpf larval zebrafish were UV crosslinked and flash frozen in liquid nitrogen. Pellets were thawed on ice and resuspended in 3 volume of ice cold CLIP lysis buffer 50 mM HEPES pH 7.5 150 mM KCl 2 mM EDTA 0.5% v/v NP 40 0.5 mM DTT 1 × Halt™ Protease and Phosphatase Inhibitor Cocktail 1 × RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 °C for 15 minutes post passing through a 26 G needle BD Biosciences. Embryo suspensions were sonicated on a bioruptor Diagenode with 30 s on/30 s off for 5 cycles. Lysates were cleared by centrifugation at 21 000 g for 15 minutes at 4 °C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 °C on an end to end rotor. Beads were washed extensively with 1 ml wash buffer 50 mM HEPES pH 7.5 300 mM KCl 0.05% v/v NP 40 1 × Halt™ Protease and Phosphatase Inhibitor Cocktail 1 × RNaseOUT Recombinant Ribonuclease Inhibitor at 4 °C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/μL RNase T1 Thermo Scientific at 22 °C for 10 minutes with shaking. Input samples are digested in parallel. Then input and IP samples were separated on an SDS PAGE gel and gel slices at corresponding size ranges were treated by proteinase K Invitrogen elution. RNA was recovered with TRIZol reagent Invitrogen. Then T4 PNK Thermo Scientific end repair was performed with purified RNA before library constructions. For [Dataset 1] RNA libraries for input samples were constructed by SMARTer Stranded Total RNA Seq Kit v2 TaKaRa 634417 with ribo minus RNA as input. For [Dataset 2] RNA libraries were constructed with NEB small RNA kit NEB. Libraries were pooled and sequenced on a NovaSeq 6000 sequencer with paired end mode 50 bp setting.	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP417272	loader:fastq load.py	ctrl_clip_rep1.r1.fastq.gz ctrl_clip_rep1.r2.fastq.gz	fastq fastq	3392768880.0	28273074.0	GSM6932542 r1	0:60 1:60	A:795387316;C:918606802;G:949982957;T:728782720;N:9085	60	60	795387316	918606802	949982957	728782720	9085	SRX19025108	SRS16444157	SRA1573941	University of Chicago	University of Chicago	2	0.92844	0.92193	0.20693	0.22683	0.90826	0.91297	0.68754	0.67062	60	60	B	B	biological fallback assumption	illumina	novaseq_era	full_length	small_rna	smarter	bulk	unknown	unknown	United States	2023-01-12	Multi-stage	Multi-stage	Whole Organism	All anatomical structures

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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");;