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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. 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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. 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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. 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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. 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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. 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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. 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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. 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Studies of these pollutants' toxic effects on development have not fully elucidated the potential underlying mechanisms. Therefore  in this study  we aim at investigate the developmental toxicity induced by cigarette smoke extract CSE at concentrations of 0.25%  1%  and 2.5% using a zebrafish embryo toxicity test and integrated transcriptomic analysis of microRNA miRNA and messenger RNA mRNA. The findings revealed that CSE caused developmental toxicity  including increased mortality and decreased incubation rate  in a dose dependent manner. Moreover  CSE induced malformations and apoptosis  specifically in the head and heart of zebrafish larvae. We used mRNA and miRNA sequencing analyses to compare changes in the expression of genes and miRNAs in zebrafish larvae. The bioinformatics analysis indicates that the mechanism underlying CSE induced developmental toxicity was associated with genetic repair impairment  apoptosis disorder  and lipid metabolism disturbance. The enrichment analysis and RT qPCR show that the ctsba gene plays a crucial function in embryo developmental apoptosis  and the fads2 gene mainly regulates lipid metabolic toxicity. The results of this study improve the understanding of CSE induced developmental toxicity in zebrafish embryos and contribute insights into the formulation of novel preventive strategies against tobacco pollutants during early embryonic development.", null, null, null, null, "S21K1230", null, "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", null, null, null, null, null, null, null, null, "High 3", "H 3", "H 3", "missing", null, null, "RNA-Seq", "METATRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP491086", null, null, "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, null, null, 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", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-02-22", "Undetermined", "Multi-stage", "Undetermined", "Undetermined"], [30659, "SRR28054754", "SRX23704451", "SRS20534446", "SRP491086", "PRJNA1078753", "Integrated mRNA  and miRNA  sequencing analyses unveil the underlying mechanism of tobacco pollutant induced developmental toxicity in zebrafish embryos", "PRJNA1078753", "Other", "Tobacco pollutants are prevalent in the environment  leading to inadvertent exposure of pregnant females. Studies of these pollutants' toxic effects on development have not fully elucidated the potential underlying mechanisms. Therefore  in this study  we aim at investigate the developmental toxicity induced by cigarette smoke extract CSE at concentrations of 0.25%  1%  and 2.5% using a zebrafish embryo toxicity test and integrated transcriptomic analysis of microRNA miRNA and messenger RNA mRNA. The findings revealed that CSE caused developmental toxicity  including increased mortality and decreased incubation rate  in a dose dependent manner. Moreover  CSE induced malformations and apoptosis  specifically in the head and heart of zebrafish larvae. We used mRNA and miRNA sequencing analyses to compare changes in the expression of genes and miRNAs in zebrafish larvae. The bioinformatics analysis indicates that the mechanism underlying CSE induced developmental toxicity was associated with genetic repair impairment  apoptosis disorder  and lipid metabolism disturbance. The enrichment analysis and RT qPCR show that the ctsba gene plays a crucial function in embryo developmental apoptosis  and the fads2 gene mainly regulates lipid metabolic toxicity. The results of this study improve the understanding of CSE induced developmental toxicity in zebrafish embryos and contribute insights into the formulation of novel preventive strategies against tobacco pollutants during early embryonic development.", null, null, null, null, "S21K1229", null, "library ID:H 2|title:High 2|library strategy:OTHER|library source:METATRANSCRIPTIOMIC|library selection:other|library layout:paired|platform:ILLUMINA|instrument model:RNA seq|filetype:fastq|filename:S21K1229 rep1 1 URNA S73 L003 R1 001.fastq|filename2:S21K1229 rep1 1 URNA S73 L003 R2 001.fastq|host:missing|isolation source:missing|collection date:missing|geographic location:missing|latitude and longitude:missing|age:missing|breed:missing|cultivar:missing|dev stage:missing|ecotype:missing|isolate:missing|sex:missing|strain:missing|tissue:missing|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "High 2", "H 2", "H 2", "missing", null, null, "RNA-Seq", "METATRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP491086", null, null, "S21K1229_rep1_1_URNA_S73_L003_R1_001.fastq.gz S21K1229_rep1_1_URNA_S73_L003_R2_001.fastq.gz", "fastq fastq", 7164803100.0, 23882677.0, "S21K1229 rep1 1 URNA S73 L003 R1 001.fastq.gz", "0:150 1:150", "A:1920286881;C:1649856655;G:1697032084;T:1897610671;N:16809", 150, 150, null, null, 1920286881, 1649856655, 1697032084, 1897610671, 16809, "SRX23704451", "SRS20534446", "SRA1806456", "The Second Affiliated Hospital of Shantou University Medical College|Department of Burns and Plastic Surgery", "The Second Affiliated Hospital of Shantou University Medical College", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-02-22", "Undetermined", "Multi-stage", "Undetermined", "Undetermined"], [30660, "SRR28054755", "SRX23704450", "SRS20534445", "SRP491086", "PRJNA1078753", "Integrated mRNA  and miRNA  sequencing analyses unveil the underlying mechanism of tobacco pollutant induced developmental toxicity in zebrafish embryos", "PRJNA1078753", "Other", "Tobacco pollutants are prevalent in the environment  leading to inadvertent exposure of pregnant females. Studies of these pollutants' toxic effects on development have not fully elucidated the potential underlying mechanisms. Therefore  in this study  we aim at investigate the developmental toxicity induced by cigarette smoke extract CSE at concentrations of 0.25%  1%  and 2.5% using a zebrafish embryo toxicity test and integrated transcriptomic analysis of microRNA miRNA and messenger RNA mRNA. The findings revealed that CSE caused developmental toxicity  including increased mortality and decreased incubation rate  in a dose dependent manner. Moreover  CSE induced malformations and apoptosis  specifically in the head and heart of zebrafish larvae. We used mRNA and miRNA sequencing analyses to compare changes in the expression of genes and miRNAs in zebrafish larvae. The bioinformatics analysis indicates that the mechanism underlying CSE induced developmental toxicity was associated with genetic repair impairment  apoptosis disorder  and lipid metabolism disturbance. The enrichment analysis and RT qPCR show that the ctsba gene plays a crucial function in embryo developmental apoptosis  and the fads2 gene mainly regulates lipid metabolic toxicity. The results of this study improve the understanding of CSE induced developmental toxicity in zebrafish embryos and contribute insights into the formulation of novel preventive strategies against tobacco pollutants during early embryonic development.", null, null, null, null, "S21K1220", null, "library ID:C 2|title:Control 2|library strategy:OTHER|library source:METATRANSCRIPTIOMIC|library selection:other|library layout:paired|platform:ILLUMINA|instrument model:RNA seq|filetype:fastq|filename:S21K1220 rep1 1 URNA S64 L003 R1 001.fastq|filename2:S21K1220 rep1 1 URNA S64 L003 R2 001.fastq|host:missing|isolation source:missing|collection date:missing|geographic location:missing|latitude and longitude:missing|age:missing|breed:missing|cultivar:missing|dev stage:missing|ecotype:missing|isolate:missing|sex:missing|strain:missing|tissue:missing|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Control 2", "C 2", "C 2", "missing", null, null, "RNA-Seq", "METATRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP491086", null, null, "S21K1220_rep1_1_URNA_S64_L003_R1_001.fastq.gz S21K1220_rep1_1_URNA_S64_L003_R2_001.fastq.gz", "fastq fastq", 6790504800.0, 22635016.0, "S21K1220 rep1 1 URNA S64 L003 R1 001.fastq.gz", "0:150 1:150", "A:1784553430;C:1593393319;G:1650087761;T:1762454671;N:15619", 150, 150, null, null, 1784553430, 1593393319, 1650087761, 1762454671, 15619, "SRX23704450", "SRS20534445", "SRA1806456", "The Second Affiliated Hospital of Shantou University Medical College|Department of Burns and Plastic Surgery", "The Second Affiliated Hospital of Shantou University Medical College", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-02-22", "Undetermined", "Multi-stage", "Undetermined", "Undetermined"], [30661, "SRR28054756", "SRX23704449", "SRS20534444", "SRP491086", "PRJNA1078753", "Integrated mRNA  and miRNA  sequencing analyses unveil the underlying mechanism of tobacco pollutant induced developmental toxicity in zebrafish embryos", "PRJNA1078753", "Other", "Tobacco pollutants are prevalent in the environment  leading to inadvertent exposure of pregnant females. Studies of these pollutants' toxic effects on development have not fully elucidated the potential underlying mechanisms. Therefore  in this study  we aim at investigate the developmental toxicity induced by cigarette smoke extract CSE at concentrations of 0.25%  1%  and 2.5% using a zebrafish embryo toxicity test and integrated transcriptomic analysis of microRNA miRNA and messenger RNA mRNA. The findings revealed that CSE caused developmental toxicity  including increased mortality and decreased incubation rate  in a dose dependent manner. Moreover  CSE induced malformations and apoptosis  specifically in the head and heart of zebrafish larvae. We used mRNA and miRNA sequencing analyses to compare changes in the expression of genes and miRNAs in zebrafish larvae. The bioinformatics analysis indicates that the mechanism underlying CSE induced developmental toxicity was associated with genetic repair impairment  apoptosis disorder  and lipid metabolism disturbance. The enrichment analysis and RT qPCR show that the ctsba gene plays a crucial function in embryo developmental apoptosis  and the fads2 gene mainly regulates lipid metabolic toxicity. The results of this study improve the understanding of CSE induced developmental toxicity in zebrafish embryos and contribute insights into the formulation of novel preventive strategies against tobacco pollutants during early embryonic development.", null, null, null, null, "S21K1219", null, "library ID:C 1|title:Control 1|library strategy:OTHER|library source:METATRANSCRIPTIOMIC|library selection:other|library layout:paired|platform:ILLUMINA|instrument model:RNA seq|filetype:fastq|filename:S21K1219 rep1 1 URNA S63 L003 R1 001.fastq|filename2:S21K1219 rep1 1 URNA S63 L003 R2 001.fastq|host:missing|isolation source:missing|collection date:missing|geographic location:missing|latitude and longitude:missing|age:missing|breed:missing|cultivar:missing|dev stage:missing|ecotype:missing|isolate:missing|sex:missing|strain:missing|tissue:missing|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Control 1", "C 1", "C 1", "missing", null, null, "RNA-Seq", "METATRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP491086", null, null, "S21K1219_rep1_1_URNA_S63_L003_R1_001.fastq.gz S21K1219_rep1_1_URNA_S63_L003_R2_001.fastq.gz", "fastq fastq", 7498264200.0, 24994214.0, "S21K1219 rep1 1 URNA S63 L003 R1 001.fastq.gz", "0:150 1:150", "A:2002773492;C:1716996682;G:1800329295;T:1978147319;N:17412", 150, 150, null, null, 2002773492, 1716996682, 1800329295, 1978147319, 17412, "SRX23704449", "SRS20534444", "SRA1806456", "The Second Affiliated Hospital of Shantou University Medical College|Department of Burns and Plastic Surgery", "The Second Affiliated Hospital of Shantou University Medical College", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-02-22", "Undetermined", "Multi-stage", "Undetermined", "Undetermined"], [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.", null, null, null, null, "6WT 3", null, "strain:AB|isolate:replicate3|ecotype:wt|age:post fertilization day 22|dev stage:juvenile|sex:missing|tissue:Gonad|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "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.", null, null, "ncRNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP359829", null, null, "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, null, null, 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", null, "China", "2022-02-14", "Multi-stage", "Multi-stage", "Gonad", "Reproductive System"], [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.", null, null, null, null, "5WT 2", null, "strain:AB|isolate:replicate2|ecotype:wt|age:post fertilization day 22|dev stage:juvenile|sex:missing|tissue:Gonad|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "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.", null, null, "ncRNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP359829", null, null, "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, null, null, 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", null, "China", "2022-02-14", "Multi-stage", "Multi-stage", "Gonad", "Reproductive System"], [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.", null, null, null, null, "4WT 1", null, "strain:AB|isolate:replicate1|ecotype:wt|age:post fertilization day 22|dev stage:juvenile|sex:missing|tissue:Gonad|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "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.", null, null, "ncRNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP359829", null, null, "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, null, null, 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", null, "China", "2022-02-14", "Multi-stage", "Multi-stage", "Gonad", "Reproductive System"], [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.", null, null, null, null, "3PLD6 3", null, "strain:AB|isolate:replicate3|ecotype:pld6 / |age:post fertilization day 22|dev stage:juvenile|sex:missing|tissue:Gonad|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "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.", null, null, "ncRNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP359829", null, null, "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, null, null, 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", null, "China", "2022-02-14", "Multi-stage", "Multi-stage", "Gonad", "Reproductive System"], [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.", null, null, null, null, "2PLD6 2", null, "strain:AB|isolate:replicate2|ecotype:pld6 / |age:post fertilization day 22|dev stage:juvenile|sex:missing|tissue:Gonad|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "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.", null, null, "ncRNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP359829", null, null, "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, null, null, 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", null, "China", "2022-02-14", "Multi-stage", "Multi-stage", "Gonad", "Reproductive System"], [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.", null, null, null, null, "1PLD6 1", null, "strain:AB|isolate:replicate1|ecotype:pld6 / |age:post fertilization day 22|dev stage:juvenile|sex:missing|tissue:Gonad|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "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.", null, null, "ncRNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP359829", null, null, "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, null, null, 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", null, "China", "2022-02-14", "Multi-stage", "Multi-stage", "Gonad", "Reproductive System"], [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.", null, "pubmed:37306388", null, "zebrafish  Ribo seq  Eif4e1c  /  rep2 [r mR2]", "GSM6502516", null, "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", null, "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\u00b0C 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\u2019s instructions. 100 \u00b5ls 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 \u00b5l of chloroform was added and incubated for 2 min. Samples were centrifuged for 15 min. at 12 000 rpm 4\u00b0C. The aqueous phase was extracted and precipitated overnight at  20\u00b0C 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\u00b0C 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 \u00b5ls 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 \u00b5l of chloroform was added and incubated for 2 min. Samples were centrifuged for 15 min. at 12 000 rpm 4\u00b0C. The aqueous phase was extracted and precipitated overnight at  20\u00b0C 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", null, "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "NextSeq 550", null, "SRP394145", null, null, "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, null, null, 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, null, 0.0, null, 1.0, null, null, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "United States", "2022-08-22", "Undetermined", "Multi-stage", "Heart", "Cardiovascular System"], [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.", null, "pubmed:37306388", null, "zebrafish  Ribo seq  Eif4e1c  /   rep 1 [r mR1]", "GSM6502515", null, "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", null, "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\u00b0C 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\u2019s instructions. 100 \u00b5ls 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 \u00b5l of chloroform was added and incubated for 2 min. Samples were centrifuged for 15 min. at 12 000 rpm 4\u00b0C. The aqueous phase was extracted and precipitated overnight at  20\u00b0C 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\u00b0C 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 \u00b5ls 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 \u00b5l of chloroform was added and incubated for 2 min. Samples were centrifuged for 15 min. at 12 000 rpm 4\u00b0C. The aqueous phase was extracted and precipitated overnight at  20\u00b0C 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", null, "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "NextSeq 550", null, "SRP394145", null, null, "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, null, null, 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, null, 0.0, null, 1.0, null, null, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "United States", "2022-08-22", "Undetermined", "Multi-stage", "Heart", "Cardiovascular System"], [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.", null, "pubmed:37306388", null, "zebrafish  Ribo seq  Eif4e1c +/+  rep 2 [r pR2]", "GSM6502514", null, "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", null, "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\u00b0C 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\u2019s instructions. 100 \u00b5ls 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 \u00b5l of chloroform was added and incubated for 2 min. Samples were centrifuged for 15 min. at 12 000 rpm 4\u00b0C. The aqueous phase was extracted and precipitated overnight at  20\u00b0C 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\u00b0C 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 \u00b5ls 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 \u00b5l of chloroform was added and incubated for 2 min. Samples were centrifuged for 15 min. at 12 000 rpm 4\u00b0C. The aqueous phase was extracted and precipitated overnight at  20\u00b0C 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", null, "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "NextSeq 550", null, "SRP394145", null, null, "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, null, null, 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, null, 0.0, null, 0.99997, null, 1.0, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "United States", "2022-08-22", "Undetermined", "Multi-stage", "Heart", "Cardiovascular System"], [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.", null, "pubmed:37306388", null, "zebrafish  Ribo seq  Eif4e1c +/+  rep 1 [r pR1]", "GSM6502513", null, "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", null, "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\u00b0C 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\u2019s instructions. 100 \u00b5ls 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 \u00b5l of chloroform was added and incubated for 2 min. Samples were centrifuged for 15 min. at 12 000 rpm 4\u00b0C. The aqueous phase was extracted and precipitated overnight at  20\u00b0C 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\u00b0C 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 \u00b5ls 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 \u00b5l of chloroform was added and incubated for 2 min. Samples were centrifuged for 15 min. at 12 000 rpm 4\u00b0C. The aqueous phase was extracted and precipitated overnight at  20\u00b0C 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", null, "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "NextSeq 550", null, "SRP394145", null, null, "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, null, null, 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, null, 0.0, null, 0.99997, null, 0.0, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "United States", "2022-08-22", "Undetermined", "Multi-stage", "Heart", "Cardiovascular System"], [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", null, "pubmed:38366571", null, "fac input rep2", "GSM6932553", null, "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\u00b0C. 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\u00b0C. 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 \u00d7 Halt\u2122 Protease and Phosphatase Inhibitor Cocktail  1 \u00d7 RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 \u00b0C 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 \u00b0C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 \u00b0C 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 \u00d7 Halt\u2122 Protease and Phosphatase Inhibitor Cocktail  1 \u00d7 RNaseOUT Recombinant Ribonuclease Inhibitor at 4 \u00b0C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/\u03bcL RNase T1 Thermo Scientific at 22 \u00b0C 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 \u00d7 Halt\u2122 Protease and Phosphatase Inhibitor Cocktail  1 \u00d7 RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 \u00b0C 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 \u00b0C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 \u00b0C 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 \u00d7 Halt\u2122 Protease and Phosphatase Inhibitor Cocktail  1 \u00d7 RNaseOUT Recombinant Ribonuclease Inhibitor at 4 \u00b0C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/\u03bcL RNase T1 Thermo Scientific at 22 \u00b0C 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.", null, "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP417272", null, "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, null, null, 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", null, "United States", "2023-01-12", "Multi-stage", "Multi-stage", "Whole Organism", "All anatomical structures"], [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", null, "pubmed:38366571", null, "fac input rep1", "GSM6932552", null, "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\u00b0C. 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\u00b0C. 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 \u00d7 Halt\u2122 Protease and Phosphatase Inhibitor Cocktail  1 \u00d7 RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 \u00b0C 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 \u00b0C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 \u00b0C 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 \u00d7 Halt\u2122 Protease and Phosphatase Inhibitor Cocktail  1 \u00d7 RNaseOUT Recombinant Ribonuclease Inhibitor at 4 \u00b0C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/\u03bcL RNase T1 Thermo Scientific at 22 \u00b0C 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 \u00d7 Halt\u2122 Protease and Phosphatase Inhibitor Cocktail  1 \u00d7 RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 \u00b0C 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 \u00b0C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 \u00b0C 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 \u00d7 Halt\u2122 Protease and Phosphatase Inhibitor Cocktail  1 \u00d7 RNaseOUT Recombinant Ribonuclease Inhibitor at 4 \u00b0C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/\u03bcL RNase T1 Thermo Scientific at 22 \u00b0C 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.", null, "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP417272", null, "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, null, null, 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", null, "United States", "2023-01-12", "Multi-stage", "Multi-stage", "Whole Organism", "All anatomical structures"], [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", null, "pubmed:38366571", null, "fac clip rep2", "GSM6932551", null, "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\u00b0C. 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\u00b0C. 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 \u00d7 Halt\u2122 Protease and Phosphatase Inhibitor Cocktail  1 \u00d7 RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 \u00b0C 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 \u00b0C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 \u00b0C 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 \u00d7 Halt\u2122 Protease and Phosphatase Inhibitor Cocktail  1 \u00d7 RNaseOUT Recombinant Ribonuclease Inhibitor at 4 \u00b0C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/\u03bcL RNase T1 Thermo Scientific at 22 \u00b0C 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 \u00d7 Halt\u2122 Protease and Phosphatase Inhibitor Cocktail  1 \u00d7 RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 \u00b0C 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 \u00b0C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 \u00b0C 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 \u00d7 Halt\u2122 Protease and Phosphatase Inhibitor Cocktail  1 \u00d7 RNaseOUT Recombinant Ribonuclease Inhibitor at 4 \u00b0C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/\u03bcL RNase T1 Thermo Scientific at 22 \u00b0C 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.", null, "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP417272", null, "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, null, null, 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", null, "United States", "2023-01-12", "Multi-stage", "Multi-stage", "Whole Organism", "All anatomical structures"], [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", null, "pubmed:38366571", null, "fac clip rep1", "GSM6932550", null, "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\u00b0C. 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\u00b0C. 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 \u00d7 Halt\u2122 Protease and Phosphatase Inhibitor Cocktail  1 \u00d7 RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 \u00b0C 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 \u00b0C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 \u00b0C 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 \u00d7 Halt\u2122 Protease and Phosphatase Inhibitor Cocktail  1 \u00d7 RNaseOUT Recombinant Ribonuclease Inhibitor at 4 \u00b0C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/\u03bcL RNase T1 Thermo Scientific at 22 \u00b0C 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 \u00d7 Halt\u2122 Protease and Phosphatase Inhibitor Cocktail  1 \u00d7 RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 \u00b0C 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 \u00b0C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 \u00b0C 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 \u00d7 Halt\u2122 Protease and Phosphatase Inhibitor Cocktail  1 \u00d7 RNaseOUT Recombinant Ribonuclease Inhibitor at 4 \u00b0C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/\u03bcL RNase T1 Thermo Scientific at 22 \u00b0C 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.", null, "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP417272", null, "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, null, null, 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", null, "United States", "2023-01-12", "Multi-stage", "Multi-stage", "Whole Organism", "All anatomical structures"], [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", null, "pubmed:38366571", null, "dfo input rep2", "GSM6932549", null, "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\u00b0C. 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\u00b0C. 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 \u00d7 Halt\u2122 Protease and Phosphatase Inhibitor Cocktail  1 \u00d7 RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 \u00b0C 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 \u00b0C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 \u00b0C 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 \u00d7 Halt\u2122 Protease and Phosphatase Inhibitor Cocktail  1 \u00d7 RNaseOUT Recombinant Ribonuclease Inhibitor at 4 \u00b0C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/\u03bcL RNase T1 Thermo Scientific at 22 \u00b0C 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 \u00d7 Halt\u2122 Protease and Phosphatase Inhibitor Cocktail  1 \u00d7 RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 \u00b0C 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 \u00b0C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 \u00b0C 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 \u00d7 Halt\u2122 Protease and Phosphatase Inhibitor Cocktail  1 \u00d7 RNaseOUT Recombinant Ribonuclease Inhibitor at 4 \u00b0C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/\u03bcL RNase T1 Thermo Scientific at 22 \u00b0C 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.", null, "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP417272", null, "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, null, null, 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", null, "United States", "2023-01-12", "Multi-stage", "Multi-stage", "Whole Organism", "All anatomical structures"], [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", null, "pubmed:38366571", null, "dfo input rep1", "GSM6932548", null, "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\u00b0C. 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\u00b0C. 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 \u00d7 Halt\u2122 Protease and Phosphatase Inhibitor Cocktail  1 \u00d7 RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 \u00b0C 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 \u00b0C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 \u00b0C 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 \u00d7 Halt\u2122 Protease and Phosphatase Inhibitor Cocktail  1 \u00d7 RNaseOUT Recombinant Ribonuclease Inhibitor at 4 \u00b0C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/\u03bcL RNase T1 Thermo Scientific at 22 \u00b0C 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 \u00d7 Halt\u2122 Protease and Phosphatase Inhibitor Cocktail  1 \u00d7 RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 \u00b0C 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 \u00b0C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 \u00b0C 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 \u00d7 Halt\u2122 Protease and Phosphatase Inhibitor Cocktail  1 \u00d7 RNaseOUT Recombinant Ribonuclease Inhibitor at 4 \u00b0C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/\u03bcL RNase T1 Thermo Scientific at 22 \u00b0C 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.", null, "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP417272", null, "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, null, null, 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", null, "United States", "2023-01-12", "Multi-stage", "Multi-stage", "Whole Organism", "All anatomical structures"], [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", null, "pubmed:38366571", null, "dfo clip rep2", "GSM6932547", null, "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\u00b0C. 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\u00b0C. 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 \u00d7 Halt\u2122 Protease and Phosphatase Inhibitor Cocktail  1 \u00d7 RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 \u00b0C 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 \u00b0C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 \u00b0C 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 \u00d7 Halt\u2122 Protease and Phosphatase Inhibitor Cocktail  1 \u00d7 RNaseOUT Recombinant Ribonuclease Inhibitor at 4 \u00b0C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/\u03bcL RNase T1 Thermo Scientific at 22 \u00b0C 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 \u00d7 Halt\u2122 Protease and Phosphatase Inhibitor Cocktail  1 \u00d7 RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 \u00b0C 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 \u00b0C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 \u00b0C 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 \u00d7 Halt\u2122 Protease and Phosphatase Inhibitor Cocktail  1 \u00d7 RNaseOUT Recombinant Ribonuclease Inhibitor at 4 \u00b0C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/\u03bcL RNase T1 Thermo Scientific at 22 \u00b0C 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.", null, "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP417272", null, "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, null, null, 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", null, "United States", "2023-01-12", "Multi-stage", "Multi-stage", "Whole Organism", "All anatomical structures"], [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", null, "pubmed:38366571", null, "dfo clip rep1", "GSM6932546", null, "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\u00b0C. 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\u00b0C. 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 \u00d7 Halt\u2122 Protease and Phosphatase Inhibitor Cocktail  1 \u00d7 RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 \u00b0C 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 \u00b0C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 \u00b0C 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 \u00d7 Halt\u2122 Protease and Phosphatase Inhibitor Cocktail  1 \u00d7 RNaseOUT Recombinant Ribonuclease Inhibitor at 4 \u00b0C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/\u03bcL RNase T1 Thermo Scientific at 22 \u00b0C 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 \u00d7 Halt\u2122 Protease and Phosphatase Inhibitor Cocktail  1 \u00d7 RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 \u00b0C 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 \u00b0C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 \u00b0C 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 \u00d7 Halt\u2122 Protease and Phosphatase Inhibitor Cocktail  1 \u00d7 RNaseOUT Recombinant Ribonuclease Inhibitor at 4 \u00b0C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/\u03bcL RNase T1 Thermo Scientific at 22 \u00b0C 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.", null, "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP417272", null, "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, null, null, 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", null, "United States", "2023-01-12", "Multi-stage", "Multi-stage", "Whole Organism", "All anatomical structures"], [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", null, "pubmed:38366571", null, "ctrl input rep2", "GSM6932545", null, "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\u00b0C. 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\u00b0C. 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 \u00d7 Halt\u2122 Protease and Phosphatase Inhibitor Cocktail  1 \u00d7 RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 \u00b0C 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 \u00b0C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 \u00b0C 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 \u00d7 Halt\u2122 Protease and Phosphatase Inhibitor Cocktail  1 \u00d7 RNaseOUT Recombinant Ribonuclease Inhibitor at 4 \u00b0C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/\u03bcL RNase T1 Thermo Scientific at 22 \u00b0C 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 \u00d7 Halt\u2122 Protease and Phosphatase Inhibitor Cocktail  1 \u00d7 RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 \u00b0C 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 \u00b0C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 \u00b0C 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 \u00d7 Halt\u2122 Protease and Phosphatase Inhibitor Cocktail  1 \u00d7 RNaseOUT Recombinant Ribonuclease Inhibitor at 4 \u00b0C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/\u03bcL RNase T1 Thermo Scientific at 22 \u00b0C 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.", null, "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP417272", null, "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, null, null, 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", null, "United States", "2023-01-12", "Multi-stage", "Multi-stage", "Whole Organism", "All anatomical structures"], [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", null, "pubmed:38366571", null, "ctrl input rep1", "GSM6932544", null, "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\u00b0C. 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\u00b0C. 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 \u00d7 Halt\u2122 Protease and Phosphatase Inhibitor Cocktail  1 \u00d7 RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 \u00b0C 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 \u00b0C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 \u00b0C 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 \u00d7 Halt\u2122 Protease and Phosphatase Inhibitor Cocktail  1 \u00d7 RNaseOUT Recombinant Ribonuclease Inhibitor at 4 \u00b0C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/\u03bcL RNase T1 Thermo Scientific at 22 \u00b0C 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 \u00d7 Halt\u2122 Protease and Phosphatase Inhibitor Cocktail  1 \u00d7 RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 \u00b0C 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 \u00b0C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 \u00b0C 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 \u00d7 Halt\u2122 Protease and Phosphatase Inhibitor Cocktail  1 \u00d7 RNaseOUT Recombinant Ribonuclease Inhibitor at 4 \u00b0C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/\u03bcL RNase T1 Thermo Scientific at 22 \u00b0C 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.", null, "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP417272", null, "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, null, null, 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", null, "United States", "2023-01-12", "Multi-stage", "Multi-stage", "Whole Organism", "All anatomical structures"], [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", null, "pubmed:38366571", null, "ctrl clip rep2", "GSM6932543", null, "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\u00b0C. 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\u00b0C. 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 \u00d7 Halt\u2122 Protease and Phosphatase Inhibitor Cocktail  1 \u00d7 RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 \u00b0C 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 \u00b0C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 \u00b0C 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 \u00d7 Halt\u2122 Protease and Phosphatase Inhibitor Cocktail  1 \u00d7 RNaseOUT Recombinant Ribonuclease Inhibitor at 4 \u00b0C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/\u03bcL RNase T1 Thermo Scientific at 22 \u00b0C 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 \u00d7 Halt\u2122 Protease and Phosphatase Inhibitor Cocktail  1 \u00d7 RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 \u00b0C 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 \u00b0C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 \u00b0C 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 \u00d7 Halt\u2122 Protease and Phosphatase Inhibitor Cocktail  1 \u00d7 RNaseOUT Recombinant Ribonuclease Inhibitor at 4 \u00b0C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/\u03bcL RNase T1 Thermo Scientific at 22 \u00b0C 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.", null, "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP417272", null, "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, null, null, 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", null, "United States", "2023-01-12", "Multi-stage", "Multi-stage", "Whole Organism", "All anatomical structures"], [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", null, "pubmed:38366571", null, "ctrl clip rep1", "GSM6932542", null, "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\u00b0C. 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\u00b0C. 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 \u00d7 Halt\u2122 Protease and Phosphatase Inhibitor Cocktail  1 \u00d7 RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 \u00b0C 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 \u00b0C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 \u00b0C 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 \u00d7 Halt\u2122 Protease and Phosphatase Inhibitor Cocktail  1 \u00d7 RNaseOUT Recombinant Ribonuclease Inhibitor at 4 \u00b0C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/\u03bcL RNase T1 Thermo Scientific at 22 \u00b0C 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 \u00d7 Halt\u2122 Protease and Phosphatase Inhibitor Cocktail  1 \u00d7 RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 \u00b0C 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 \u00b0C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 \u00b0C 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 \u00d7 Halt\u2122 Protease and Phosphatase Inhibitor Cocktail  1 \u00d7 RNaseOUT Recombinant Ribonuclease Inhibitor at 4 \u00b0C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/\u03bcL RNase T1 Thermo Scientific at 22 \u00b0C 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.", null, "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP417272", null, "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, null, null, 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", null, "United States", "2023-01-12", "Multi-stage", "Multi-stage", "Whole Organism", "All anatomical structures"]], "truncated": false, "filtered_table_rows_count": 34, "expanded_columns": [], "expandable_columns": [], "columns": ["rowid", "run.accession", "experiment.accession", "sample.accession", "study.accession", "bioproject", "study.title", "study.alias", "study.type", "study.abstract", "study.attributes", "study.PMIDs", "sample.description", "sample.title", "sample.alias", "sample.centername", "sample.attributes", "GEOsample.title", "GEOsample.dataprocessing", "GEOsample.source", "GEOsample.treatmentprotocol", "GEOsample.extractprotocol", "GEOsample.growthprotocol", "GEOsample.characteristics", "GEOsample.accession", "experiment.title", "experiment.alias", "experiment.library_name", "experiment.design_description", "experiment.library_construction_protocol", "experiment.attributes", "experiment.library_strategy", "experiment.library_source", "experiment.library_selection", "experiment.library_layout", "experiment.platform", "experiment.instrument_model", "experiment.spot_descriptor", "experiment.study_ref", "run.title", "run.attributes", "run.filename", "run.semantic_name", "run.total_bases", "run.total_spots", "run.alias", "run.read_lengths", "run.base_counts", "run.r1_length", "run.r2_length", "run.r3_length", "run.r4_length", "run.Acount", "run.Ccount", "run.Gcount", "run.Tcount", "run.Ncount", "run.experiment", "run.pool_member", "submission.accession", "submission.srasource", "submission.bioprojectsource", "seqdetective.n_mates", "seqdetective.mapping_rate.mate1", "seqdetective.mapping_rate.mate2", "seqdetective.nofeature_rate.mate1", "seqdetective.nofeature_rate.mate2", "seqdetective.sparsity.mate1", "seqdetective.sparsity.mate2", "seqdetective.pos_strand_rate.mate1", "seqdetective.pos_strand_rate.mate2", "seqdetective.readlen.mate1", "seqdetective.readlen.mate2", "seqdetective.judgement.mate1", "seqdetective.judgement.mate2", "seqdetective.judgement.reason", "platform_family", "instrument_generation", "read_bias", "selection_class", "prep_kit", "sc_or_bulk", "tech_class", "technology", "tech_variant", "submission.bioprojectsource.country", "earliest_date", "devstage_curation", "devstage_curation_coarse", "tissue_curation", "tissue_curation_coarse"], "primary_keys": [], "units": {}, "query": {"sql": "select rowid, [run.accession], [experiment.accession], [sample.accession], [study.accession], bioproject, [study.title], [study.alias], [study.type], [study.abstract], [study.attributes], [study.PMIDs], [sample.description], [sample.title], [sample.alias], [sample.centername], [sample.attributes], [GEOsample.title], [GEOsample.dataprocessing], [GEOsample.source], [GEOsample.treatmentprotocol], [GEOsample.extractprotocol], [GEOsample.growthprotocol], [GEOsample.characteristics], [GEOsample.accession], [experiment.title], [experiment.alias], [experiment.library_name], [experiment.design_description], [experiment.library_construction_protocol], [experiment.attributes], [experiment.library_strategy], [experiment.library_source], [experiment.library_selection], [experiment.library_layout], [experiment.platform], [experiment.instrument_model], [experiment.spot_descriptor], [experiment.study_ref], [run.title], [run.attributes], [run.filename], [run.semantic_name], [run.total_bases], [run.total_spots], [run.alias], [run.read_lengths], [run.base_counts], [run.r1_length], [run.r2_length], [run.r3_length], [run.r4_length], [run.Acount], [run.Ccount], [run.Gcount], [run.Tcount], [run.Ncount], [run.experiment], [run.pool_member], [submission.accession], [submission.srasource], [submission.bioprojectsource], [seqdetective.n_mates], [seqdetective.mapping_rate.mate1], [seqdetective.mapping_rate.mate2], [seqdetective.nofeature_rate.mate1], [seqdetective.nofeature_rate.mate2], [seqdetective.sparsity.mate1], [seqdetective.sparsity.mate2], [seqdetective.pos_strand_rate.mate1], [seqdetective.pos_strand_rate.mate2], [seqdetective.readlen.mate1], [seqdetective.readlen.mate2], [seqdetective.judgement.mate1], [seqdetective.judgement.mate2], [seqdetective.judgement.reason], platform_family, 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