{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where technology = \"bulk\" and tissue_curation = \"Trunk\"", "rows": [[25329, "SRR25868071", "SRX21589492", "SRS18767065", "SRP457981", "PRJNA1011838", "fhl2b expression ameliorates muscular dystrophy [5dpf trunk]", "GSE242135", "Transcriptome Analysis", "In muscle dystrophies muscle fibers loose integrity and die leading to significant suffering and a shorter life. Strikingly the extraocular muscles EOMs controlling eye movements are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin plectin and obscurin intermediate filament proteins causing different muscle dystrophies and contributes to disease protection of the EOMs. Moreover we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje significantly improving their survival rate. Therefore fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. 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Strikingly the extraocular muscles EOMs controlling eye movements are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin plectin and obscurin intermediate filament proteins causing different muscle dystrophies and contributes to disease protection of the EOMs. Moreover we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje significantly improving their survival rate. Therefore fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. 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Strikingly the extraocular muscles EOMs controlling eye movements are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin plectin and obscurin intermediate filament proteins causing different muscle dystrophies and contributes to disease protection of the EOMs. Moreover we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje significantly improving their survival rate. Therefore fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. 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Strikingly the extraocular muscles EOMs controlling eye movements are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin plectin and obscurin intermediate filament proteins causing different muscle dystrophies and contributes to disease protection of the EOMs. Moreover we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje significantly improving their survival rate. Therefore fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the effect of fhl2b overexpression in muscle in the background of the dmd/sapje mutant line at 5 dpf", "parent bioproject:PRJNA1011837", "pubmed:38431640", null, "sibCGFP1", "GSM7749554", null, "source name:5 dpf trunk|tissue:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd+/ ;Tg503unc:fhl2b T2A EGFP|geo loc name:missing|collection date:missing", "sibCGFP1", "Sequence reads were mapped to GRCz11 using STAR options: outSAMtype BAM SortedByCoordinate seedSearchStartLmax 12 outFilterScoreMinOverLread 0.3 alignSJoverhangMin 15 outFilterMismatchNmax 33 outFilterMatchNminOverLread 0 outFilterType BySJout outSAMunmapped Within outSAMattributes NH HI AS NM MD outSAMstrandField intronMotif quantMode GeneCounts Read count extraction and normalization were performed using R package DeSEQ2 Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts", "5 dpf trunk", null, "Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at 80C. 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Strikingly the extraocular muscles EOMs controlling eye movements are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin plectin and obscurin intermediate filament proteins causing different muscle dystrophies and contributes to disease protection of the EOMs. Moreover we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje significantly improving their survival rate. Therefore fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the effect of fhl2b overexpression in muscle in the background of the dmd/sapje mutant line at 5 dpf", "parent bioproject:PRJNA1011837", "pubmed:38431640", null, "sibC4", "GSM7749553", null, "source name:5 dpf trunk|tissue:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd+/ |geo loc name:missing|collection date:missing", "sibC4", "Sequence reads were mapped to GRCz11 using STAR options: outSAMtype BAM SortedByCoordinate seedSearchStartLmax 12 outFilterScoreMinOverLread 0.3 alignSJoverhangMin 15 outFilterMismatchNmax 33 outFilterMatchNminOverLread 0 outFilterType BySJout outSAMunmapped Within outSAMattributes NH HI AS NM MD outSAMstrandField intronMotif quantMode GeneCounts Read count extraction and normalization were performed using R package DeSEQ2 Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts", "5 dpf trunk", null, "Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at 80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA poly A selection", "WT AB zebrafish used originated from the same line utilized when generating the desma / ;desmb / double mutant. Zebrafish were maintained by standard procedures on a 10/14h dark/light cycle at 28\u00b0C", "tissue:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd+/ ", "GSM7749553", "GSM7749553: sibC4; Danio rerio; RNA Seq", "GSM7749553 r1", "GSM7749553", "1", "Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at 80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. 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Strikingly the extraocular muscles EOMs controlling eye movements are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin plectin and obscurin intermediate filament proteins causing different muscle dystrophies and contributes to disease protection of the EOMs. Moreover we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje significantly improving their survival rate. Therefore fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the effect of fhl2b overexpression in muscle in the background of the dmd/sapje mutant line at 5 dpf", "parent bioproject:PRJNA1011837", "pubmed:38431640", null, "sibC3", "GSM7749552", null, "source name:5 dpf trunk|tissue:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd+/ |geo loc name:missing|collection date:missing", "sibC3", "Sequence reads were mapped to GRCz11 using STAR options: outSAMtype BAM SortedByCoordinate seedSearchStartLmax 12 outFilterScoreMinOverLread 0.3 alignSJoverhangMin 15 outFilterMismatchNmax 33 outFilterMatchNminOverLread 0 outFilterType BySJout outSAMunmapped Within outSAMattributes NH HI AS NM MD outSAMstrandField intronMotif quantMode GeneCounts Read count extraction and normalization were performed using R package DeSEQ2 Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts", "5 dpf trunk", null, "Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at 80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA poly A selection", "WT AB zebrafish used originated from the same line utilized when generating the desma / ;desmb / double mutant. Zebrafish were maintained by standard procedures on a 10/14h dark/light cycle at 28\u00b0C", "tissue:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd+/ ", "GSM7749552", "GSM7749552: sibC3; Danio rerio; RNA Seq", "GSM7749552 r1", "GSM7749552", "1", "Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at 80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. 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Strikingly the extraocular muscles EOMs controlling eye movements are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin plectin and obscurin intermediate filament proteins causing different muscle dystrophies and contributes to disease protection of the EOMs. Moreover we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje significantly improving their survival rate. Therefore fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the effect of fhl2b overexpression in muscle in the background of the dmd/sapje mutant line at 5 dpf", "parent bioproject:PRJNA1011837", "pubmed:38431640", null, "sibC2", "GSM7749551", null, "source name:5 dpf trunk|tissue:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd+/ |geo loc name:missing|collection date:missing", "sibC2", "Sequence reads were mapped to GRCz11 using STAR options: outSAMtype BAM SortedByCoordinate seedSearchStartLmax 12 outFilterScoreMinOverLread 0.3 alignSJoverhangMin 15 outFilterMismatchNmax 33 outFilterMatchNminOverLread 0 outFilterType BySJout outSAMunmapped Within outSAMattributes NH HI AS NM MD outSAMstrandField intronMotif quantMode GeneCounts Read count extraction and normalization were performed using R package DeSEQ2 Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts", "5 dpf trunk", null, "Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at 80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA poly A selection", "WT AB zebrafish used originated from the same line utilized when generating the desma / ;desmb / double mutant. Zebrafish were maintained by standard procedures on a 10/14h dark/light cycle at 28\u00b0C", "tissue:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd+/ ", "GSM7749551", "GSM7749551: sibC2; Danio rerio; RNA Seq", "GSM7749551 r1", "GSM7749551", "1", "Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at 80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA poly A selection", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP457981", null, "loader:fastq load.py", "WA-3548-sibC2_S40_L002_R1_001.fastq.gz WA-3548-sibC2_S40_L002_R2_001.fastq.gz", "fastq fastq", 9464242402.0, 31338551.0, "GSM7749551 r1", "0:151 1:151", "A:2497543137;C:2235078067;G:2319534414;T:2411649747;N:437037", 151, 151, null, null, 2497543137, 2235078067, 2319534414, 2411649747, 437037, "SRX21589486", "SRS18767057", "SRA1703879", "Ume\u00e5 Univeristy", "Ume\u00e5 Univeristy", 2, 0.96464, 0.965, 0.06696, 0.06563, 0.7138, 0.71512, 0.46359, 0.46601, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "Sweden", "2023-09-01", "Larval", "Larval", "Trunk", "Surface Structure"], [25336, "SRR25868078", "SRX21589485", "SRS18767061", "SRP457981", "PRJNA1011838", "fhl2b expression ameliorates muscular dystrophy [5dpf trunk]", "GSE242135", "Transcriptome Analysis", "In muscle dystrophies muscle fibers loose integrity and die leading to significant suffering and a shorter life. Strikingly the extraocular muscles EOMs controlling eye movements are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin plectin and obscurin intermediate filament proteins causing different muscle dystrophies and contributes to disease protection of the EOMs. Moreover we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje significantly improving their survival rate. Therefore fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the effect of fhl2b overexpression in muscle in the background of the dmd/sapje mutant line at 5 dpf", "parent bioproject:PRJNA1011837", "pubmed:38431640", null, "sibC1", "GSM7749550", null, "source name:5 dpf trunk|tissue:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd+/ |geo loc name:missing|collection date:missing", "sibC1", "Sequence reads were mapped to GRCz11 using STAR options: outSAMtype BAM SortedByCoordinate seedSearchStartLmax 12 outFilterScoreMinOverLread 0.3 alignSJoverhangMin 15 outFilterMismatchNmax 33 outFilterMatchNminOverLread 0 outFilterType BySJout outSAMunmapped Within outSAMattributes NH HI AS NM MD outSAMstrandField intronMotif quantMode GeneCounts Read count extraction and normalization were performed using R package DeSEQ2 Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts", "5 dpf trunk", null, "Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at 80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA poly A selection", "WT AB zebrafish used originated from the same line utilized when generating the desma / ;desmb / double mutant. Zebrafish were maintained by standard procedures on a 10/14h dark/light cycle at 28\u00b0C", "tissue:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd+/ ", "GSM7749550", "GSM7749550: sibC1; Danio rerio; RNA Seq", "GSM7749550 r1", "GSM7749550", "1", "Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at 80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA poly A selection", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP457981", null, "loader:fastq load.py", "WA-3548-sibC1_S39_L002_R1_001.fastq.gz WA-3548-sibC1_S39_L002_R2_001.fastq.gz", "fastq fastq", 11153872908.0, 36933354.0, "GSM7749550 r1", "0:151 1:151", "A:2966120106;C:2600333644;G:2710289968;T:2876608337;N:520853", 151, 151, null, null, 2966120106, 2600333644, 2710289968, 2876608337, 520853, "SRX21589485", "SRS18767061", "SRA1703879", "Ume\u00e5 Univeristy", "Ume\u00e5 Univeristy", 2, 0.96189, 0.96306, 0.07632, 0.07512, 0.70749, 0.70818, 0.46784, 0.4683, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "Sweden", "2023-09-01", "Larval", "Larval", "Trunk", "Surface Structure"], [25337, "SRR25868079", "SRX21589484", "SRS18767058", "SRP457981", "PRJNA1011838", "fhl2b expression ameliorates muscular dystrophy [5dpf trunk]", "GSE242135", "Transcriptome Analysis", "In muscle dystrophies muscle fibers loose integrity and die leading to significant suffering and a shorter life. Strikingly the extraocular muscles EOMs controlling eye movements are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin plectin and obscurin intermediate filament proteins causing different muscle dystrophies and contributes to disease protection of the EOMs. Moreover we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje significantly improving their survival rate. Therefore fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the effect of fhl2b overexpression in muscle in the background of the dmd/sapje mutant line at 5 dpf", "parent bioproject:PRJNA1011837", "pubmed:38431640", null, "dmdGFP4", "GSM7749549", null, "source name:5 dpf trunk|tissue:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd / ;Tg503unc:fhl2b T2A EGFP|geo loc name:missing|collection date:missing", "dmdGFP4", "Sequence reads were mapped to GRCz11 using STAR options: outSAMtype BAM SortedByCoordinate seedSearchStartLmax 12 outFilterScoreMinOverLread 0.3 alignSJoverhangMin 15 outFilterMismatchNmax 33 outFilterMatchNminOverLread 0 outFilterType BySJout outSAMunmapped Within outSAMattributes NH HI AS NM MD outSAMstrandField intronMotif quantMode GeneCounts Read count extraction and normalization were performed using R package DeSEQ2 Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts", "5 dpf trunk", null, "Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at 80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA poly A selection", "WT AB zebrafish used originated from the same line utilized when generating the desma / ;desmb / double mutant. Zebrafish were maintained by standard procedures on a 10/14h dark/light cycle at 28\u00b0C", "tissue:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd / ;Tg503unc:fhl2b T2A EGFP", "GSM7749549", "GSM7749549: dmdGFP4; Danio rerio; RNA Seq", "GSM7749549 r1", "GSM7749549", "1", "Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at 80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA poly A selection", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP457981", null, "loader:fastq load.py", "WA-3548-dmdGFP4_S54_L002_R1_001.fastq.gz WA-3548-dmdGFP4_S54_L002_R2_001.fastq.gz", "fastq fastq", 6593937762.0, 21834231.0, "GSM7749549 r1", "0:151 1:151", "A:1745786828;C:1531704556;G:1637507801;T:1678632967;N:305610", 151, 151, null, null, 1745786828, 1531704556, 1637507801, 1678632967, 305610, "SRX21589484", "SRS18767058", "SRA1703879", "Ume\u00e5 Univeristy", "Ume\u00e5 Univeristy", 2, 0.9626, 0.96282, 0.08653, 0.08533, 0.70433, 0.70636, 0.47707, 0.46994, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "Sweden", "2023-09-01", "Larval", "Larval", "Trunk", "Surface Structure"], [25338, "SRR25868080", "SRX21589483", "SRS18767056", "SRP457981", "PRJNA1011838", "fhl2b expression ameliorates muscular dystrophy [5dpf trunk]", "GSE242135", "Transcriptome Analysis", "In muscle dystrophies muscle fibers loose integrity and die leading to significant suffering and a shorter life. Strikingly the extraocular muscles EOMs controlling eye movements are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin plectin and obscurin intermediate filament proteins causing different muscle dystrophies and contributes to disease protection of the EOMs. Moreover we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje significantly improving their survival rate. Therefore fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the effect of fhl2b overexpression in muscle in the background of the dmd/sapje mutant line at 5 dpf", "parent bioproject:PRJNA1011837", "pubmed:38431640", null, "dmdGFP3", "GSM7749548", null, "source name:5 dpf trunk|tissue:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd / ;Tg503unc:fhl2b T2A EGFP|geo loc name:missing|collection date:missing", "dmdGFP3", "Sequence reads were mapped to GRCz11 using STAR options: outSAMtype BAM SortedByCoordinate seedSearchStartLmax 12 outFilterScoreMinOverLread 0.3 alignSJoverhangMin 15 outFilterMismatchNmax 33 outFilterMatchNminOverLread 0 outFilterType BySJout outSAMunmapped Within outSAMattributes NH HI AS NM MD outSAMstrandField intronMotif quantMode GeneCounts Read count extraction and normalization were performed using R package DeSEQ2 Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts", "5 dpf trunk", null, "Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at 80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA poly A selection", "WT AB zebrafish used originated from the same line utilized when generating the desma / ;desmb / double mutant. Zebrafish were maintained by standard procedures on a 10/14h dark/light cycle at 28\u00b0C", "tissue:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd / ;Tg503unc:fhl2b T2A EGFP", "GSM7749548", "GSM7749548: dmdGFP3; Danio rerio; RNA Seq", "GSM7749548 r1", "GSM7749548", "1", "Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at 80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA poly A selection", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP457981", null, "loader:fastq load.py", "WA-3548-dmdGFP3_S53_L002_R1_001.fastq.gz WA-3548-dmdGFP3_S53_L002_R2_001.fastq.gz", "fastq fastq", 9250573476.0, 30631038.0, "GSM7749548 r1", "0:151 1:151", "A:2485551140;C:2135752367;G:2259698711;T:2369143289;N:427969", 151, 151, null, null, 2485551140, 2135752367, 2259698711, 2369143289, 427969, "SRX21589483", "SRS18767056", "SRA1703879", "Ume\u00e5 Univeristy", "Ume\u00e5 Univeristy", 2, 0.96118, 0.96196, 0.0946, 0.09271, 0.69702, 0.69834, 0.47168, 0.47515, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "Sweden", "2023-09-01", "Larval", "Larval", "Trunk", "Surface Structure"], [25339, "SRR25868081", "SRX21589482", "SRS18767055", "SRP457981", "PRJNA1011838", "fhl2b expression ameliorates muscular dystrophy [5dpf trunk]", "GSE242135", "Transcriptome Analysis", "In muscle dystrophies muscle fibers loose integrity and die leading to significant suffering and a shorter life. Strikingly the extraocular muscles EOMs controlling eye movements are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin plectin and obscurin intermediate filament proteins causing different muscle dystrophies and contributes to disease protection of the EOMs. Moreover we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje significantly improving their survival rate. Therefore fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the effect of fhl2b overexpression in muscle in the background of the dmd/sapje mutant line at 5 dpf", "parent bioproject:PRJNA1011837", "pubmed:38431640", null, "dmdGFP2", "GSM7749547", null, "source name:5 dpf trunk|tissue:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd / ;Tg503unc:fhl2b T2A EGFP|geo loc name:missing|collection date:missing", "dmdGFP2", "Sequence reads were mapped to GRCz11 using STAR options: outSAMtype BAM SortedByCoordinate seedSearchStartLmax 12 outFilterScoreMinOverLread 0.3 alignSJoverhangMin 15 outFilterMismatchNmax 33 outFilterMatchNminOverLread 0 outFilterType BySJout outSAMunmapped Within outSAMattributes NH HI AS NM MD outSAMstrandField intronMotif quantMode GeneCounts Read count extraction and normalization were performed using R package DeSEQ2 Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts", "5 dpf trunk", null, "Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at 80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA poly A selection", "WT AB zebrafish used originated from the same line utilized when generating the desma / ;desmb / double mutant. Zebrafish were maintained by standard procedures on a 10/14h dark/light cycle at 28\u00b0C", "tissue:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd / ;Tg503unc:fhl2b T2A EGFP", "GSM7749547", "GSM7749547: dmdGFP2; Danio rerio; RNA Seq", "GSM7749547 r1", "GSM7749547", "1", "Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at 80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA poly A selection", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP457981", null, "loader:fastq load.py", "WA-3548-dmdGFP2_S52_L002_R1_001.fastq.gz WA-3548-dmdGFP2_S52_L002_R2_001.fastq.gz", "fastq fastq", 8584886654.0, 28426777.0, "GSM7749547 r1", "0:151 1:151", "A:2310205296;C:1982936514;G:2071907465;T:2219441471;N:395908", 151, 151, null, null, 2310205296, 1982936514, 2071907465, 2219441471, 395908, "SRX21589482", "SRS18767055", "SRA1703879", "Ume\u00e5 Univeristy", "Ume\u00e5 Univeristy", 2, 0.9586, 0.95966, 0.09636, 0.09473, 0.69881, 0.6997, 0.47446, 0.47409, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "Sweden", "2023-09-01", "Larval", "Larval", "Trunk", "Surface Structure"], [25340, "SRR25868082", "SRX21589481", "SRS18767052", "SRP457981", "PRJNA1011838", "fhl2b expression ameliorates muscular dystrophy [5dpf trunk]", "GSE242135", "Transcriptome Analysis", "In muscle dystrophies muscle fibers loose integrity and die leading to significant suffering and a shorter life. Strikingly the extraocular muscles EOMs controlling eye movements are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin plectin and obscurin intermediate filament proteins causing different muscle dystrophies and contributes to disease protection of the EOMs. Moreover we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje significantly improving their survival rate. Therefore fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the effect of fhl2b overexpression in muscle in the background of the dmd/sapje mutant line at 5 dpf", "parent bioproject:PRJNA1011837", "pubmed:38431640", null, "dmdGFP1", "GSM7749546", null, "source name:5 dpf trunk|tissue:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd / ;Tg503unc:fhl2b T2A EGFP|geo loc name:missing|collection date:missing", "dmdGFP1", "Sequence reads were mapped to GRCz11 using STAR options: outSAMtype BAM SortedByCoordinate seedSearchStartLmax 12 outFilterScoreMinOverLread 0.3 alignSJoverhangMin 15 outFilterMismatchNmax 33 outFilterMatchNminOverLread 0 outFilterType BySJout outSAMunmapped Within outSAMattributes NH HI AS NM MD outSAMstrandField intronMotif quantMode GeneCounts Read count extraction and normalization were performed using R package DeSEQ2 Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts", "5 dpf trunk", null, "Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at 80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA poly A selection", "WT AB zebrafish used originated from the same line utilized when generating the desma / ;desmb / double mutant. Zebrafish were maintained by standard procedures on a 10/14h dark/light cycle at 28\u00b0C", "tissue:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd / ;Tg503unc:fhl2b T2A EGFP", "GSM7749546", "GSM7749546: dmdGFP1; Danio rerio; RNA Seq", "GSM7749546 r1", "GSM7749546", "1", "Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at 80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA poly A selection", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP457981", null, "loader:fastq load.py", "WA-3548-dmdGFP1_S51_L002_R1_001.fastq.gz WA-3548-dmdGFP1_S51_L002_R2_001.fastq.gz", "fastq fastq", 7573189674.0, 25076787.0, "GSM7749546 r1", "0:151 1:151", "A:2025587174;C:1735604560;G:1848622101;T:1963022142;N:353697", 151, 151, null, null, 2025587174, 1735604560, 1848622101, 1963022142, 353697, "SRX21589481", "SRS18767052", "SRA1703879", "Ume\u00e5 Univeristy", "Ume\u00e5 Univeristy", 2, 0.95942, 0.96073, 0.08752, 0.08624, 0.69863, 0.69822, 0.4733, 0.47454, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "Sweden", "2023-09-01", "Larval", "Larval", "Trunk", "Surface Structure"], [25341, "SRR25868083", "SRX21589480", "SRS18767054", "SRP457981", "PRJNA1011838", "fhl2b expression ameliorates muscular dystrophy [5dpf trunk]", "GSE242135", "Transcriptome Analysis", "In muscle dystrophies muscle fibers loose integrity and die leading to significant suffering and a shorter life. Strikingly the extraocular muscles EOMs controlling eye movements are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin plectin and obscurin intermediate filament proteins causing different muscle dystrophies and contributes to disease protection of the EOMs. Moreover we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje significantly improving their survival rate. Therefore fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the effect of fhl2b overexpression in muscle in the background of the dmd/sapje mutant line at 5 dpf", "parent bioproject:PRJNA1011837", "pubmed:38431640", null, "dmd4", "GSM7749545", null, "source name:5 dpf trunk|tissue:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd / |geo loc name:missing|collection date:missing", "dmd4", "Sequence reads were mapped to GRCz11 using STAR options: outSAMtype BAM SortedByCoordinate seedSearchStartLmax 12 outFilterScoreMinOverLread 0.3 alignSJoverhangMin 15 outFilterMismatchNmax 33 outFilterMatchNminOverLread 0 outFilterType BySJout outSAMunmapped Within outSAMattributes NH HI AS NM MD outSAMstrandField intronMotif quantMode GeneCounts Read count extraction and normalization were performed using R package DeSEQ2 Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts", "5 dpf trunk", null, "Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at 80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA poly A selection", "WT AB zebrafish used originated from the same line utilized when generating the desma / ;desmb / double mutant. Zebrafish were maintained by standard procedures on a 10/14h dark/light cycle at 28\u00b0C", "tissue:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd / ", "GSM7749545", "GSM7749545: dmd4; Danio rerio; RNA Seq", "GSM7749545 r1", "GSM7749545", "1", "Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at 80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA poly A selection", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP457981", null, "loader:fastq load.py", "WA-3548-dmd4_S50_L002_R1_001.fastq.gz WA-3548-dmd4_S50_L002_R2_001.fastq.gz", "fastq fastq", 9121652998.0, 30204149.0, "GSM7749545 r1", "0:151 1:151", "A:2438907102;C:2114952319;G:2225797925;T:2341561511;N:434141", 151, 151, null, null, 2438907102, 2114952319, 2225797925, 2341561511, 434141, "SRX21589480", "SRS18767054", "SRA1703879", "Ume\u00e5 Univeristy", "Ume\u00e5 Univeristy", 2, 0.961, 0.96258, 0.08366, 0.08276, 0.69787, 0.69856, 0.47181, 0.46112, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "Sweden", "2023-09-01", "Larval", "Larval", "Trunk", "Surface Structure"], [25342, "SRR25868084", "SRX21589479", "SRS18767053", "SRP457981", "PRJNA1011838", "fhl2b expression ameliorates muscular dystrophy [5dpf trunk]", "GSE242135", "Transcriptome Analysis", "In muscle dystrophies muscle fibers loose integrity and die leading to significant suffering and a shorter life. Strikingly the extraocular muscles EOMs controlling eye movements are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin plectin and obscurin intermediate filament proteins causing different muscle dystrophies and contributes to disease protection of the EOMs. Moreover we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje significantly improving their survival rate. Therefore fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the effect of fhl2b overexpression in muscle in the background of the dmd/sapje mutant line at 5 dpf", "parent bioproject:PRJNA1011837", "pubmed:38431640", null, "dmd3", "GSM7749544", null, "source name:5 dpf trunk|tissue:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd / |geo loc name:missing|collection date:missing", "dmd3", "Sequence reads were mapped to GRCz11 using STAR options: outSAMtype BAM SortedByCoordinate seedSearchStartLmax 12 outFilterScoreMinOverLread 0.3 alignSJoverhangMin 15 outFilterMismatchNmax 33 outFilterMatchNminOverLread 0 outFilterType BySJout outSAMunmapped Within outSAMattributes NH HI AS NM MD outSAMstrandField intronMotif quantMode GeneCounts Read count extraction and normalization were performed using R package DeSEQ2 Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts", "5 dpf trunk", null, "Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at 80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA poly A selection", "WT AB zebrafish used originated from the same line utilized when generating the desma / ;desmb / double mutant. Zebrafish were maintained by standard procedures on a 10/14h dark/light cycle at 28\u00b0C", "tissue:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd / ", "GSM7749544", "GSM7749544: dmd3; Danio rerio; RNA Seq", "GSM7749544 r1", "GSM7749544", "1", "Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at 80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA poly A selection", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP457981", null, "loader:fastq load.py", "WA-3548-dmd3_S49_L002_R1_001.fastq.gz WA-3548-dmd3_S49_L002_R2_001.fastq.gz", "fastq fastq", 7896671538.0, 26147919.0, "GSM7749544 r1", "0:151 1:151", "A:2104101125;C:1828908837;G:1933039401;T:2030257090;N:365085", 151, 151, null, null, 2104101125, 1828908837, 1933039401, 2030257090, 365085, "SRX21589479", "SRS18767053", "SRA1703879", "Ume\u00e5 Univeristy", "Ume\u00e5 Univeristy", 2, 0.96014, 0.96084, 0.08575, 0.08475, 0.70082, 0.70108, 0.47254, 0.47153, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "Sweden", "2023-09-01", "Larval", "Larval", "Trunk", "Surface Structure"], [25343, "SRR25868085", "SRX21589478", "SRS18767051", "SRP457981", "PRJNA1011838", "fhl2b expression ameliorates muscular dystrophy [5dpf trunk]", "GSE242135", "Transcriptome Analysis", "In muscle dystrophies muscle fibers loose integrity and die leading to significant suffering and a shorter life. Strikingly the extraocular muscles EOMs controlling eye movements are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin plectin and obscurin intermediate filament proteins causing different muscle dystrophies and contributes to disease protection of the EOMs. Moreover we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje significantly improving their survival rate. Therefore fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the effect of fhl2b overexpression in muscle in the background of the dmd/sapje mutant line at 5 dpf", "parent bioproject:PRJNA1011837", "pubmed:38431640", null, "dmd2", "GSM7749543", null, "source name:5 dpf trunk|tissue:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd / |geo loc name:missing|collection date:missing", "dmd2", "Sequence reads were mapped to GRCz11 using STAR options: outSAMtype BAM SortedByCoordinate seedSearchStartLmax 12 outFilterScoreMinOverLread 0.3 alignSJoverhangMin 15 outFilterMismatchNmax 33 outFilterMatchNminOverLread 0 outFilterType BySJout outSAMunmapped Within outSAMattributes NH HI AS NM MD outSAMstrandField intronMotif quantMode GeneCounts Read count extraction and normalization were performed using R package DeSEQ2 Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts", "5 dpf trunk", null, "Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at 80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA poly A selection", "WT AB zebrafish used originated from the same line utilized when generating the desma / ;desmb / double mutant. Zebrafish were maintained by standard procedures on a 10/14h dark/light cycle at 28\u00b0C", "tissue:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd / ", "GSM7749543", "GSM7749543: dmd2; Danio rerio; RNA Seq", "GSM7749543 r1", "GSM7749543", "1", "Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at 80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA poly A selection", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP457981", null, "loader:fastq load.py", "WA-3548-dmd2_S48_L002_R1_001.fastq.gz WA-3548-dmd2_S48_L002_R2_001.fastq.gz", "fastq fastq", 9484006792.0, 31403996.0, "GSM7749543 r1", "0:151 1:151", "A:2518758838;C:2211640185;G:2303907076;T:2449259369;N:441324", 151, 151, null, null, 2518758838, 2211640185, 2303907076, 2449259369, 441324, "SRX21589478", "SRS18767051", "SRA1703879", "Ume\u00e5 Univeristy", "Ume\u00e5 Univeristy", 2, 0.96047, 0.96128, 0.09081, 0.09031, 0.69603, 0.69605, 0.46706, 0.47077, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "Sweden", "2023-09-01", "Larval", "Larval", "Trunk", "Surface Structure"], [25344, "SRR25868086", "SRX21589477", "SRS18767050", "SRP457981", "PRJNA1011838", "fhl2b expression ameliorates muscular dystrophy [5dpf trunk]", "GSE242135", "Transcriptome Analysis", "In muscle dystrophies muscle fibers loose integrity and die leading to significant suffering and a shorter life. Strikingly the extraocular muscles EOMs controlling eye movements are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin plectin and obscurin intermediate filament proteins causing different muscle dystrophies and contributes to disease protection of the EOMs. Moreover we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje significantly improving their survival rate. Therefore fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the effect of fhl2b overexpression in muscle in the background of the dmd/sapje mutant line at 5 dpf", "parent bioproject:PRJNA1011837", "pubmed:38431640", null, "dmd1", "GSM7749542", null, "source name:5 dpf trunk|tissue:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd / |geo loc name:missing|collection date:missing", "dmd1", "Sequence reads were mapped to GRCz11 using STAR options: outSAMtype BAM SortedByCoordinate seedSearchStartLmax 12 outFilterScoreMinOverLread 0.3 alignSJoverhangMin 15 outFilterMismatchNmax 33 outFilterMatchNminOverLread 0 outFilterType BySJout outSAMunmapped Within outSAMattributes NH HI AS NM MD outSAMstrandField intronMotif quantMode GeneCounts Read count extraction and normalization were performed using R package DeSEQ2 Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts", "5 dpf trunk", null, "Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at 80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA poly A selection", "WT AB zebrafish used originated from the same line utilized when generating the desma / ;desmb / double mutant. Zebrafish were maintained by standard procedures on a 10/14h dark/light cycle at 28\u00b0C", "tissue:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd / ", "GSM7749542", "GSM7749542: dmd1; Danio rerio; RNA Seq", "GSM7749542 r1", "GSM7749542", "1", "Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at 80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA poly A selection", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP457981", null, "loader:fastq load.py", "WA-3548-dmd1_S47_L002_R1_001.fastq.gz WA-3548-dmd1_S47_L002_R2_001.fastq.gz", "fastq fastq", 8411057568.0, 27851184.0, "GSM7749542 r1", "0:151 1:151", "A:2239146475;C:1963458820;G:2046268505;T:2161796444;N:387324", 151, 151, null, null, 2239146475, 1963458820, 2046268505, 2161796444, 387324, "SRX21589477", "SRS18767050", "SRA1703879", "Ume\u00e5 Univeristy", "Ume\u00e5 Univeristy", 2, 0.96292, 0.96424, 0.07952, 0.07845, 0.70473, 0.70467, 0.47569, 0.47555, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "Sweden", "2023-09-01", "Larval", "Larval", "Trunk", "Surface Structure"], [32488, "SRR29285561", "SRX24802703", "SRS21518811", "SRP511787", "PRJNA1120060", "O GlcNAcylation Modulates Expression and Abundance of N Glycosylation Machinery in an Inherited Glycosylation Disorder", "GSE269074", "Transcriptome Analysis", "Much of the N glycosylation machinery was identified decades ago but the regulatory mechanisms influencing normal and disease states are only beginning to be discovered. Recent studies highlight a role for key metabolites and metabolic enzymes in this process revising the view of the relationship between different metabolic pathways. Using a multi omic approach in a zebrafish we discovered a mechanism where O GlcNAcylation directly influences the expression and abundance of two enzymes essential for the earliest steps of N linked glycosylation the nus1 encoded NgBR and Dpagt1. Here we show that phosphomannomutase pmm2 deficiency is associated with increased levels of UDP GlcNAc and protein O GlcNAcylation. Biochemical studies show that O GlcNAc modification of the NgBR and Dpagt1 increases their abundance in pmm2m/m mutants. Modulating O GlcNAc levels NgBR abundance or Dpagt1 activity exacerbated cartilage phenotypes in pmm2 mutants suggesting that O GlcNAc mediated increases in the N glycosylation machinery protects against more severe pathology. These findings highlight nucleotide sugar donors as metabolic sensors that coordinate two different glycosylation pathways demonstrating how their interplay is relevant to disease outcome in the most common congenital disorder of glycosylation. Overall design: We did bulk total RNA seq with ribo depletion of whole zebrafish larvae at 2 ages 5dpf and 8dpf for two genotypes wildtype WT and Mutant where the mutant is a loss of function of Pmm2. Each sample consisted of 15 larvae and we sequenced 5 biological replicates per genotype and age combination.", null, "pubmed:39561044", null, "Mutant 8dpf 5", "GSM8305920", null, "source name:whole body|tissue:whole body|genotype:Mutant|age:8dpf|genotype:Mutant|replicate:5|geo loc name:missing|collection date:missing", "Mutant 8dpf 5", "FASTQ QC by fastp adapter trimming and assessment of ribo depletion by bbduk alignment by STAR BAM indexing by samtools counting of reads in each gene by subread Assembly: GRCz11 Supplementary files format and content: The counts table contains raw counts of reads aligning to genes generated by subread. It is a tab delimited text file", "whole body", "For the sample preparation 3dpf larvae were genotyped using the assay described see the qRT PCR analyses and genotyping section subsequently pooled by genotype and collected and snap frozen in liquid nitrogen 5 and 8dpf. 15 larvae per genotype per sample were collected.", "Direct zol RNA microprep kit KTC UNIV RNA Seq NUQ AD A01 with NuQuant Custom deplete ADU033 D. rerio kit", "Animals were maintained according to standard protocols", "tissue:whole body|genotype:Mutant|age:8dpf|genotype:Mutant|replicate:5", "GSM8305920", "GSM8305920: Mutant 8dpf 5; Danio rerio; RNA Seq", "GSM8305920 r1", "GSM8305920", "1", "Direct zol RNA microprep kit KTC UNIV RNA Seq NUQ AD A01 with NuQuant Custom deplete ADU033 D. rerio kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP511787", null, null, "30_S30_R1_001.fastq.gz 30_S30_R2_001.fastq.gz", "fastq fastq", 6296757573.0, 23640034.0, "GSM8305920 r1", "0:133.22 1:133.14", "A:1705780530;C:1407325553;G:1444855023;T:1711961543;N:26834924", 133, 133, null, null, 1705780530, 1407325553, 1444855023, 1711961543, 26834924, "SRX24802703", "SRS21518811", "SRA1889334", "Greenwood Genetic Center", "Greenwood Genetic Center", 2, 0.72886, 0.72666, 0.24329, 0.24823, 0.73529, 0.74146, 0.51326, 0.51598, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2024-06-04", "Larval", "Larval", "Trunk", "Surface Structure"], [32489, "SRR29285562", "SRX24802702", "SRS21518810", "SRP511787", "PRJNA1120060", "O GlcNAcylation Modulates Expression and Abundance of N Glycosylation Machinery in an Inherited Glycosylation Disorder", "GSE269074", "Transcriptome Analysis", "Much of the N glycosylation machinery was identified decades ago but the regulatory mechanisms influencing normal and disease states are only beginning to be discovered. Recent studies highlight a role for key metabolites and metabolic enzymes in this process revising the view of the relationship between different metabolic pathways. Using a multi omic approach in a zebrafish we discovered a mechanism where O GlcNAcylation directly influences the expression and abundance of two enzymes essential for the earliest steps of N linked glycosylation the nus1 encoded NgBR and Dpagt1. Here we show that phosphomannomutase pmm2 deficiency is associated with increased levels of UDP GlcNAc and protein O GlcNAcylation. Biochemical studies show that O GlcNAc modification of the NgBR and Dpagt1 increases their abundance in pmm2m/m mutants. Modulating O GlcNAc levels NgBR abundance or Dpagt1 activity exacerbated cartilage phenotypes in pmm2 mutants suggesting that O GlcNAc mediated increases in the N glycosylation machinery protects against more severe pathology. These findings highlight nucleotide sugar donors as metabolic sensors that coordinate two different glycosylation pathways demonstrating how their interplay is relevant to disease outcome in the most common congenital disorder of glycosylation. Overall design: We did bulk total RNA seq with ribo depletion of whole zebrafish larvae at 2 ages 5dpf and 8dpf for two genotypes wildtype WT and Mutant where the mutant is a loss of function of Pmm2. Each sample consisted of 15 larvae and we sequenced 5 biological replicates per genotype and age combination.", null, "pubmed:39561044", null, "Mutant 8dpf 4", "GSM8305919", null, "source name:whole body|tissue:whole body|genotype:Mutant|age:8dpf|genotype:Mutant|replicate:4|geo loc name:missing|collection date:missing", "Mutant 8dpf 4", "FASTQ QC by fastp adapter trimming and assessment of ribo depletion by bbduk alignment by STAR BAM indexing by samtools counting of reads in each gene by subread Assembly: GRCz11 Supplementary files format and content: The counts table contains raw counts of reads aligning to genes generated by subread. It is a tab delimited text file", "whole body", "For the sample preparation 3dpf larvae were genotyped using the assay described see the qRT PCR analyses and genotyping section subsequently pooled by genotype and collected and snap frozen in liquid nitrogen 5 and 8dpf. 15 larvae per genotype per sample were collected.", "Direct zol RNA microprep kit KTC UNIV RNA Seq NUQ AD A01 with NuQuant Custom deplete ADU033 D. rerio kit", "Animals were maintained according to standard protocols", "tissue:whole body|genotype:Mutant|age:8dpf|genotype:Mutant|replicate:4", "GSM8305919", "GSM8305919: Mutant 8dpf 4; Danio rerio; RNA Seq", "GSM8305919 r1", "GSM8305919", "1", "Direct zol RNA microprep kit KTC UNIV RNA Seq NUQ AD A01 with NuQuant Custom deplete ADU033 D. rerio kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP511787", null, null, "29_S29_R1_001.fastq.gz 29_S29_R2_001.fastq.gz", "fastq fastq", 3977478302.0, 15484604.0, "GSM8305919 r1", "0:128.40 1:128.47", "A:1153124522;C:795067209;G:830421153;T:1174546124;N:24319294", 128, 128, null, null, 1153124522, 795067209, 830421153, 1174546124, 24319294, "SRX24802702", "SRS21518810", "SRA1889334", "Greenwood Genetic Center", "Greenwood Genetic Center", 2, 0.75548, 0.75663, 0.31871, 0.33308, 0.72275, 0.73411, 0.59066, 0.60265, 148, 148, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2024-06-04", "Larval", "Larval", "Trunk", "Surface Structure"], [32490, "SRR29285563", "SRX24802701", "SRS21518809", "SRP511787", "PRJNA1120060", "O GlcNAcylation Modulates Expression and Abundance of N Glycosylation Machinery in an Inherited Glycosylation Disorder", "GSE269074", "Transcriptome Analysis", "Much of the N glycosylation machinery was identified decades ago but the regulatory mechanisms influencing normal and disease states are only beginning to be discovered. Recent studies highlight a role for key metabolites and metabolic enzymes in this process revising the view of the relationship between different metabolic pathways. Using a multi omic approach in a zebrafish we discovered a mechanism where O GlcNAcylation directly influences the expression and abundance of two enzymes essential for the earliest steps of N linked glycosylation the nus1 encoded NgBR and Dpagt1. Here we show that phosphomannomutase pmm2 deficiency is associated with increased levels of UDP GlcNAc and protein O GlcNAcylation. Biochemical studies show that O GlcNAc modification of the NgBR and Dpagt1 increases their abundance in pmm2m/m mutants. Modulating O GlcNAc levels NgBR abundance or Dpagt1 activity exacerbated cartilage phenotypes in pmm2 mutants suggesting that O GlcNAc mediated increases in the N glycosylation machinery protects against more severe pathology. These findings highlight nucleotide sugar donors as metabolic sensors that coordinate two different glycosylation pathways demonstrating how their interplay is relevant to disease outcome in the most common congenital disorder of glycosylation. Overall design: We did bulk total RNA seq with ribo depletion of whole zebrafish larvae at 2 ages 5dpf and 8dpf for two genotypes wildtype WT and Mutant where the mutant is a loss of function of Pmm2. Each sample consisted of 15 larvae and we sequenced 5 biological replicates per genotype and age combination.", null, "pubmed:39561044", null, "Mutant 8dpf 3", "GSM8305918", null, "source name:whole body|tissue:whole body|genotype:Mutant|age:8dpf|genotype:Mutant|replicate:3|geo loc name:missing|collection date:missing", "Mutant 8dpf 3", "FASTQ QC by fastp adapter trimming and assessment of ribo depletion by bbduk alignment by STAR BAM indexing by samtools counting of reads in each gene by subread Assembly: GRCz11 Supplementary files format and content: The counts table contains raw counts of reads aligning to genes generated by subread. It is a tab delimited text file", "whole body", "For the sample preparation 3dpf larvae were genotyped using the assay described see the qRT PCR analyses and genotyping section subsequently pooled by genotype and collected and snap frozen in liquid nitrogen 5 and 8dpf. 15 larvae per genotype per sample were collected.", "Direct zol RNA microprep kit KTC UNIV RNA Seq NUQ AD A01 with NuQuant Custom deplete ADU033 D. rerio kit", "Animals were maintained according to standard protocols", "tissue:whole body|genotype:Mutant|age:8dpf|genotype:Mutant|replicate:3", "GSM8305918", "GSM8305918: Mutant 8dpf 3; Danio rerio; RNA Seq", "GSM8305918 r1", "GSM8305918", "1", "Direct zol RNA microprep kit KTC UNIV RNA Seq NUQ AD A01 with NuQuant Custom deplete ADU033 D. rerio kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP511787", null, null, "28_S28_R1_001.fastq.gz 28_S28_R2_001.fastq.gz", "fastq fastq", 1621059592.0, 6158743.0, "GSM8305918 r1", "0:131.56 1:131.65", "A:440443017;C:360750685;G:369447031;T:443711271;N:6707588", 131, 131, null, null, 440443017, 360750685, 369447031, 443711271, 6707588, "SRX24802701", "SRS21518809", "SRA1889334", "Greenwood Genetic Center", "Greenwood Genetic Center", 2, 0.80702, 0.80741, 0.30093, 0.30284, 0.72563, 0.73269, 0.58822, 0.62115, 121, 121, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2024-06-04", "Larval", "Larval", "Trunk", "Surface Structure"], [32491, "SRR29285564", "SRX24802700", "SRS21518808", "SRP511787", "PRJNA1120060", "O GlcNAcylation Modulates Expression and Abundance of N Glycosylation Machinery in an Inherited Glycosylation Disorder", "GSE269074", "Transcriptome Analysis", "Much of the N glycosylation machinery was identified decades ago but the regulatory mechanisms influencing normal and disease states are only beginning to be discovered. Recent studies highlight a role for key metabolites and metabolic enzymes in this process revising the view of the relationship between different metabolic pathways. Using a multi omic approach in a zebrafish we discovered a mechanism where O GlcNAcylation directly influences the expression and abundance of two enzymes essential for the earliest steps of N linked glycosylation the nus1 encoded NgBR and Dpagt1. Here we show that phosphomannomutase pmm2 deficiency is associated with increased levels of UDP GlcNAc and protein O GlcNAcylation. Biochemical studies show that O GlcNAc modification of the NgBR and Dpagt1 increases their abundance in pmm2m/m mutants. Modulating O GlcNAc levels NgBR abundance or Dpagt1 activity exacerbated cartilage phenotypes in pmm2 mutants suggesting that O GlcNAc mediated increases in the N glycosylation machinery protects against more severe pathology. These findings highlight nucleotide sugar donors as metabolic sensors that coordinate two different glycosylation pathways demonstrating how their interplay is relevant to disease outcome in the most common congenital disorder of glycosylation. Overall design: We did bulk total RNA seq with ribo depletion of whole zebrafish larvae at 2 ages 5dpf and 8dpf for two genotypes wildtype WT and Mutant where the mutant is a loss of function of Pmm2. Each sample consisted of 15 larvae and we sequenced 5 biological replicates per genotype and age combination.", null, "pubmed:39561044", null, "Mutant 8dpf 2", "GSM8305917", null, "source name:whole body|tissue:whole body|genotype:Mutant|age:8dpf|genotype:Mutant|replicate:2|geo loc name:missing|collection date:missing", "Mutant 8dpf 2", "FASTQ QC by fastp adapter trimming and assessment of ribo depletion by bbduk alignment by STAR BAM indexing by samtools counting of reads in each gene by subread Assembly: GRCz11 Supplementary files format and content: The counts table contains raw counts of reads aligning to genes generated by subread. It is a tab delimited text file", "whole body", "For the sample preparation 3dpf larvae were genotyped using the assay described see the qRT PCR analyses and genotyping section subsequently pooled by genotype and collected and snap frozen in liquid nitrogen 5 and 8dpf. 15 larvae per genotype per sample were collected.", "Direct zol RNA microprep kit KTC UNIV RNA Seq NUQ AD A01 with NuQuant Custom deplete ADU033 D. rerio kit", "Animals were maintained according to standard protocols", "tissue:whole body|genotype:Mutant|age:8dpf|genotype:Mutant|replicate:2", "GSM8305917", "GSM8305917: Mutant 8dpf 2; Danio rerio; RNA Seq", "GSM8305917 r1", "GSM8305917", "1", "Direct zol RNA microprep kit KTC UNIV RNA Seq NUQ AD A01 with NuQuant Custom deplete ADU033 D. rerio kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP511787", null, null, "27_S27_R1_001.fastq.gz 27_S27_R2_001.fastq.gz", "fastq fastq", 14150299985.0, 54393342.0, "GSM8305917 r1", "0:130.00 1:130.15", "A:4019553056;C:2916143925;G:3025489536;T:4096585966;N:92527502", 130, 130, null, null, 4019553056, 2916143925, 3025489536, 4096585966, 92527502, "SRX24802700", "SRS21518808", "SRA1889334", "Greenwood Genetic Center", "Greenwood Genetic Center", 2, 0.7951, 0.79615, 0.295, 0.30615, 0.72516, 0.73367, 0.59737, 0.60496, 70, 70, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2024-06-04", "Larval", "Larval", "Trunk", "Surface Structure"], [32492, "SRR29285565", "SRX24802699", "SRS21518807", "SRP511787", "PRJNA1120060", "O GlcNAcylation Modulates Expression and Abundance of N Glycosylation Machinery in an Inherited Glycosylation Disorder", "GSE269074", "Transcriptome Analysis", "Much of the N glycosylation machinery was identified decades ago but the regulatory mechanisms influencing normal and disease states are only beginning to be discovered. Recent studies highlight a role for key metabolites and metabolic enzymes in this process revising the view of the relationship between different metabolic pathways. Using a multi omic approach in a zebrafish we discovered a mechanism where O GlcNAcylation directly influences the expression and abundance of two enzymes essential for the earliest steps of N linked glycosylation the nus1 encoded NgBR and Dpagt1. Here we show that phosphomannomutase pmm2 deficiency is associated with increased levels of UDP GlcNAc and protein O GlcNAcylation. Biochemical studies show that O GlcNAc modification of the NgBR and Dpagt1 increases their abundance in pmm2m/m mutants. Modulating O GlcNAc levels NgBR abundance or Dpagt1 activity exacerbated cartilage phenotypes in pmm2 mutants suggesting that O GlcNAc mediated increases in the N glycosylation machinery protects against more severe pathology. These findings highlight nucleotide sugar donors as metabolic sensors that coordinate two different glycosylation pathways demonstrating how their interplay is relevant to disease outcome in the most common congenital disorder of glycosylation. Overall design: We did bulk total RNA seq with ribo depletion of whole zebrafish larvae at 2 ages 5dpf and 8dpf for two genotypes wildtype WT and Mutant where the mutant is a loss of function of Pmm2. Each sample consisted of 15 larvae and we sequenced 5 biological replicates per genotype and age combination.", null, "pubmed:39561044", null, "Mutant 8dpf 1", "GSM8305916", null, "source name:whole body|tissue:whole body|genotype:Mutant|age:8dpf|genotype:Mutant|replicate:1|geo loc name:missing|collection date:missing", "Mutant 8dpf 1", "FASTQ QC by fastp adapter trimming and assessment of ribo depletion by bbduk alignment by STAR BAM indexing by samtools counting of reads in each gene by subread Assembly: GRCz11 Supplementary files format and content: The counts table contains raw counts of reads aligning to genes generated by subread. It is a tab delimited text file", "whole body", "For the sample preparation 3dpf larvae were genotyped using the assay described see the qRT PCR analyses and genotyping section subsequently pooled by genotype and collected and snap frozen in liquid nitrogen 5 and 8dpf. 15 larvae per genotype per sample were collected.", "Direct zol RNA microprep kit KTC UNIV RNA Seq NUQ AD A01 with NuQuant Custom deplete ADU033 D. rerio kit", "Animals were maintained according to standard protocols", "tissue:whole body|genotype:Mutant|age:8dpf|genotype:Mutant|replicate:1", "GSM8305916", "GSM8305916: Mutant 8dpf 1; Danio rerio; RNA Seq", "GSM8305916 r1", "GSM8305916", "1", "Direct zol RNA microprep kit KTC UNIV RNA Seq NUQ AD A01 with NuQuant Custom deplete ADU033 D. rerio kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP511787", null, null, "26_S26_R1_001.fastq.gz 26_S26_R2_001.fastq.gz", "fastq fastq", 1761064863.0, 6874590.0, "GSM8305916 r1", "0:127.98 1:128.19", "A:497556179;C:351357168;G:364495411;T:507457398;N:40198707", 127, 128, null, null, 497556179, 351357168, 364495411, 507457398, 40198707, "SRX24802699", "SRS21518807", "SRA1889334", "Greenwood Genetic Center", "Greenwood Genetic Center", 2, 0.61484, 0.60165, 0.21597, 0.22261, 0.7614, 0.77402, 0.57726, 0.59475, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2024-06-04", "Larval", "Larval", "Trunk", "Surface Structure"], [32493, "SRR29285566", "SRX24802698", "SRS21518806", "SRP511787", "PRJNA1120060", "O GlcNAcylation Modulates Expression and Abundance of N Glycosylation Machinery in an Inherited Glycosylation Disorder", "GSE269074", "Transcriptome Analysis", "Much of the N glycosylation machinery was identified decades ago but the regulatory mechanisms influencing normal and disease states are only beginning to be discovered. Recent studies highlight a role for key metabolites and metabolic enzymes in this process revising the view of the relationship between different metabolic pathways. Using a multi omic approach in a zebrafish we discovered a mechanism where O GlcNAcylation directly influences the expression and abundance of two enzymes essential for the earliest steps of N linked glycosylation the nus1 encoded NgBR and Dpagt1. Here we show that phosphomannomutase pmm2 deficiency is associated with increased levels of UDP GlcNAc and protein O GlcNAcylation. Biochemical studies show that O GlcNAc modification of the NgBR and Dpagt1 increases their abundance in pmm2m/m mutants. Modulating O GlcNAc levels NgBR abundance or Dpagt1 activity exacerbated cartilage phenotypes in pmm2 mutants suggesting that O GlcNAc mediated increases in the N glycosylation machinery protects against more severe pathology. These findings highlight nucleotide sugar donors as metabolic sensors that coordinate two different glycosylation pathways demonstrating how their interplay is relevant to disease outcome in the most common congenital disorder of glycosylation. Overall design: We did bulk total RNA seq with ribo depletion of whole zebrafish larvae at 2 ages 5dpf and 8dpf for two genotypes wildtype WT and Mutant where the mutant is a loss of function of Pmm2. Each sample consisted of 15 larvae and we sequenced 5 biological replicates per genotype and age combination.", null, "pubmed:39561044", null, "Mutant 5dpf 5", "GSM8305915", null, "source name:whole body|tissue:whole body|genotype:Mutant|age:5dpf|genotype:WT|replicate:5|geo loc name:missing|collection date:missing", "Mutant 5dpf 5", "FASTQ QC by fastp adapter trimming and assessment of ribo depletion by bbduk alignment by STAR BAM indexing by samtools counting of reads in each gene by subread Assembly: GRCz11 Supplementary files format and content: The counts table contains raw counts of reads aligning to genes generated by subread. It is a tab delimited text file", "whole body", "For the sample preparation 3dpf larvae were genotyped using the assay described see the qRT PCR analyses and genotyping section subsequently pooled by genotype and collected and snap frozen in liquid nitrogen 5 and 8dpf. 15 larvae per genotype per sample were collected.", "Direct zol RNA microprep kit KTC UNIV RNA Seq NUQ AD A01 with NuQuant Custom deplete ADU033 D. rerio kit", "Animals were maintained according to standard protocols", "tissue:whole body|genotype:Mutant|age:5dpf|genotype:WT|replicate:5", "GSM8305915", "GSM8305915: Mutant 5dpf 5; Danio rerio; RNA Seq", "GSM8305915 r1", "GSM8305915", "1", "Direct zol RNA microprep kit KTC UNIV RNA Seq NUQ AD A01 with NuQuant Custom deplete ADU033 D. rerio kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP511787", null, null, "20_S20_R1_001.fastq.gz 20_S20_R2_001.fastq.gz", "fastq fastq", 44861994269.0, 170464414.0, "GSM8305915 r1", "0:131.53 1:131.64", "A:12814834357;C:9164689606;G:9481668356;T:13176021007;N:224780943", 131, 131, null, null, 12814834357, 9164689606, 9481668356, 13176021007, 224780943, "SRX24802698", "SRS21518806", "SRA1889334", "Greenwood Genetic Center", "Greenwood Genetic Center", 2, 0.76449, 0.75903, 0.29761, 0.31015, 0.72088, 0.73399, 0.58295, 0.58975, 78, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2024-06-04", "Larval", "Larval", "Trunk", "Surface Structure"], [32494, "SRR29285567", "SRX24802697", "SRS21518805", "SRP511787", "PRJNA1120060", "O GlcNAcylation Modulates Expression and Abundance of N Glycosylation Machinery in an Inherited Glycosylation Disorder", "GSE269074", "Transcriptome Analysis", "Much of the N glycosylation machinery was identified decades ago but the regulatory mechanisms influencing normal and disease states are only beginning to be discovered. Recent studies highlight a role for key metabolites and metabolic enzymes in this process revising the view of the relationship between different metabolic pathways. Using a multi omic approach in a zebrafish we discovered a mechanism where O GlcNAcylation directly influences the expression and abundance of two enzymes essential for the earliest steps of N linked glycosylation the nus1 encoded NgBR and Dpagt1. Here we show that phosphomannomutase pmm2 deficiency is associated with increased levels of UDP GlcNAc and protein O GlcNAcylation. Biochemical studies show that O GlcNAc modification of the NgBR and Dpagt1 increases their abundance in pmm2m/m mutants. Modulating O GlcNAc levels NgBR abundance or Dpagt1 activity exacerbated cartilage phenotypes in pmm2 mutants suggesting that O GlcNAc mediated increases in the N glycosylation machinery protects against more severe pathology. These findings highlight nucleotide sugar donors as metabolic sensors that coordinate two different glycosylation pathways demonstrating how their interplay is relevant to disease outcome in the most common congenital disorder of glycosylation. Overall design: We did bulk total RNA seq with ribo depletion of whole zebrafish larvae at 2 ages 5dpf and 8dpf for two genotypes wildtype WT and Mutant where the mutant is a loss of function of Pmm2. Each sample consisted of 15 larvae and we sequenced 5 biological replicates per genotype and age combination.", null, "pubmed:39561044", null, "Mutant 5dpf 4", "GSM8305914", null, "source name:whole body|tissue:whole body|genotype:Mutant|age:5dpf|genotype:WT|replicate:4|geo loc name:missing|collection date:missing", "Mutant 5dpf 4", "FASTQ QC by fastp adapter trimming and assessment of ribo depletion by bbduk alignment by STAR BAM indexing by samtools counting of reads in each gene by subread Assembly: GRCz11 Supplementary files format and content: The counts table contains raw counts of reads aligning to genes generated by subread. It is a tab delimited text file", "whole body", "For the sample preparation 3dpf larvae were genotyped using the assay described see the qRT PCR analyses and genotyping section subsequently pooled by genotype and collected and snap frozen in liquid nitrogen 5 and 8dpf. 15 larvae per genotype per sample were collected.", "Direct zol RNA microprep kit KTC UNIV RNA Seq NUQ AD A01 with NuQuant Custom deplete ADU033 D. rerio kit", "Animals were maintained according to standard protocols", "tissue:whole body|genotype:Mutant|age:5dpf|genotype:WT|replicate:4", "GSM8305914", "GSM8305914: Mutant 5dpf 4; Danio rerio; RNA Seq", "GSM8305914 r1", "GSM8305914", "1", "Direct zol RNA microprep kit KTC UNIV RNA Seq NUQ AD A01 with NuQuant Custom deplete ADU033 D. rerio kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP511787", null, null, "19_S19_R1_001.fastq.gz 19_S19_R2_001.fastq.gz", "fastq fastq", 5607120194.0, 22270005.0, "GSM8305914 r1", "0:125.80 1:125.98", "A:1567782157;C:1175882461;G:1212477800;T:1586827542;N:64150234", 125, 125, null, null, 1567782157, 1175882461, 1212477800, 1586827542, 64150234, "SRX24802697", "SRS21518805", "SRA1889334", "Greenwood Genetic Center", "Greenwood Genetic Center", 2, 0.73788, 0.74164, 0.26347, 0.27285, 0.73914, 0.74688, 0.59711, 0.60862, 150, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2024-06-04", "Larval", "Larval", "Trunk", "Surface Structure"], [32495, "SRR29285568", "SRX24802696", "SRS21518804", "SRP511787", "PRJNA1120060", "O GlcNAcylation Modulates Expression and Abundance of N Glycosylation Machinery in an Inherited Glycosylation Disorder", "GSE269074", "Transcriptome Analysis", "Much of the N glycosylation machinery was identified decades ago but the regulatory mechanisms influencing normal and disease states are only beginning to be discovered. Recent studies highlight a role for key metabolites and metabolic enzymes in this process revising the view of the relationship between different metabolic pathways. Using a multi omic approach in a zebrafish we discovered a mechanism where O GlcNAcylation directly influences the expression and abundance of two enzymes essential for the earliest steps of N linked glycosylation the nus1 encoded NgBR and Dpagt1. Here we show that phosphomannomutase pmm2 deficiency is associated with increased levels of UDP GlcNAc and protein O GlcNAcylation. Biochemical studies show that O GlcNAc modification of the NgBR and Dpagt1 increases their abundance in pmm2m/m mutants. Modulating O GlcNAc levels NgBR abundance or Dpagt1 activity exacerbated cartilage phenotypes in pmm2 mutants suggesting that O GlcNAc mediated increases in the N glycosylation machinery protects against more severe pathology. These findings highlight nucleotide sugar donors as metabolic sensors that coordinate two different glycosylation pathways demonstrating how their interplay is relevant to disease outcome in the most common congenital disorder of glycosylation. Overall design: We did bulk total RNA seq with ribo depletion of whole zebrafish larvae at 2 ages 5dpf and 8dpf for two genotypes wildtype WT and Mutant where the mutant is a loss of function of Pmm2. Each sample consisted of 15 larvae and we sequenced 5 biological replicates per genotype and age combination.", null, "pubmed:39561044", null, "Mutant 5dpf 3", "GSM8305913", null, "source name:whole body|tissue:whole body|genotype:Mutant|age:5dpf|genotype:WT|replicate:3|geo loc name:missing|collection date:missing", "Mutant 5dpf 3", "FASTQ QC by fastp adapter trimming and assessment of ribo depletion by bbduk alignment by STAR BAM indexing by samtools counting of reads in each gene by subread Assembly: GRCz11 Supplementary files format and content: The counts table contains raw counts of reads aligning to genes generated by subread. It is a tab delimited text file", "whole body", "For the sample preparation 3dpf larvae were genotyped using the assay described see the qRT PCR analyses and genotyping section subsequently pooled by genotype and collected and snap frozen in liquid nitrogen 5 and 8dpf. 15 larvae per genotype per sample were collected.", "Direct zol RNA microprep kit KTC UNIV RNA Seq NUQ AD A01 with NuQuant Custom deplete ADU033 D. rerio kit", "Animals were maintained according to standard protocols", "tissue:whole body|genotype:Mutant|age:5dpf|genotype:WT|replicate:3", "GSM8305913", "GSM8305913: Mutant 5dpf 3; Danio rerio; RNA Seq", "GSM8305913 r1", "GSM8305913", "1", "Direct zol RNA microprep kit KTC UNIV RNA Seq NUQ AD A01 with NuQuant Custom deplete ADU033 D. rerio kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP511787", null, null, "18_S18_R1_001.fastq.gz 18_S18_R2_001.fastq.gz", "fastq fastq", 35413242014.0, 147228358.0, "GSM8305913 r1", null, null, null, null, null, null, null, null, null, null, null, "SRX24802696", "SRS21518804", "SRA1889334", "Greenwood Genetic Center", "Greenwood Genetic Center", 2, 0.62906, 0.62092, 0.3537, 0.37017, 0.75465, 0.76822, 0.54776, 0.569, 137, 137, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2024-06-04", "Larval", "Larval", "Trunk", "Surface Structure"], [32496, "SRR29285569", "SRX24802695", "SRS21518803", "SRP511787", "PRJNA1120060", "O GlcNAcylation Modulates Expression and Abundance of N Glycosylation Machinery in an Inherited Glycosylation Disorder", "GSE269074", "Transcriptome Analysis", "Much of the N glycosylation machinery was identified decades ago but the regulatory mechanisms influencing normal and disease states are only beginning to be discovered. Recent studies highlight a role for key metabolites and metabolic enzymes in this process revising the view of the relationship between different metabolic pathways. Using a multi omic approach in a zebrafish we discovered a mechanism where O GlcNAcylation directly influences the expression and abundance of two enzymes essential for the earliest steps of N linked glycosylation the nus1 encoded NgBR and Dpagt1. Here we show that phosphomannomutase pmm2 deficiency is associated with increased levels of UDP GlcNAc and protein O GlcNAcylation. Biochemical studies show that O GlcNAc modification of the NgBR and Dpagt1 increases their abundance in pmm2m/m mutants. Modulating O GlcNAc levels NgBR abundance or Dpagt1 activity exacerbated cartilage phenotypes in pmm2 mutants suggesting that O GlcNAc mediated increases in the N glycosylation machinery protects against more severe pathology. These findings highlight nucleotide sugar donors as metabolic sensors that coordinate two different glycosylation pathways demonstrating how their interplay is relevant to disease outcome in the most common congenital disorder of glycosylation. Overall design: We did bulk total RNA seq with ribo depletion of whole zebrafish larvae at 2 ages 5dpf and 8dpf for two genotypes wildtype WT and Mutant where the mutant is a loss of function of Pmm2. Each sample consisted of 15 larvae and we sequenced 5 biological replicates per genotype and age combination.", null, "pubmed:39561044", null, "Mutant 5dpf 2", "GSM8305912", null, "source name:whole body|tissue:whole body|genotype:Mutant|age:5dpf|genotype:WT|replicate:2|geo loc name:missing|collection date:missing", "Mutant 5dpf 2", "FASTQ QC by fastp adapter trimming and assessment of ribo depletion by bbduk alignment by STAR BAM indexing by samtools counting of reads in each gene by subread Assembly: GRCz11 Supplementary files format and content: The counts table contains raw counts of reads aligning to genes generated by subread. It is a tab delimited text file", "whole body", "For the sample preparation 3dpf larvae were genotyped using the assay described see the qRT PCR analyses and genotyping section subsequently pooled by genotype and collected and snap frozen in liquid nitrogen 5 and 8dpf. 15 larvae per genotype per sample were collected.", "Direct zol RNA microprep kit KTC UNIV RNA Seq NUQ AD A01 with NuQuant Custom deplete ADU033 D. rerio kit", "Animals were maintained according to standard protocols", "tissue:whole body|genotype:Mutant|age:5dpf|genotype:WT|replicate:2", "GSM8305912", "GSM8305912: Mutant 5dpf 2; Danio rerio; RNA Seq", "GSM8305912 r1", "GSM8305912", "1", "Direct zol RNA microprep kit KTC UNIV RNA Seq NUQ AD A01 with NuQuant Custom deplete ADU033 D. rerio kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP511787", null, null, "17_S17_R1_001.fastq.gz 17_S17_R2_001.fastq.gz", "fastq fastq", 35865106141.0, 138431350.0, "GSM8305912 r1", "0:129.49 1:129.59", "A:10011943989;C:7650430976;G:7850227100;T:10118820207;N:233683869", 129, 129, null, null, 10011943989, 7650430976, 7850227100, 10118820207, 233683869, "SRX24802695", "SRS21518803", "SRA1889334", "Greenwood Genetic Center", "Greenwood Genetic Center", 2, 0.59494, 0.59416, 0.20522, 0.21104, 0.77297, 0.781, 0.63558, 0.6401, 150, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2024-06-04", "Larval", "Larval", "Trunk", "Surface Structure"], [32497, "SRR29285570", "SRX24802694", "SRS21518802", "SRP511787", "PRJNA1120060", "O GlcNAcylation Modulates Expression and Abundance of N Glycosylation Machinery in an Inherited Glycosylation Disorder", "GSE269074", "Transcriptome Analysis", "Much of the N glycosylation machinery was identified decades ago but the regulatory mechanisms influencing normal and disease states are only beginning to be discovered. Recent studies highlight a role for key metabolites and metabolic enzymes in this process revising the view of the relationship between different metabolic pathways. Using a multi omic approach in a zebrafish we discovered a mechanism where O GlcNAcylation directly influences the expression and abundance of two enzymes essential for the earliest steps of N linked glycosylation the nus1 encoded NgBR and Dpagt1. Here we show that phosphomannomutase pmm2 deficiency is associated with increased levels of UDP GlcNAc and protein O GlcNAcylation. Biochemical studies show that O GlcNAc modification of the NgBR and Dpagt1 increases their abundance in pmm2m/m mutants. Modulating O GlcNAc levels NgBR abundance or Dpagt1 activity exacerbated cartilage phenotypes in pmm2 mutants suggesting that O GlcNAc mediated increases in the N glycosylation machinery protects against more severe pathology. These findings highlight nucleotide sugar donors as metabolic sensors that coordinate two different glycosylation pathways demonstrating how their interplay is relevant to disease outcome in the most common congenital disorder of glycosylation. Overall design: We did bulk total RNA seq with ribo depletion of whole zebrafish larvae at 2 ages 5dpf and 8dpf for two genotypes wildtype WT and Mutant where the mutant is a loss of function of Pmm2. Each sample consisted of 15 larvae and we sequenced 5 biological replicates per genotype and age combination.", null, "pubmed:39561044", null, "Mutant 5dpf 1", "GSM8305911", null, "source name:whole body|tissue:whole body|genotype:Mutant|age:5dpf|genotype:WT|replicate:1|geo loc name:missing|collection date:missing", "Mutant 5dpf 1", "FASTQ QC by fastp adapter trimming and assessment of ribo depletion by bbduk alignment by STAR BAM indexing by samtools counting of reads in each gene by subread Assembly: GRCz11 Supplementary files format and content: The counts table contains raw counts of reads aligning to genes generated by subread. It is a tab delimited text file", "whole body", "For the sample preparation 3dpf larvae were genotyped using the assay described see the qRT PCR analyses and genotyping section subsequently pooled by genotype and collected and snap frozen in liquid nitrogen 5 and 8dpf. 15 larvae per genotype per sample were collected.", "Direct zol RNA microprep kit KTC UNIV RNA Seq NUQ AD A01 with NuQuant Custom deplete ADU033 D. rerio kit", "Animals were maintained according to standard protocols", "tissue:whole body|genotype:Mutant|age:5dpf|genotype:WT|replicate:1", "GSM8305911", "GSM8305911: Mutant 5dpf 1; Danio rerio; RNA Seq", "GSM8305911 r1", "GSM8305911", "1", "Direct zol RNA microprep kit KTC UNIV RNA Seq NUQ AD A01 with NuQuant Custom deplete ADU033 D. rerio kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP511787", null, null, "16_S16_R1_001.fastq.gz 16_S16_R2_001.fastq.gz", "fastq fastq", 11424421439.0, 43844065.0, "GSM8305911 r1", "0:130.34 1:130.23", "A:3153455776;C:2478215013;G:2568391366;T:3186999856;N:37359428", 130, 130, null, null, 3153455776, 2478215013, 2568391366, 3186999856, 37359428, "SRX24802694", "SRS21518802", "SRA1889334", "Greenwood Genetic Center", "Greenwood Genetic Center", 2, 0.80218, 0.80263, 0.28757, 0.2949, 0.73442, 0.74474, 0.61946, 0.63013, 150, 149, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2024-06-04", "Larval", "Larval", "Trunk", "Surface Structure"], [32498, "SRR29285571", "SRX24802693", "SRS21518801", "SRP511787", "PRJNA1120060", "O GlcNAcylation Modulates Expression and Abundance of N Glycosylation Machinery in an Inherited Glycosylation Disorder", "GSE269074", "Transcriptome Analysis", "Much of the N glycosylation machinery was identified decades ago but the regulatory mechanisms influencing normal and disease states are only beginning to be discovered. Recent studies highlight a role for key metabolites and metabolic enzymes in this process revising the view of the relationship between different metabolic pathways. Using a multi omic approach in a zebrafish we discovered a mechanism where O GlcNAcylation directly influences the expression and abundance of two enzymes essential for the earliest steps of N linked glycosylation the nus1 encoded NgBR and Dpagt1. Here we show that phosphomannomutase pmm2 deficiency is associated with increased levels of UDP GlcNAc and protein O GlcNAcylation. Biochemical studies show that O GlcNAc modification of the NgBR and Dpagt1 increases their abundance in pmm2m/m mutants. Modulating O GlcNAc levels NgBR abundance or Dpagt1 activity exacerbated cartilage phenotypes in pmm2 mutants suggesting that O GlcNAc mediated increases in the N glycosylation machinery protects against more severe pathology. These findings highlight nucleotide sugar donors as metabolic sensors that coordinate two different glycosylation pathways demonstrating how their interplay is relevant to disease outcome in the most common congenital disorder of glycosylation. Overall design: We did bulk total RNA seq with ribo depletion of whole zebrafish larvae at 2 ages 5dpf and 8dpf for two genotypes wildtype WT and Mutant where the mutant is a loss of function of Pmm2. Each sample consisted of 15 larvae and we sequenced 5 biological replicates per genotype and age combination.", null, "pubmed:39561044", null, "WT 8dpf 5", "GSM8305910", null, "source name:whole body|tissue:whole body|genotype:WT|age:8dpf|genotype:Mutant|replicate:5|geo loc name:missing|collection date:missing", "WT 8dpf 5", "FASTQ QC by fastp adapter trimming and assessment of ribo depletion by bbduk alignment by STAR BAM indexing by samtools counting of reads in each gene by subread Assembly: GRCz11 Supplementary files format and content: The counts table contains raw counts of reads aligning to genes generated by subread. It is a tab delimited text file", "whole body", "For the sample preparation 3dpf larvae were genotyped using the assay described see the qRT PCR analyses and genotyping section subsequently pooled by genotype and collected and snap frozen in liquid nitrogen 5 and 8dpf. 15 larvae per genotype per sample were collected.", "Direct zol RNA microprep kit KTC UNIV RNA Seq NUQ AD A01 with NuQuant Custom deplete ADU033 D. rerio kit", "Animals were maintained according to standard protocols", "tissue:whole body|genotype:WT|age:8dpf|genotype:Mutant|replicate:5", "GSM8305910", "GSM8305910: WT 8dpf 5; Danio rerio; RNA Seq", "GSM8305910 r1", "GSM8305910", "1", "Direct zol RNA microprep kit KTC UNIV RNA Seq NUQ AD A01 with NuQuant Custom deplete ADU033 D. rerio kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP511787", null, null, "15_S15_R1_001.fastq.gz 15_S15_R2_001.fastq.gz", "fastq fastq", 7264574863.0, 26944269.0, "GSM8305910 r1", "0:134.76 1:134.85", "A:2143925256;C:1439783329;G:1477108393;T:2165189668;N:38568217", 134, 134, null, null, 2143925256, 1439783329, 1477108393, 2165189668, 38568217, "SRX24802693", "SRS21518801", "SRA1889334", "Greenwood Genetic Center", "Greenwood Genetic Center", 2, 0.37678, 0.37076, 0.18096, 0.18839, 0.80211, 0.81373, 0.56741, 0.58443, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2024-06-04", "Larval", "Larval", "Trunk", "Surface Structure"], [32499, "SRR29285572", "SRX24802692", "SRS21518800", "SRP511787", "PRJNA1120060", "O GlcNAcylation Modulates Expression and Abundance of N Glycosylation Machinery in an Inherited Glycosylation Disorder", "GSE269074", "Transcriptome Analysis", "Much of the N glycosylation machinery was identified decades ago but the regulatory mechanisms influencing normal and disease states are only beginning to be discovered. Recent studies highlight a role for key metabolites and metabolic enzymes in this process revising the view of the relationship between different metabolic pathways. Using a multi omic approach in a zebrafish we discovered a mechanism where O GlcNAcylation directly influences the expression and abundance of two enzymes essential for the earliest steps of N linked glycosylation the nus1 encoded NgBR and Dpagt1. Here we show that phosphomannomutase pmm2 deficiency is associated with increased levels of UDP GlcNAc and protein O GlcNAcylation. Biochemical studies show that O GlcNAc modification of the NgBR and Dpagt1 increases their abundance in pmm2m/m mutants. Modulating O GlcNAc levels NgBR abundance or Dpagt1 activity exacerbated cartilage phenotypes in pmm2 mutants suggesting that O GlcNAc mediated increases in the N glycosylation machinery protects against more severe pathology. These findings highlight nucleotide sugar donors as metabolic sensors that coordinate two different glycosylation pathways demonstrating how their interplay is relevant to disease outcome in the most common congenital disorder of glycosylation. Overall design: We did bulk total RNA seq with ribo depletion of whole zebrafish larvae at 2 ages 5dpf and 8dpf for two genotypes wildtype WT and Mutant where the mutant is a loss of function of Pmm2. Each sample consisted of 15 larvae and we sequenced 5 biological replicates per genotype and age combination.", null, "pubmed:39561044", null, "WT 8dpf 4", "GSM8305909", null, "source name:whole body|tissue:whole body|genotype:WT|age:8dpf|genotype:Mutant|replicate:4|geo loc name:missing|collection date:missing", "WT 8dpf 4", "FASTQ QC by fastp adapter trimming and assessment of ribo depletion by bbduk alignment by STAR BAM indexing by samtools counting of reads in each gene by subread Assembly: GRCz11 Supplementary files format and content: The counts table contains raw counts of reads aligning to genes generated by subread. It is a tab delimited text file", "whole body", "For the sample preparation 3dpf larvae were genotyped using the assay described see the qRT PCR analyses and genotyping section subsequently pooled by genotype and collected and snap frozen in liquid nitrogen 5 and 8dpf. 15 larvae per genotype per sample were collected.", "Direct zol RNA microprep kit KTC UNIV RNA Seq NUQ AD A01 with NuQuant Custom deplete ADU033 D. rerio kit", "Animals were maintained according to standard protocols", "tissue:whole body|genotype:WT|age:8dpf|genotype:Mutant|replicate:4", "GSM8305909", "GSM8305909: WT 8dpf 4; Danio rerio; RNA Seq", "GSM8305909 r1", "GSM8305909", "1", "Direct zol RNA microprep kit KTC UNIV RNA Seq NUQ AD A01 with NuQuant Custom deplete ADU033 D. rerio kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP511787", null, null, "14_S14_R1_001.fastq.gz 14_S14_R2_001.fastq.gz", "fastq fastq", 32778065815.0, 131056842.0, "GSM8305909 r1", null, null, null, null, null, null, null, null, null, null, null, "SRX24802692", "SRS21518800", "SRA1889334", "Greenwood Genetic Center", "Greenwood Genetic Center", 2, 0.78701, 0.78678, 0.27772, 0.2804, 0.74507, 0.75122, 0.62456, 0.6297, 151, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2024-06-04", "Larval", "Larval", "Trunk", "Surface Structure"], [32500, "SRR29285573", "SRX24802691", "SRS21518799", "SRP511787", "PRJNA1120060", "O GlcNAcylation Modulates Expression and Abundance of N Glycosylation Machinery in an Inherited Glycosylation Disorder", "GSE269074", "Transcriptome Analysis", "Much of the N glycosylation machinery was identified decades ago but the regulatory mechanisms influencing normal and disease states are only beginning to be discovered. Recent studies highlight a role for key metabolites and metabolic enzymes in this process revising the view of the relationship between different metabolic pathways. Using a multi omic approach in a zebrafish we discovered a mechanism where O GlcNAcylation directly influences the expression and abundance of two enzymes essential for the earliest steps of N linked glycosylation the nus1 encoded NgBR and Dpagt1. Here we show that phosphomannomutase pmm2 deficiency is associated with increased levels of UDP GlcNAc and protein O GlcNAcylation. Biochemical studies show that O GlcNAc modification of the NgBR and Dpagt1 increases their abundance in pmm2m/m mutants. Modulating O GlcNAc levels NgBR abundance or Dpagt1 activity exacerbated cartilage phenotypes in pmm2 mutants suggesting that O GlcNAc mediated increases in the N glycosylation machinery protects against more severe pathology. These findings highlight nucleotide sugar donors as metabolic sensors that coordinate two different glycosylation pathways demonstrating how their interplay is relevant to disease outcome in the most common congenital disorder of glycosylation. Overall design: We did bulk total RNA seq with ribo depletion of whole zebrafish larvae at 2 ages 5dpf and 8dpf for two genotypes wildtype WT and Mutant where the mutant is a loss of function of Pmm2. Each sample consisted of 15 larvae and we sequenced 5 biological replicates per genotype and age combination.", null, "pubmed:39561044", null, "WT 8dpf 3", "GSM8305908", null, "source name:whole body|tissue:whole body|genotype:WT|age:8dpf|genotype:Mutant|replicate:3|geo loc name:missing|collection date:missing", "WT 8dpf 3", "FASTQ QC by fastp adapter trimming and assessment of ribo depletion by bbduk alignment by STAR BAM indexing by samtools counting of reads in each gene by subread Assembly: GRCz11 Supplementary files format and content: The counts table contains raw counts of reads aligning to genes generated by subread. It is a tab delimited text file", "whole body", "For the sample preparation 3dpf larvae were genotyped using the assay described see the qRT PCR analyses and genotyping section subsequently pooled by genotype and collected and snap frozen in liquid nitrogen 5 and 8dpf. 15 larvae per genotype per sample were collected.", "Direct zol RNA microprep kit KTC UNIV RNA Seq NUQ AD A01 with NuQuant Custom deplete ADU033 D. rerio kit", "Animals were maintained according to standard protocols", "tissue:whole body|genotype:WT|age:8dpf|genotype:Mutant|replicate:3", "GSM8305908", "GSM8305908: WT 8dpf 3; Danio rerio; RNA Seq", "GSM8305908 r1", "GSM8305908", "1", "Direct zol RNA microprep kit KTC UNIV RNA Seq NUQ AD A01 with NuQuant Custom deplete ADU033 D. rerio kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP511787", null, null, "13_S13_R1_001.fastq.gz 13_S13_R2_001.fastq.gz", "fastq fastq", 2715775308.0, 12018782.0, "GSM8305908 r1", "0:112.87 1:113.09", "A:793819995;C:525097564;G:555570458;T:797117723;N:44169568", 112, 113, null, null, 793819995, 525097564, 555570458, 797117723, 44169568, "SRX24802691", "SRS21518799", "SRA1889334", "Greenwood Genetic Center", "Greenwood Genetic Center", 2, 0.6927, 0.68987, 0.40365, 0.41469, 0.74276, 0.75175, 0.57052, 0.56713, 108, 108, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2024-06-04", "Larval", "Larval", "Trunk", "Surface Structure"], [32501, "SRR29285574", "SRX24802690", "SRS21518798", "SRP511787", "PRJNA1120060", "O GlcNAcylation Modulates Expression and Abundance of N Glycosylation Machinery in an Inherited Glycosylation Disorder", "GSE269074", "Transcriptome Analysis", "Much of the N glycosylation machinery was identified decades ago but the regulatory mechanisms influencing normal and disease states are only beginning to be discovered. Recent studies highlight a role for key metabolites and metabolic enzymes in this process revising the view of the relationship between different metabolic pathways. Using a multi omic approach in a zebrafish we discovered a mechanism where O GlcNAcylation directly influences the expression and abundance of two enzymes essential for the earliest steps of N linked glycosylation the nus1 encoded NgBR and Dpagt1. Here we show that phosphomannomutase pmm2 deficiency is associated with increased levels of UDP GlcNAc and protein O GlcNAcylation. Biochemical studies show that O GlcNAc modification of the NgBR and Dpagt1 increases their abundance in pmm2m/m mutants. Modulating O GlcNAc levels NgBR abundance or Dpagt1 activity exacerbated cartilage phenotypes in pmm2 mutants suggesting that O GlcNAc mediated increases in the N glycosylation machinery protects against more severe pathology. These findings highlight nucleotide sugar donors as metabolic sensors that coordinate two different glycosylation pathways demonstrating how their interplay is relevant to disease outcome in the most common congenital disorder of glycosylation. Overall design: We did bulk total RNA seq with ribo depletion of whole zebrafish larvae at 2 ages 5dpf and 8dpf for two genotypes wildtype WT and Mutant where the mutant is a loss of function of Pmm2. Each sample consisted of 15 larvae and we sequenced 5 biological replicates per genotype and age combination.", null, "pubmed:39561044", null, "WT 8dpf 2", "GSM8305907", null, "source name:whole body|tissue:whole body|genotype:WT|age:8dpf|genotype:Mutant|replicate:2|geo loc name:missing|collection date:missing", "WT 8dpf 2", "FASTQ QC by fastp adapter trimming and assessment of ribo depletion by bbduk alignment by STAR BAM indexing by samtools counting of reads in each gene by subread Assembly: GRCz11 Supplementary files format and content: The counts table contains raw counts of reads aligning to genes generated by subread. It is a tab delimited text file", "whole body", "For the sample preparation 3dpf larvae were genotyped using the assay described see the qRT PCR analyses and genotyping section subsequently pooled by genotype and collected and snap frozen in liquid nitrogen 5 and 8dpf. 15 larvae per genotype per sample were collected.", "Direct zol RNA microprep kit KTC UNIV RNA Seq NUQ AD A01 with NuQuant Custom deplete ADU033 D. rerio kit", "Animals were maintained according to standard protocols", "tissue:whole body|genotype:WT|age:8dpf|genotype:Mutant|replicate:2", "GSM8305907", "GSM8305907: WT 8dpf 2; Danio rerio; RNA Seq", "GSM8305907 r1", "GSM8305907", "1", "Direct zol RNA microprep kit KTC UNIV RNA Seq NUQ AD A01 with NuQuant Custom deplete ADU033 D. rerio kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP511787", null, null, "12_S12_R1_001.fastq.gz 12_S12_R2_001.fastq.gz", "fastq fastq", 13984059501.0, 53799424.0, "GSM8305907 r1", "0:129.96 1:129.97", "A:3756098800;C:3181863043;G:3231146344;T:3789534545;N:25416769", 129, 129, null, null, 3756098800, 3181863043, 3231146344, 3789534545, 25416769, "SRX24802690", "SRS21518798", "SRA1889334", "Greenwood Genetic Center", "Greenwood Genetic Center", 2, 0.86656, 0.86486, 0.30024, 0.30172, 0.72537, 0.72914, 0.61466, 0.62287, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2024-06-04", "Larval", "Larval", "Trunk", "Surface Structure"], [32502, "SRR29285575", "SRX24802689", "SRS21518797", "SRP511787", "PRJNA1120060", "O GlcNAcylation Modulates Expression and Abundance of N Glycosylation Machinery in an Inherited Glycosylation Disorder", "GSE269074", "Transcriptome Analysis", "Much of the N glycosylation machinery was identified decades ago but the regulatory mechanisms influencing normal and disease states are only beginning to be discovered. Recent studies highlight a role for key metabolites and metabolic enzymes in this process revising the view of the relationship between different metabolic pathways. Using a multi omic approach in a zebrafish we discovered a mechanism where O GlcNAcylation directly influences the expression and abundance of two enzymes essential for the earliest steps of N linked glycosylation the nus1 encoded NgBR and Dpagt1. Here we show that phosphomannomutase pmm2 deficiency is associated with increased levels of UDP GlcNAc and protein O GlcNAcylation. Biochemical studies show that O GlcNAc modification of the NgBR and Dpagt1 increases their abundance in pmm2m/m mutants. Modulating O GlcNAc levels NgBR abundance or Dpagt1 activity exacerbated cartilage phenotypes in pmm2 mutants suggesting that O GlcNAc mediated increases in the N glycosylation machinery protects against more severe pathology. These findings highlight nucleotide sugar donors as metabolic sensors that coordinate two different glycosylation pathways demonstrating how their interplay is relevant to disease outcome in the most common congenital disorder of glycosylation. Overall design: We did bulk total RNA seq with ribo depletion of whole zebrafish larvae at 2 ages 5dpf and 8dpf for two genotypes wildtype WT and Mutant where the mutant is a loss of function of Pmm2. Each sample consisted of 15 larvae and we sequenced 5 biological replicates per genotype and age combination.", null, "pubmed:39561044", null, "WT 8dpf 1", "GSM8305906", null, "source name:whole body|tissue:whole body|genotype:WT|age:8dpf|genotype:Mutant|replicate:1|geo loc name:missing|collection date:missing", "WT 8dpf 1", "FASTQ QC by fastp adapter trimming and assessment of ribo depletion by bbduk alignment by STAR BAM indexing by samtools counting of reads in each gene by subread Assembly: GRCz11 Supplementary files format and content: The counts table contains raw counts of reads aligning to genes generated by subread. It is a tab delimited text file", "whole body", "For the sample preparation 3dpf larvae were genotyped using the assay described see the qRT PCR analyses and genotyping section subsequently pooled by genotype and collected and snap frozen in liquid nitrogen 5 and 8dpf. 15 larvae per genotype per sample were collected.", "Direct zol RNA microprep kit KTC UNIV RNA Seq NUQ AD A01 with NuQuant Custom deplete ADU033 D. rerio kit", "Animals were maintained according to standard protocols", "tissue:whole body|genotype:WT|age:8dpf|genotype:Mutant|replicate:1", "GSM8305906", "GSM8305906: WT 8dpf 1; Danio rerio; RNA Seq", "GSM8305906 r1", "GSM8305906", "1", "Direct zol RNA microprep kit KTC UNIV RNA Seq NUQ AD A01 with NuQuant Custom deplete ADU033 D. rerio kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP511787", null, null, "11_S11_R1_001.fastq.gz 11_S11_R2_001.fastq.gz", "fastq fastq", 5388226113.0, 22114932.0, "GSM8305906 r1", "0:121.71 1:121.94", "A:1571088373;C:1056285467;G:1094594072;T:1584231174;N:82027027", 121, 121, null, null, 1571088373, 1056285467, 1094594072, 1584231174, 82027027, "SRX24802689", "SRS21518797", "SRA1889334", "Greenwood Genetic Center", "Greenwood Genetic Center", 2, 0.60126, 0.60282, 0.28098, 0.29016, 0.76337, 0.7713, 0.59511, 0.60885, 90, 90, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2024-06-04", "Larval", "Larval", "Trunk", "Surface Structure"], [32503, "SRR29285576", "SRX24802688", "SRS21518796", "SRP511787", "PRJNA1120060", "O GlcNAcylation Modulates Expression and Abundance of N Glycosylation Machinery in an Inherited Glycosylation Disorder", "GSE269074", "Transcriptome Analysis", "Much of the N glycosylation machinery was identified decades ago but the regulatory mechanisms influencing normal and disease states are only beginning to be discovered. Recent studies highlight a role for key metabolites and metabolic enzymes in this process revising the view of the relationship between different metabolic pathways. Using a multi omic approach in a zebrafish we discovered a mechanism where O GlcNAcylation directly influences the expression and abundance of two enzymes essential for the earliest steps of N linked glycosylation the nus1 encoded NgBR and Dpagt1. Here we show that phosphomannomutase pmm2 deficiency is associated with increased levels of UDP GlcNAc and protein O GlcNAcylation. Biochemical studies show that O GlcNAc modification of the NgBR and Dpagt1 increases their abundance in pmm2m/m mutants. Modulating O GlcNAc levels NgBR abundance or Dpagt1 activity exacerbated cartilage phenotypes in pmm2 mutants suggesting that O GlcNAc mediated increases in the N glycosylation machinery protects against more severe pathology. These findings highlight nucleotide sugar donors as metabolic sensors that coordinate two different glycosylation pathways demonstrating how their interplay is relevant to disease outcome in the most common congenital disorder of glycosylation. Overall design: We did bulk total RNA seq with ribo depletion of whole zebrafish larvae at 2 ages 5dpf and 8dpf for two genotypes wildtype WT and Mutant where the mutant is a loss of function of Pmm2. Each sample consisted of 15 larvae and we sequenced 5 biological replicates per genotype and age combination.", null, "pubmed:39561044", null, "WT 5dpf 5", "GSM8305905", null, "source name:whole body|tissue:whole body|genotype:WT|age:5dpf|genotype:WT|replicate:5|geo loc name:missing|collection date:missing", "WT 5dpf 5", "FASTQ QC by fastp adapter trimming and assessment of ribo depletion by bbduk alignment by STAR BAM indexing by samtools counting of reads in each gene by subread Assembly: GRCz11 Supplementary files format and content: The counts table contains raw counts of reads aligning to genes generated by subread. It is a tab delimited text file", "whole body", "For the sample preparation 3dpf larvae were genotyped using the assay described see the qRT PCR analyses and genotyping section subsequently pooled by genotype and collected and snap frozen in liquid nitrogen 5 and 8dpf. 15 larvae per genotype per sample were collected.", "Direct zol RNA microprep kit KTC UNIV RNA Seq NUQ AD A01 with NuQuant Custom deplete ADU033 D. rerio kit", "Animals were maintained according to standard protocols", "tissue:whole body|genotype:WT|age:5dpf|genotype:WT|replicate:5", "GSM8305905", "GSM8305905: WT 5dpf 5; Danio rerio; RNA Seq", "GSM8305905 r1", "GSM8305905", "1", "Direct zol RNA microprep kit KTC UNIV RNA Seq NUQ AD A01 with NuQuant Custom deplete ADU033 D. rerio kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP511787", null, null, "5_S5_R1_001.fastq.gz 5_S5_R2_001.fastq.gz", "fastq fastq", 36864973430.0, 147827522.0, "GSM8305905 r1", "0:124.60 1:124.78", "A:10882747927;C:7449801226;G:7566579083;T:10815945515;N:149899679", 124, 124, null, null, 10882747927, 7449801226, 7566579083, 10815945515, 149899679, "SRX24802688", "SRS21518796", "SRA1889334", "Greenwood Genetic Center", "Greenwood Genetic Center", 2, 0.47374, 0.48165, 0.40857, 0.41507, 0.81677, 0.81471, 0.49158, 0.49375, 150, 91, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2024-06-04", "Larval", "Larval", "Trunk", "Surface Structure"], [32504, "SRR29285577", "SRX24802687", "SRS21518795", "SRP511787", "PRJNA1120060", "O GlcNAcylation Modulates Expression and Abundance of N Glycosylation Machinery in an Inherited Glycosylation Disorder", "GSE269074", "Transcriptome Analysis", "Much of the N glycosylation machinery was identified decades ago but the regulatory mechanisms influencing normal and disease states are only beginning to be discovered. Recent studies highlight a role for key metabolites and metabolic enzymes in this process revising the view of the relationship between different metabolic pathways. Using a multi omic approach in a zebrafish we discovered a mechanism where O GlcNAcylation directly influences the expression and abundance of two enzymes essential for the earliest steps of N linked glycosylation the nus1 encoded NgBR and Dpagt1. Here we show that phosphomannomutase pmm2 deficiency is associated with increased levels of UDP GlcNAc and protein O GlcNAcylation. Biochemical studies show that O GlcNAc modification of the NgBR and Dpagt1 increases their abundance in pmm2m/m mutants. Modulating O GlcNAc levels NgBR abundance or Dpagt1 activity exacerbated cartilage phenotypes in pmm2 mutants suggesting that O GlcNAc mediated increases in the N glycosylation machinery protects against more severe pathology. These findings highlight nucleotide sugar donors as metabolic sensors that coordinate two different glycosylation pathways demonstrating how their interplay is relevant to disease outcome in the most common congenital disorder of glycosylation. Overall design: We did bulk total RNA seq with ribo depletion of whole zebrafish larvae at 2 ages 5dpf and 8dpf for two genotypes wildtype WT and Mutant where the mutant is a loss of function of Pmm2. Each sample consisted of 15 larvae and we sequenced 5 biological replicates per genotype and age combination.", null, "pubmed:39561044", null, "WT 5dpf 4", "GSM8305904", null, "source name:whole body|tissue:whole body|genotype:WT|age:5dpf|genotype:WT|replicate:4|geo loc name:missing|collection date:missing", "WT 5dpf 4", "FASTQ QC by fastp adapter trimming and assessment of ribo depletion by bbduk alignment by STAR BAM indexing by samtools counting of reads in each gene by subread Assembly: GRCz11 Supplementary files format and content: The counts table contains raw counts of reads aligning to genes generated by subread. It is a tab delimited text file", "whole body", "For the sample preparation 3dpf larvae were genotyped using the assay described see the qRT PCR analyses and genotyping section subsequently pooled by genotype and collected and snap frozen in liquid nitrogen 5 and 8dpf. 15 larvae per genotype per sample were collected.", "Direct zol RNA microprep kit KTC UNIV RNA Seq NUQ AD A01 with NuQuant Custom deplete ADU033 D. rerio kit", "Animals were maintained according to standard protocols", "tissue:whole body|genotype:WT|age:5dpf|genotype:WT|replicate:4", "GSM8305904", "GSM8305904: WT 5dpf 4; Danio rerio; RNA Seq", "GSM8305904 r1", "GSM8305904", "1", "Direct zol RNA microprep kit KTC UNIV RNA Seq NUQ AD A01 with NuQuant Custom deplete ADU033 D. rerio kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP511787", null, null, "4_S4_R1_001.fastq.gz 4_S4_R2_001.fastq.gz", "fastq fastq", 20865362996.0, 85474604.0, "GSM8305904 r1", "0:121.96 1:122.16", "A:6011091272;C:4396318913;G:4448338805;T:5974192691;N:35421315", 121, 122, null, null, 6011091272, 4396318913, 4448338805, 5974192691, 35421315, "SRX24802687", "SRS21518795", "SRA1889334", "Greenwood Genetic Center", "Greenwood Genetic Center", 2, 0.687, 0.69172, 0.58591, 0.59047, 0.76589, 0.76607, 0.51259, 0.52162, 84, 84, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2024-06-04", "Larval", "Larval", "Trunk", "Surface Structure"], [32505, "SRR29285578", "SRX24802686", "SRS21518794", "SRP511787", "PRJNA1120060", "O GlcNAcylation Modulates Expression and Abundance of N Glycosylation Machinery in an Inherited Glycosylation Disorder", "GSE269074", "Transcriptome Analysis", "Much of the N glycosylation machinery was identified decades ago but the regulatory mechanisms influencing normal and disease states are only beginning to be discovered. Recent studies highlight a role for key metabolites and metabolic enzymes in this process revising the view of the relationship between different metabolic pathways. Using a multi omic approach in a zebrafish we discovered a mechanism where O GlcNAcylation directly influences the expression and abundance of two enzymes essential for the earliest steps of N linked glycosylation the nus1 encoded NgBR and Dpagt1. Here we show that phosphomannomutase pmm2 deficiency is associated with increased levels of UDP GlcNAc and protein O GlcNAcylation. Biochemical studies show that O GlcNAc modification of the NgBR and Dpagt1 increases their abundance in pmm2m/m mutants. Modulating O GlcNAc levels NgBR abundance or Dpagt1 activity exacerbated cartilage phenotypes in pmm2 mutants suggesting that O GlcNAc mediated increases in the N glycosylation machinery protects against more severe pathology. These findings highlight nucleotide sugar donors as metabolic sensors that coordinate two different glycosylation pathways demonstrating how their interplay is relevant to disease outcome in the most common congenital disorder of glycosylation. Overall design: We did bulk total RNA seq with ribo depletion of whole zebrafish larvae at 2 ages 5dpf and 8dpf for two genotypes wildtype WT and Mutant where the mutant is a loss of function of Pmm2. Each sample consisted of 15 larvae and we sequenced 5 biological replicates per genotype and age combination.", null, "pubmed:39561044", null, "WT 5dpf 3", "GSM8305903", null, "source name:whole body|tissue:whole body|genotype:WT|age:5dpf|genotype:WT|replicate:3|geo loc name:missing|collection date:missing", "WT 5dpf 3", "FASTQ QC by fastp adapter trimming and assessment of ribo depletion by bbduk alignment by STAR BAM indexing by samtools counting of reads in each gene by subread Assembly: GRCz11 Supplementary files format and content: The counts table contains raw counts of reads aligning to genes generated by subread. It is a tab delimited text file", "whole body", "For the sample preparation 3dpf larvae were genotyped using the assay described see the qRT PCR analyses and genotyping section subsequently pooled by genotype and collected and snap frozen in liquid nitrogen 5 and 8dpf. 15 larvae per genotype per sample were collected.", "Direct zol RNA microprep kit KTC UNIV RNA Seq NUQ AD A01 with NuQuant Custom deplete ADU033 D. rerio kit", "Animals were maintained according to standard protocols", "tissue:whole body|genotype:WT|age:5dpf|genotype:WT|replicate:3", "GSM8305903", "GSM8305903: WT 5dpf 3; Danio rerio; RNA Seq", "GSM8305903 r1", "GSM8305903", "1", "Direct zol RNA microprep kit KTC UNIV RNA Seq NUQ AD A01 with NuQuant Custom deplete ADU033 D. rerio kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP511787", null, null, "3_S3_R1_001.fastq.gz 3_S3_R2_001.fastq.gz", "fastq fastq", 44771347433.0, 163809987.0, "GSM8305903 r1", "0:136.62 1:136.70", "A:13512158868;C:8775800809;G:8933321442;T:13479562694;N:70503620", 136, 136, null, null, 13512158868, 8775800809, 8933321442, 13479562694, 70503620, "SRX24802686", "SRS21518794", "SRA1889334", "Greenwood Genetic Center", "Greenwood Genetic Center", 2, 0.74877, 0.75623, 0.64593, 0.65183, 0.73434, 0.73537, 0.49765, 0.49588, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2024-06-04", "Larval", "Larval", "Trunk", "Surface Structure"], [32506, "SRR29285579", "SRX24802685", "SRS21518793", "SRP511787", "PRJNA1120060", "O GlcNAcylation Modulates Expression and Abundance of N Glycosylation Machinery in an Inherited Glycosylation Disorder", "GSE269074", "Transcriptome Analysis", "Much of the N glycosylation machinery was identified decades ago but the regulatory mechanisms influencing normal and disease states are only beginning to be discovered. Recent studies highlight a role for key metabolites and metabolic enzymes in this process revising the view of the relationship between different metabolic pathways. Using a multi omic approach in a zebrafish we discovered a mechanism where O GlcNAcylation directly influences the expression and abundance of two enzymes essential for the earliest steps of N linked glycosylation the nus1 encoded NgBR and Dpagt1. Here we show that phosphomannomutase pmm2 deficiency is associated with increased levels of UDP GlcNAc and protein O GlcNAcylation. Biochemical studies show that O GlcNAc modification of the NgBR and Dpagt1 increases their abundance in pmm2m/m mutants. Modulating O GlcNAc levels NgBR abundance or Dpagt1 activity exacerbated cartilage phenotypes in pmm2 mutants suggesting that O GlcNAc mediated increases in the N glycosylation machinery protects against more severe pathology. These findings highlight nucleotide sugar donors as metabolic sensors that coordinate two different glycosylation pathways demonstrating how their interplay is relevant to disease outcome in the most common congenital disorder of glycosylation. Overall design: We did bulk total RNA seq with ribo depletion of whole zebrafish larvae at 2 ages 5dpf and 8dpf for two genotypes wildtype WT and Mutant where the mutant is a loss of function of Pmm2. Each sample consisted of 15 larvae and we sequenced 5 biological replicates per genotype and age combination.", null, "pubmed:39561044", null, "WT 5dpf 2", "GSM8305902", null, "source name:whole body|tissue:whole body|genotype:WT|age:5dpf|genotype:WT|replicate:2|geo loc name:missing|collection date:missing", "WT 5dpf 2", "FASTQ QC by fastp adapter trimming and assessment of ribo depletion by bbduk alignment by STAR BAM indexing by samtools counting of reads in each gene by subread Assembly: GRCz11 Supplementary files format and content: The counts table contains raw counts of reads aligning to genes generated by subread. It is a tab delimited text file", "whole body", "For the sample preparation 3dpf larvae were genotyped using the assay described see the qRT PCR analyses and genotyping section subsequently pooled by genotype and collected and snap frozen in liquid nitrogen 5 and 8dpf. 15 larvae per genotype per sample were collected.", "Direct zol RNA microprep kit KTC UNIV RNA Seq NUQ AD A01 with NuQuant Custom deplete ADU033 D. rerio kit", "Animals were maintained according to standard protocols", "tissue:whole body|genotype:WT|age:5dpf|genotype:WT|replicate:2", "GSM8305902", "GSM8305902: WT 5dpf 2; Danio rerio; RNA Seq", "GSM8305902 r1", "GSM8305902", "1", "Direct zol RNA microprep kit KTC UNIV RNA Seq NUQ AD A01 with NuQuant Custom deplete ADU033 D. rerio kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP511787", null, null, "2_S2_R1_001.fastq.gz 2_S2_R2_001.fastq.gz", "fastq fastq", 52117152588.0, 201316650.0, "GSM8305902 r1", "0:129.38 1:129.51", "A:14844703814;C:10642718902;G:11093806467;T:15180220229;N:355703176", 129, 129, null, null, 14844703814, 10642718902, 11093806467, 15180220229, 355703176, "SRX24802685", "SRS21518793", "SRA1889334", "Greenwood Genetic Center", "Greenwood Genetic Center", 2, 0.77169, 0.7713, 0.2982, 0.30914, 0.72557, 0.73752, 0.59505, 0.60502, 150, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2024-06-04", "Larval", "Larval", "Trunk", "Surface Structure"], [32507, "SRR29285580", "SRX24802684", "SRS21518792", "SRP511787", "PRJNA1120060", "O GlcNAcylation Modulates Expression and Abundance of N Glycosylation Machinery in an Inherited Glycosylation Disorder", "GSE269074", "Transcriptome Analysis", "Much of the N glycosylation machinery was identified decades ago but the regulatory mechanisms influencing normal and disease states are only beginning to be discovered. Recent studies highlight a role for key metabolites and metabolic enzymes in this process revising the view of the relationship between different metabolic pathways. Using a multi omic approach in a zebrafish we discovered a mechanism where O GlcNAcylation directly influences the expression and abundance of two enzymes essential for the earliest steps of N linked glycosylation the nus1 encoded NgBR and Dpagt1. Here we show that phosphomannomutase pmm2 deficiency is associated with increased levels of UDP GlcNAc and protein O GlcNAcylation. Biochemical studies show that O GlcNAc modification of the NgBR and Dpagt1 increases their abundance in pmm2m/m mutants. Modulating O GlcNAc levels NgBR abundance or Dpagt1 activity exacerbated cartilage phenotypes in pmm2 mutants suggesting that O GlcNAc mediated increases in the N glycosylation machinery protects against more severe pathology. These findings highlight nucleotide sugar donors as metabolic sensors that coordinate two different glycosylation pathways demonstrating how their interplay is relevant to disease outcome in the most common congenital disorder of glycosylation. Overall design: We did bulk total RNA seq with ribo depletion of whole zebrafish larvae at 2 ages 5dpf and 8dpf for two genotypes wildtype WT and Mutant where the mutant is a loss of function of Pmm2. Each sample consisted of 15 larvae and we sequenced 5 biological replicates per genotype and age combination.", null, "pubmed:39561044", null, "WT 5dpf 1", "GSM8305901", null, "source name:whole body|tissue:whole body|genotype:WT|age:5dpf|genotype:WT|replicate:1|geo loc name:missing|collection date:missing", "WT 5dpf 1", "FASTQ QC by fastp adapter trimming and assessment of ribo depletion by bbduk alignment by STAR BAM indexing by samtools counting of reads in each gene by subread Assembly: GRCz11 Supplementary files format and content: The counts table contains raw counts of reads aligning to genes generated by subread. It is a tab delimited text file", "whole body", "For the sample preparation 3dpf larvae were genotyped using the assay described see the qRT PCR analyses and genotyping section subsequently pooled by genotype and collected and snap frozen in liquid nitrogen 5 and 8dpf. 15 larvae per genotype per sample were collected.", "Direct zol RNA microprep kit KTC UNIV RNA Seq NUQ AD A01 with NuQuant Custom deplete ADU033 D. rerio kit", "Animals were maintained according to standard protocols", "tissue:whole body|genotype:WT|age:5dpf|genotype:WT|replicate:1", "GSM8305901", "GSM8305901: WT 5dpf 1; Danio rerio; RNA Seq", "GSM8305901 r1", "GSM8305901", "1", "Direct zol RNA microprep kit KTC UNIV RNA Seq NUQ AD A01 with NuQuant Custom deplete ADU033 D. rerio kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP511787", null, null, "1_S1_R2_001.fastq.gz 1_S1_R1_001.fastq.gz", "fastq fastq", 41102336514.0, 146454940.0, "GSM8305901 r1", "0:140.30 1:140.35", "A:12296287974;C:8083080687;G:8218018380;T:12249171413;N:255778060", 140, 140, null, null, 12296287974, 8083080687, 8218018380, 12249171413, 255778060, "SRX24802684", "SRS21518792", "SRA1889334", "Greenwood Genetic Center", "Greenwood Genetic Center", 2, 0.07796, 0.07849, 0.03932, 0.04037, 0.93685, 0.94028, 0.58171, 0.59475, 149, 149, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2024-06-04", "Larval", "Larval", "Trunk", "Surface Structure"], [34206, "SRR31539731", "SRX26906755", "SRS23386341", "SRP548139", "PRJNA1191617", "Sox10 is required for systemic initiation of bone mineralization", "GSE283071", "Transcriptome Analysis", "Heterozygous variants in SOX10 cause syndromes affecting pigmentation digestion hearing and neural development primarily attributable to failed differentiation or loss of non skeletal neural crest derivatives. We report here an additional novel requirement for Sox10 in bone mineralization. Neither crest nor mesoderm derived bones initiate mineralization on time in zebrafish sox10 mutants despite normal osteoblast differentiation and matrix production. Mutants are deficient in the Trpv6+ ionocytes that take up calcium from the environment resulting in severe calcium deficiency. As these ionocytes derive from ectoderm not crest we hypothesized that the primary defect resides in a separate organ that systemically regulates ionocyte numbers. RNAseq revealed significantly elevated stanniocalcin Stc1a an anti hypercalcemic hormone in sox10 mutants. Stc1a inhibits calcium uptake in fish by repressing trpv6 expression and Trpv6+ ionocyte proliferation. Epistasis assays confirm excess Stc1a as the proximate cause of the calcium deficit. The pronephros derived glands that synthesize Stc1a interact with sox10+ cells but these cells are missing in mutants. We conclude that sox10+ crest derived cells non autonomously limit Stc1a production to allow the inaugural wave of calcium uptake necessary to initiate bone mineralization. Overall design: Bulk RNA seq was performed on pooled whole body zebrafish wild type and sox10 mutant larvae at 45 hpf 4 dpf and 7 dpf. Total of 18 samples. 45 hpf 3 replicates: controls n = 10 20 & 25; mutants n = 10 15 & 15 embryos 4 dpf 3 replicates: controls n = 10 15 & 12; mutants n = 10 11 & 12 embryos and 7 dpf 3 replicates: controls n = 12 30 & 18; mutants = 18 12 & 7 embryos", null, "pubmed:39791977", null, "Whole body 7 dpf sox10 mutant embryos biol rep 3", "GSM8655460", null, "source name:whole body|tissue:whole body|genotype:sox10 / |time:7 dpf|geo loc name:missing|collection date:missing", "Whole body 7 dpf sox10 mutant embryos biol rep 3", "The data was processed through the Galaxy project using Trimmomatic version 0.39 Sequences were pseudoaligned and quantified at TPM values using Kallisto. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file includes TPM values for each transcript at 45 hpf 4 dpf and 7 dpf", "whole body", null, "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina\u2019s TruSeq\u00ae stranded mRNA library preparation kit.", null, "tissue:whole body|genotype:sox10 / |time:7 dpf", "GSM8655460", "GSM8655460: Whole body 7 dpf sox10 mutant embryos biol rep 3; Danio rerio; RNA Seq", "GSM8655460 r1", "GSM8655460", "1", "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina's TruSeq\u00ae stranded mRNA library preparation kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP548139", null, null, "7 dpf_mut 3_R1.fastq.gz 7 dpf_mut 3_R2.fastq.gz", "fastq fastq", 14265929756.0, 47238178.0, "GSM8655460 r1", "0:151 1:151", "A:3890017873;C:3282588566;G:3079614796;T:4012518928;N:1189593", 151, 151, null, null, 3890017873, 3282588566, 3079614796, 4012518928, 1189593, "SRX26906755", "SRS23386341", null, null, "Barske Lab, Human Genetics, Cincinnati Children's Hospital", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-11-27", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [34207, "SRR31539732", "SRX26906754", "SRS23386340", "SRP548139", "PRJNA1191617", "Sox10 is required for systemic initiation of bone mineralization", "GSE283071", "Transcriptome Analysis", "Heterozygous variants in SOX10 cause syndromes affecting pigmentation digestion hearing and neural development primarily attributable to failed differentiation or loss of non skeletal neural crest derivatives. We report here an additional novel requirement for Sox10 in bone mineralization. Neither crest nor mesoderm derived bones initiate mineralization on time in zebrafish sox10 mutants despite normal osteoblast differentiation and matrix production. Mutants are deficient in the Trpv6+ ionocytes that take up calcium from the environment resulting in severe calcium deficiency. As these ionocytes derive from ectoderm not crest we hypothesized that the primary defect resides in a separate organ that systemically regulates ionocyte numbers. RNAseq revealed significantly elevated stanniocalcin Stc1a an anti hypercalcemic hormone in sox10 mutants. Stc1a inhibits calcium uptake in fish by repressing trpv6 expression and Trpv6+ ionocyte proliferation. Epistasis assays confirm excess Stc1a as the proximate cause of the calcium deficit. The pronephros derived glands that synthesize Stc1a interact with sox10+ cells but these cells are missing in mutants. We conclude that sox10+ crest derived cells non autonomously limit Stc1a production to allow the inaugural wave of calcium uptake necessary to initiate bone mineralization. Overall design: Bulk RNA seq was performed on pooled whole body zebrafish wild type and sox10 mutant larvae at 45 hpf 4 dpf and 7 dpf. Total of 18 samples. 45 hpf 3 replicates: controls n = 10 20 & 25; mutants n = 10 15 & 15 embryos 4 dpf 3 replicates: controls n = 10 15 & 12; mutants n = 10 11 & 12 embryos and 7 dpf 3 replicates: controls n = 12 30 & 18; mutants = 18 12 & 7 embryos", null, "pubmed:39791977", null, "Whole body 7 dpf sox10 mutant embryos biol rep 2", "GSM8655459", null, "source name:whole body|tissue:whole body|genotype:sox10 / |time:7 dpf|geo loc name:missing|collection date:missing", "Whole body 7 dpf sox10 mutant embryos biol rep 2", "The data was processed through the Galaxy project using Trimmomatic version 0.39 Sequences were pseudoaligned and quantified at TPM values using Kallisto. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file includes TPM values for each transcript at 45 hpf 4 dpf and 7 dpf", "whole body", null, "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina\u2019s TruSeq\u00ae stranded mRNA library preparation kit.", null, "tissue:whole body|genotype:sox10 / |time:7 dpf", "GSM8655459", "GSM8655459: Whole body 7 dpf sox10 mutant embryos biol rep 2; Danio rerio; RNA Seq", "GSM8655459 r1", "GSM8655459", "1", "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina's TruSeq\u00ae stranded mRNA library preparation kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP548139", null, null, "7 dpf_mut 2_R1.fastq.gz 7 dpf_mut 2_R2.fastq.gz", "fastq fastq", 16096968138.0, 53301219.0, "GSM8655459 r1", "0:151 1:151", "A:4158085994;C:3672102993;G:3915623401;T:4349806816;N:1348934", 151, 151, null, null, 4158085994, 3672102993, 3915623401, 4349806816, 1348934, "SRX26906754", "SRS23386340", null, null, "Barske Lab, Human Genetics, Cincinnati Children's Hospital", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-11-27", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [34208, "SRR31539733", "SRX26906753", "SRS23386339", "SRP548139", "PRJNA1191617", "Sox10 is required for systemic initiation of bone mineralization", "GSE283071", "Transcriptome Analysis", "Heterozygous variants in SOX10 cause syndromes affecting pigmentation digestion hearing and neural development primarily attributable to failed differentiation or loss of non skeletal neural crest derivatives. We report here an additional novel requirement for Sox10 in bone mineralization. Neither crest nor mesoderm derived bones initiate mineralization on time in zebrafish sox10 mutants despite normal osteoblast differentiation and matrix production. Mutants are deficient in the Trpv6+ ionocytes that take up calcium from the environment resulting in severe calcium deficiency. As these ionocytes derive from ectoderm not crest we hypothesized that the primary defect resides in a separate organ that systemically regulates ionocyte numbers. RNAseq revealed significantly elevated stanniocalcin Stc1a an anti hypercalcemic hormone in sox10 mutants. Stc1a inhibits calcium uptake in fish by repressing trpv6 expression and Trpv6+ ionocyte proliferation. Epistasis assays confirm excess Stc1a as the proximate cause of the calcium deficit. The pronephros derived glands that synthesize Stc1a interact with sox10+ cells but these cells are missing in mutants. We conclude that sox10+ crest derived cells non autonomously limit Stc1a production to allow the inaugural wave of calcium uptake necessary to initiate bone mineralization. Overall design: Bulk RNA seq was performed on pooled whole body zebrafish wild type and sox10 mutant larvae at 45 hpf 4 dpf and 7 dpf. Total of 18 samples. 45 hpf 3 replicates: controls n = 10 20 & 25; mutants n = 10 15 & 15 embryos 4 dpf 3 replicates: controls n = 10 15 & 12; mutants n = 10 11 & 12 embryos and 7 dpf 3 replicates: controls n = 12 30 & 18; mutants = 18 12 & 7 embryos", null, "pubmed:39791977", null, "Whole body 7 dpf sox10 mutant embryos biol rep 1", "GSM8655458", null, "source name:whole body|tissue:whole body|genotype:sox10 / |time:7 dpf|geo loc name:missing|collection date:missing", "Whole body 7 dpf sox10 mutant embryos biol rep 1", "The data was processed through the Galaxy project using Trimmomatic version 0.39 Sequences were pseudoaligned and quantified at TPM values using Kallisto. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file includes TPM values for each transcript at 45 hpf 4 dpf and 7 dpf", "whole body", null, "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina\u2019s TruSeq\u00ae stranded mRNA library preparation kit.", null, "tissue:whole body|genotype:sox10 / |time:7 dpf", "GSM8655458", "GSM8655458: Whole body 7 dpf sox10 mutant embryos biol rep 1; Danio rerio; RNA Seq", "GSM8655458 r1", "GSM8655458", "1", "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina's TruSeq\u00ae stranded mRNA library preparation kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP548139", null, null, "7 dpf_mut 1_R1.fastq.gz 7 dpf_mut 1_R2.fastq.gz", "fastq fastq", 15919165034.0, 52712467.0, "GSM8655458 r1", "0:151 1:151", "A:4153549187;C:3626188288;G:3782139805;T:4355972996;N:1314758", 151, 151, null, null, 4153549187, 3626188288, 3782139805, 4355972996, 1314758, "SRX26906753", "SRS23386339", null, null, "Barske Lab, Human Genetics, Cincinnati Children's Hospital", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-11-27", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [34209, "SRR31539734", "SRX26906752", "SRS23386338", "SRP548139", "PRJNA1191617", "Sox10 is required for systemic initiation of bone mineralization", "GSE283071", "Transcriptome Analysis", "Heterozygous variants in SOX10 cause syndromes affecting pigmentation digestion hearing and neural development primarily attributable to failed differentiation or loss of non skeletal neural crest derivatives. We report here an additional novel requirement for Sox10 in bone mineralization. Neither crest nor mesoderm derived bones initiate mineralization on time in zebrafish sox10 mutants despite normal osteoblast differentiation and matrix production. Mutants are deficient in the Trpv6+ ionocytes that take up calcium from the environment resulting in severe calcium deficiency. As these ionocytes derive from ectoderm not crest we hypothesized that the primary defect resides in a separate organ that systemically regulates ionocyte numbers. RNAseq revealed significantly elevated stanniocalcin Stc1a an anti hypercalcemic hormone in sox10 mutants. Stc1a inhibits calcium uptake in fish by repressing trpv6 expression and Trpv6+ ionocyte proliferation. Epistasis assays confirm excess Stc1a as the proximate cause of the calcium deficit. The pronephros derived glands that synthesize Stc1a interact with sox10+ cells but these cells are missing in mutants. We conclude that sox10+ crest derived cells non autonomously limit Stc1a production to allow the inaugural wave of calcium uptake necessary to initiate bone mineralization. Overall design: Bulk RNA seq was performed on pooled whole body zebrafish wild type and sox10 mutant larvae at 45 hpf 4 dpf and 7 dpf. Total of 18 samples. 45 hpf 3 replicates: controls n = 10 20 & 25; mutants n = 10 15 & 15 embryos 4 dpf 3 replicates: controls n = 10 15 & 12; mutants n = 10 11 & 12 embryos and 7 dpf 3 replicates: controls n = 12 30 & 18; mutants = 18 12 & 7 embryos", null, "pubmed:39791977", null, "Whole body 7 dpf wild type embryos biol rep 3", "GSM8655457", null, "source name:whole body|tissue:whole body|genotype:WT|time:7 dpf|geo loc name:missing|collection date:missing", "Whole body 7 dpf wild type embryos biol rep 3", "The data was processed through the Galaxy project using Trimmomatic version 0.39 Sequences were pseudoaligned and quantified at TPM values using Kallisto. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file includes TPM values for each transcript at 45 hpf 4 dpf and 7 dpf", "whole body", null, "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina\u2019s TruSeq\u00ae stranded mRNA library preparation kit.", null, "tissue:whole body|genotype:WT|time:7 dpf", "GSM8655457", "GSM8655457: Whole body 7 dpf wild type embryos biol rep 3; Danio rerio; RNA Seq", "GSM8655457 r1", "GSM8655457", "1", "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina's TruSeq\u00ae stranded mRNA library preparation kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP548139", null, null, "7 dpf_WT 3_R1.fastq.gz 7 dpf_WT 3_R2.fastq.gz", "fastq fastq", 15543953590.0, 51470045.0, "GSM8655457 r1", "0:151 1:151", "A:4031818994;C:3704599213;G:3577251498;T:4228986622;N:1297263", 151, 151, null, null, 4031818994, 3704599213, 3577251498, 4228986622, 1297263, "SRX26906752", "SRS23386338", null, null, "Barske Lab, Human Genetics, Cincinnati Children's Hospital", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-11-27", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [34210, "SRR31539735", "SRX26906751", "SRS23386337", "SRP548139", "PRJNA1191617", "Sox10 is required for systemic initiation of bone mineralization", "GSE283071", "Transcriptome Analysis", "Heterozygous variants in SOX10 cause syndromes affecting pigmentation digestion hearing and neural development primarily attributable to failed differentiation or loss of non skeletal neural crest derivatives. We report here an additional novel requirement for Sox10 in bone mineralization. Neither crest nor mesoderm derived bones initiate mineralization on time in zebrafish sox10 mutants despite normal osteoblast differentiation and matrix production. Mutants are deficient in the Trpv6+ ionocytes that take up calcium from the environment resulting in severe calcium deficiency. As these ionocytes derive from ectoderm not crest we hypothesized that the primary defect resides in a separate organ that systemically regulates ionocyte numbers. RNAseq revealed significantly elevated stanniocalcin Stc1a an anti hypercalcemic hormone in sox10 mutants. Stc1a inhibits calcium uptake in fish by repressing trpv6 expression and Trpv6+ ionocyte proliferation. Epistasis assays confirm excess Stc1a as the proximate cause of the calcium deficit. The pronephros derived glands that synthesize Stc1a interact with sox10+ cells but these cells are missing in mutants. We conclude that sox10+ crest derived cells non autonomously limit Stc1a production to allow the inaugural wave of calcium uptake necessary to initiate bone mineralization. Overall design: Bulk RNA seq was performed on pooled whole body zebrafish wild type and sox10 mutant larvae at 45 hpf 4 dpf and 7 dpf. Total of 18 samples. 45 hpf 3 replicates: controls n = 10 20 & 25; mutants n = 10 15 & 15 embryos 4 dpf 3 replicates: controls n = 10 15 & 12; mutants n = 10 11 & 12 embryos and 7 dpf 3 replicates: controls n = 12 30 & 18; mutants = 18 12 & 7 embryos", null, "pubmed:39791977", null, "Whole body 7 dpf wild type embryos biol rep 2", "GSM8655456", null, "source name:whole body|tissue:whole body|genotype:WT|time:7 dpf|geo loc name:missing|collection date:missing", "Whole body 7 dpf wild type embryos biol rep 2", "The data was processed through the Galaxy project using Trimmomatic version 0.39 Sequences were pseudoaligned and quantified at TPM values using Kallisto. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file includes TPM values for each transcript at 45 hpf 4 dpf and 7 dpf", "whole body", null, "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina\u2019s TruSeq\u00ae stranded mRNA library preparation kit.", null, "tissue:whole body|genotype:WT|time:7 dpf", "GSM8655456", "GSM8655456: Whole body 7 dpf wild type embryos biol rep 2; Danio rerio; RNA Seq", "GSM8655456 r1", "GSM8655456", "1", "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina's TruSeq\u00ae stranded mRNA library preparation kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP548139", null, null, "7 dpf_WT 2_R1.fastq.gz 7 dpf_WT 2_R2.fastq.gz", "fastq fastq", 14325089744.0, 47434072.0, "GSM8655456 r1", "0:151 1:151", "A:3806636861;C:3343198938;G:3185927363;T:3988104951;N:1221631", 151, 151, null, null, 3806636861, 3343198938, 3185927363, 3988104951, 1221631, "SRX26906751", "SRS23386337", null, null, "Barske Lab, Human Genetics, Cincinnati Children's Hospital", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-11-27", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [34211, "SRR31539736", "SRX26906750", "SRS23386333", "SRP548139", "PRJNA1191617", "Sox10 is required for systemic initiation of bone mineralization", "GSE283071", "Transcriptome Analysis", "Heterozygous variants in SOX10 cause syndromes affecting pigmentation digestion hearing and neural development primarily attributable to failed differentiation or loss of non skeletal neural crest derivatives. We report here an additional novel requirement for Sox10 in bone mineralization. Neither crest nor mesoderm derived bones initiate mineralization on time in zebrafish sox10 mutants despite normal osteoblast differentiation and matrix production. Mutants are deficient in the Trpv6+ ionocytes that take up calcium from the environment resulting in severe calcium deficiency. As these ionocytes derive from ectoderm not crest we hypothesized that the primary defect resides in a separate organ that systemically regulates ionocyte numbers. RNAseq revealed significantly elevated stanniocalcin Stc1a an anti hypercalcemic hormone in sox10 mutants. Stc1a inhibits calcium uptake in fish by repressing trpv6 expression and Trpv6+ ionocyte proliferation. Epistasis assays confirm excess Stc1a as the proximate cause of the calcium deficit. The pronephros derived glands that synthesize Stc1a interact with sox10+ cells but these cells are missing in mutants. We conclude that sox10+ crest derived cells non autonomously limit Stc1a production to allow the inaugural wave of calcium uptake necessary to initiate bone mineralization. Overall design: Bulk RNA seq was performed on pooled whole body zebrafish wild type and sox10 mutant larvae at 45 hpf 4 dpf and 7 dpf. Total of 18 samples. 45 hpf 3 replicates: controls n = 10 20 & 25; mutants n = 10 15 & 15 embryos 4 dpf 3 replicates: controls n = 10 15 & 12; mutants n = 10 11 & 12 embryos and 7 dpf 3 replicates: controls n = 12 30 & 18; mutants = 18 12 & 7 embryos", null, "pubmed:39791977", null, "Whole body 7 dpf wild type embryos biol rep 1", "GSM8655455", null, "source name:whole body|tissue:whole body|genotype:WT|time:7 dpf|geo loc name:missing|collection date:missing", "Whole body 7 dpf wild type embryos biol rep 1", "The data was processed through the Galaxy project using Trimmomatic version 0.39 Sequences were pseudoaligned and quantified at TPM values using Kallisto. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file includes TPM values for each transcript at 45 hpf 4 dpf and 7 dpf", "whole body", null, "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina\u2019s TruSeq\u00ae stranded mRNA library preparation kit.", null, "tissue:whole body|genotype:WT|time:7 dpf", "GSM8655455", "GSM8655455: Whole body 7 dpf wild type embryos biol rep 1; Danio rerio; RNA Seq", "GSM8655455 r1", "GSM8655455", "1", "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina's TruSeq\u00ae stranded mRNA library preparation kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP548139", null, null, "7 dpf_WT 1_R1.fastq.gz 7 dpf_WT 1_R2.fastq.gz", "fastq fastq", 16398118008.0, 54298404.0, "GSM8655455 r1", "0:151 1:151", "A:4341778579;C:3858758690;G:3657590940;T:4538608543;N:1381256", 151, 151, null, null, 4341778579, 3858758690, 3657590940, 4538608543, 1381256, "SRX26906750", "SRS23386333", null, null, "Barske Lab, Human Genetics, Cincinnati Children's Hospital", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-11-27", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [34212, "SRR31539737", "SRX26906749", "SRS23386334", "SRP548139", "PRJNA1191617", "Sox10 is required for systemic initiation of bone mineralization", "GSE283071", "Transcriptome Analysis", "Heterozygous variants in SOX10 cause syndromes affecting pigmentation digestion hearing and neural development primarily attributable to failed differentiation or loss of non skeletal neural crest derivatives. We report here an additional novel requirement for Sox10 in bone mineralization. Neither crest nor mesoderm derived bones initiate mineralization on time in zebrafish sox10 mutants despite normal osteoblast differentiation and matrix production. Mutants are deficient in the Trpv6+ ionocytes that take up calcium from the environment resulting in severe calcium deficiency. As these ionocytes derive from ectoderm not crest we hypothesized that the primary defect resides in a separate organ that systemically regulates ionocyte numbers. RNAseq revealed significantly elevated stanniocalcin Stc1a an anti hypercalcemic hormone in sox10 mutants. Stc1a inhibits calcium uptake in fish by repressing trpv6 expression and Trpv6+ ionocyte proliferation. Epistasis assays confirm excess Stc1a as the proximate cause of the calcium deficit. The pronephros derived glands that synthesize Stc1a interact with sox10+ cells but these cells are missing in mutants. We conclude that sox10+ crest derived cells non autonomously limit Stc1a production to allow the inaugural wave of calcium uptake necessary to initiate bone mineralization. Overall design: Bulk RNA seq was performed on pooled whole body zebrafish wild type and sox10 mutant larvae at 45 hpf 4 dpf and 7 dpf. Total of 18 samples. 45 hpf 3 replicates: controls n = 10 20 & 25; mutants n = 10 15 & 15 embryos 4 dpf 3 replicates: controls n = 10 15 & 12; mutants n = 10 11 & 12 embryos and 7 dpf 3 replicates: controls n = 12 30 & 18; mutants = 18 12 & 7 embryos", null, "pubmed:39791977", null, "Whole body 4 dpf sox10 mutant embryos biol rep 3", "GSM8655454", null, "source name:whole body|tissue:whole body|genotype:sox10 / |time:4 dpf|geo loc name:missing|collection date:missing", "Whole body 4 dpf sox10 mutant embryos biol rep 3", "The data was processed through the Galaxy project using Trimmomatic version 0.39 Sequences were pseudoaligned and quantified at TPM values using Kallisto. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file includes TPM values for each transcript at 45 hpf 4 dpf and 7 dpf", "whole body", null, "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina\u2019s TruSeq\u00ae stranded mRNA library preparation kit.", null, "tissue:whole body|genotype:sox10 / |time:4 dpf", "GSM8655454", "GSM8655454: Whole body 4 dpf sox10 mutant embryos biol rep 3; Danio rerio; RNA Seq", "GSM8655454 r1", "GSM8655454", "1", "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina's TruSeq\u00ae stranded mRNA library preparation kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP548139", null, null, "4 dpf_mut 3_R1.fastq.gz 4 dpf_mut 3_R2.fastq.gz", "fastq fastq", 15071278894.0, 49904897.0, "GSM8655454 r1", "0:151 1:151", "A:3996223512;C:3537174277;G:3398338576;T:4138304072;N:1238457", 151, 151, null, null, 3996223512, 3537174277, 3398338576, 4138304072, 1238457, "SRX26906749", "SRS23386334", null, null, "Barske Lab, Human Genetics, Cincinnati Children's Hospital", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-11-27", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [34213, "SRR31539738", "SRX26906748", "SRS23386336", "SRP548139", "PRJNA1191617", "Sox10 is required for systemic initiation of bone mineralization", "GSE283071", "Transcriptome Analysis", "Heterozygous variants in SOX10 cause syndromes affecting pigmentation digestion hearing and neural development primarily attributable to failed differentiation or loss of non skeletal neural crest derivatives. We report here an additional novel requirement for Sox10 in bone mineralization. Neither crest nor mesoderm derived bones initiate mineralization on time in zebrafish sox10 mutants despite normal osteoblast differentiation and matrix production. Mutants are deficient in the Trpv6+ ionocytes that take up calcium from the environment resulting in severe calcium deficiency. As these ionocytes derive from ectoderm not crest we hypothesized that the primary defect resides in a separate organ that systemically regulates ionocyte numbers. RNAseq revealed significantly elevated stanniocalcin Stc1a an anti hypercalcemic hormone in sox10 mutants. Stc1a inhibits calcium uptake in fish by repressing trpv6 expression and Trpv6+ ionocyte proliferation. Epistasis assays confirm excess Stc1a as the proximate cause of the calcium deficit. The pronephros derived glands that synthesize Stc1a interact with sox10+ cells but these cells are missing in mutants. We conclude that sox10+ crest derived cells non autonomously limit Stc1a production to allow the inaugural wave of calcium uptake necessary to initiate bone mineralization. Overall design: Bulk RNA seq was performed on pooled whole body zebrafish wild type and sox10 mutant larvae at 45 hpf 4 dpf and 7 dpf. Total of 18 samples. 45 hpf 3 replicates: controls n = 10 20 & 25; mutants n = 10 15 & 15 embryos 4 dpf 3 replicates: controls n = 10 15 & 12; mutants n = 10 11 & 12 embryos and 7 dpf 3 replicates: controls n = 12 30 & 18; mutants = 18 12 & 7 embryos", null, "pubmed:39791977", null, "Whole body 4 dpf sox10 mutant embryos biol rep 2", "GSM8655453", null, "source name:whole body|tissue:whole body|genotype:sox10 / |time:4 dpf|geo loc name:missing|collection date:missing", "Whole body 4 dpf sox10 mutant embryos biol rep 2", "The data was processed through the Galaxy project using Trimmomatic version 0.39 Sequences were pseudoaligned and quantified at TPM values using Kallisto. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file includes TPM values for each transcript at 45 hpf 4 dpf and 7 dpf", "whole body", null, "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina\u2019s TruSeq\u00ae stranded mRNA library preparation kit.", null, "tissue:whole body|genotype:sox10 / |time:4 dpf", "GSM8655453", "GSM8655453: Whole body 4 dpf sox10 mutant embryos biol rep 2; Danio rerio; RNA Seq", "GSM8655453 r1", "GSM8655453", "1", "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina's TruSeq\u00ae stranded mRNA library preparation kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP548139", null, null, "4 dpf_mut 2_R1.fastq.gz 4 dpf_mut 2_R2.fastq.gz", "fastq fastq", 14918687958.0, 49399629.0, "GSM8655453 r1", "0:151 1:151", "A:3994132161;C:3464356999;G:3293001897;T:4165943265;N:1253636", 151, 151, null, null, 3994132161, 3464356999, 3293001897, 4165943265, 1253636, "SRX26906748", "SRS23386336", null, null, "Barske Lab, Human Genetics, Cincinnati Children's Hospital", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-11-27", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [34214, "SRR31539739", "SRX26906747", "SRS23386332", "SRP548139", "PRJNA1191617", "Sox10 is required for systemic initiation of bone mineralization", "GSE283071", "Transcriptome Analysis", "Heterozygous variants in SOX10 cause syndromes affecting pigmentation digestion hearing and neural development primarily attributable to failed differentiation or loss of non skeletal neural crest derivatives. We report here an additional novel requirement for Sox10 in bone mineralization. Neither crest nor mesoderm derived bones initiate mineralization on time in zebrafish sox10 mutants despite normal osteoblast differentiation and matrix production. Mutants are deficient in the Trpv6+ ionocytes that take up calcium from the environment resulting in severe calcium deficiency. As these ionocytes derive from ectoderm not crest we hypothesized that the primary defect resides in a separate organ that systemically regulates ionocyte numbers. RNAseq revealed significantly elevated stanniocalcin Stc1a an anti hypercalcemic hormone in sox10 mutants. Stc1a inhibits calcium uptake in fish by repressing trpv6 expression and Trpv6+ ionocyte proliferation. Epistasis assays confirm excess Stc1a as the proximate cause of the calcium deficit. The pronephros derived glands that synthesize Stc1a interact with sox10+ cells but these cells are missing in mutants. We conclude that sox10+ crest derived cells non autonomously limit Stc1a production to allow the inaugural wave of calcium uptake necessary to initiate bone mineralization. Overall design: Bulk RNA seq was performed on pooled whole body zebrafish wild type and sox10 mutant larvae at 45 hpf 4 dpf and 7 dpf. Total of 18 samples. 45 hpf 3 replicates: controls n = 10 20 & 25; mutants n = 10 15 & 15 embryos 4 dpf 3 replicates: controls n = 10 15 & 12; mutants n = 10 11 & 12 embryos and 7 dpf 3 replicates: controls n = 12 30 & 18; mutants = 18 12 & 7 embryos", null, "pubmed:39791977", null, "Whole body 4 dpf sox10 mutant embryos biol rep 1", "GSM8655452", null, "source name:whole body|tissue:whole body|genotype:sox10 / |time:4 dpf|geo loc name:missing|collection date:missing", "Whole body 4 dpf sox10 mutant embryos biol rep 1", "The data was processed through the Galaxy project using Trimmomatic version 0.39 Sequences were pseudoaligned and quantified at TPM values using Kallisto. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file includes TPM values for each transcript at 45 hpf 4 dpf and 7 dpf", "whole body", null, "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina\u2019s TruSeq\u00ae stranded mRNA library preparation kit.", null, "tissue:whole body|genotype:sox10 / |time:4 dpf", "GSM8655452", "GSM8655452: Whole body 4 dpf sox10 mutant embryos biol rep 1; Danio rerio; RNA Seq", "GSM8655452 r1", "GSM8655452", "1", "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina's TruSeq\u00ae stranded mRNA library preparation kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP548139", null, null, "4 dpf_mut 1_R1.fastq.gz 4 dpf_mut 1_R2.fastq.gz", "fastq fastq", 14573247372.0, 48255786.0, "GSM8655452 r1", "0:151 1:151", "A:3964700989;C:3340575136;G:3128233836;T:4138502375;N:1235036", 151, 151, null, null, 3964700989, 3340575136, 3128233836, 4138502375, 1235036, "SRX26906747", "SRS23386332", null, null, "Barske Lab, Human Genetics, Cincinnati Children's Hospital", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-11-27", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [34215, "SRR31539740", "SRX26906746", "SRS23386331", "SRP548139", "PRJNA1191617", "Sox10 is required for systemic initiation of bone mineralization", "GSE283071", "Transcriptome Analysis", "Heterozygous variants in SOX10 cause syndromes affecting pigmentation digestion hearing and neural development primarily attributable to failed differentiation or loss of non skeletal neural crest derivatives. We report here an additional novel requirement for Sox10 in bone mineralization. Neither crest nor mesoderm derived bones initiate mineralization on time in zebrafish sox10 mutants despite normal osteoblast differentiation and matrix production. Mutants are deficient in the Trpv6+ ionocytes that take up calcium from the environment resulting in severe calcium deficiency. As these ionocytes derive from ectoderm not crest we hypothesized that the primary defect resides in a separate organ that systemically regulates ionocyte numbers. RNAseq revealed significantly elevated stanniocalcin Stc1a an anti hypercalcemic hormone in sox10 mutants. Stc1a inhibits calcium uptake in fish by repressing trpv6 expression and Trpv6+ ionocyte proliferation. Epistasis assays confirm excess Stc1a as the proximate cause of the calcium deficit. The pronephros derived glands that synthesize Stc1a interact with sox10+ cells but these cells are missing in mutants. We conclude that sox10+ crest derived cells non autonomously limit Stc1a production to allow the inaugural wave of calcium uptake necessary to initiate bone mineralization. Overall design: Bulk RNA seq was performed on pooled whole body zebrafish wild type and sox10 mutant larvae at 45 hpf 4 dpf and 7 dpf. Total of 18 samples. 45 hpf 3 replicates: controls n = 10 20 & 25; mutants n = 10 15 & 15 embryos 4 dpf 3 replicates: controls n = 10 15 & 12; mutants n = 10 11 & 12 embryos and 7 dpf 3 replicates: controls n = 12 30 & 18; mutants = 18 12 & 7 embryos", null, "pubmed:39791977", null, "Whole body 4 dpf wild type embryos biol rep 3", "GSM8655451", null, "source name:whole body|tissue:whole body|genotype:WT|time:4 dpf|geo loc name:missing|collection date:missing", "Whole body 4 dpf wild type embryos biol rep 3", "The data was processed through the Galaxy project using Trimmomatic version 0.39 Sequences were pseudoaligned and quantified at TPM values using Kallisto. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file includes TPM values for each transcript at 45 hpf 4 dpf and 7 dpf", "whole body", null, "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina\u2019s TruSeq\u00ae stranded mRNA library preparation kit.", null, "tissue:whole body|genotype:WT|time:4 dpf", "GSM8655451", "GSM8655451: Whole body 4 dpf wild type embryos biol rep 3; Danio rerio; RNA Seq", "GSM8655451 r1", "GSM8655451", "1", "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina's TruSeq\u00ae stranded mRNA library preparation kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP548139", null, null, "4 dpf_WT 3_R1.fastq.gz 4 dpf_WT 3_R2.fastq.gz", "fastq fastq", 15132219172.0, 50106686.0, "GSM8655451 r1", "0:151 1:151", "A:4030654907;C:3519071260;G:3404455031;T:4176756699;N:1281275", 151, 151, null, null, 4030654907, 3519071260, 3404455031, 4176756699, 1281275, "SRX26906746", "SRS23386331", null, null, "Barske Lab, Human Genetics, Cincinnati Children's Hospital", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-11-27", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [34216, "SRR31539741", "SRX26906745", "SRS23386335", "SRP548139", "PRJNA1191617", "Sox10 is required for systemic initiation of bone mineralization", "GSE283071", "Transcriptome Analysis", "Heterozygous variants in SOX10 cause syndromes affecting pigmentation digestion hearing and neural development primarily attributable to failed differentiation or loss of non skeletal neural crest derivatives. We report here an additional novel requirement for Sox10 in bone mineralization. Neither crest nor mesoderm derived bones initiate mineralization on time in zebrafish sox10 mutants despite normal osteoblast differentiation and matrix production. Mutants are deficient in the Trpv6+ ionocytes that take up calcium from the environment resulting in severe calcium deficiency. As these ionocytes derive from ectoderm not crest we hypothesized that the primary defect resides in a separate organ that systemically regulates ionocyte numbers. RNAseq revealed significantly elevated stanniocalcin Stc1a an anti hypercalcemic hormone in sox10 mutants. Stc1a inhibits calcium uptake in fish by repressing trpv6 expression and Trpv6+ ionocyte proliferation. Epistasis assays confirm excess Stc1a as the proximate cause of the calcium deficit. The pronephros derived glands that synthesize Stc1a interact with sox10+ cells but these cells are missing in mutants. We conclude that sox10+ crest derived cells non autonomously limit Stc1a production to allow the inaugural wave of calcium uptake necessary to initiate bone mineralization. Overall design: Bulk RNA seq was performed on pooled whole body zebrafish wild type and sox10 mutant larvae at 45 hpf 4 dpf and 7 dpf. Total of 18 samples. 45 hpf 3 replicates: controls n = 10 20 & 25; mutants n = 10 15 & 15 embryos 4 dpf 3 replicates: controls n = 10 15 & 12; mutants n = 10 11 & 12 embryos and 7 dpf 3 replicates: controls n = 12 30 & 18; mutants = 18 12 & 7 embryos", null, "pubmed:39791977", null, "Whole body 4 dpf wild type embryos biol rep 2", "GSM8655450", null, "source name:whole body|tissue:whole body|genotype:WT|time:4 dpf|geo loc name:missing|collection date:missing", "Whole body 4 dpf wild type embryos biol rep 2", "The data was processed through the Galaxy project using Trimmomatic version 0.39 Sequences were pseudoaligned and quantified at TPM values using Kallisto. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file includes TPM values for each transcript at 45 hpf 4 dpf and 7 dpf", "whole body", null, "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina\u2019s TruSeq\u00ae stranded mRNA library preparation kit.", null, "tissue:whole body|genotype:WT|time:4 dpf", "GSM8655450", "GSM8655450: Whole body 4 dpf wild type embryos biol rep 2; Danio rerio; RNA Seq", "GSM8655450 r1", "GSM8655450", "1", "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina's TruSeq\u00ae stranded mRNA library preparation kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP548139", null, null, "4 dpf_WT 2_R1.fastq.gz 4 dpf_WT 2_R2.fastq.gz", "fastq fastq", 15546478914.0, 51478407.0, "GSM8655450 r1", "0:151 1:151", "A:4105803894;C:3606318412;G:3589944905;T:4243130619;N:1281084", 151, 151, null, null, 4105803894, 3606318412, 3589944905, 4243130619, 1281084, "SRX26906745", "SRS23386335", null, null, "Barske Lab, Human Genetics, Cincinnati Children's Hospital", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-11-27", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [34217, "SRR31539742", "SRX26906744", "SRS23386330", "SRP548139", "PRJNA1191617", "Sox10 is required for systemic initiation of bone mineralization", "GSE283071", "Transcriptome Analysis", "Heterozygous variants in SOX10 cause syndromes affecting pigmentation digestion hearing and neural development primarily attributable to failed differentiation or loss of non skeletal neural crest derivatives. We report here an additional novel requirement for Sox10 in bone mineralization. Neither crest nor mesoderm derived bones initiate mineralization on time in zebrafish sox10 mutants despite normal osteoblast differentiation and matrix production. Mutants are deficient in the Trpv6+ ionocytes that take up calcium from the environment resulting in severe calcium deficiency. As these ionocytes derive from ectoderm not crest we hypothesized that the primary defect resides in a separate organ that systemically regulates ionocyte numbers. RNAseq revealed significantly elevated stanniocalcin Stc1a an anti hypercalcemic hormone in sox10 mutants. Stc1a inhibits calcium uptake in fish by repressing trpv6 expression and Trpv6+ ionocyte proliferation. Epistasis assays confirm excess Stc1a as the proximate cause of the calcium deficit. The pronephros derived glands that synthesize Stc1a interact with sox10+ cells but these cells are missing in mutants. We conclude that sox10+ crest derived cells non autonomously limit Stc1a production to allow the inaugural wave of calcium uptake necessary to initiate bone mineralization. Overall design: Bulk RNA seq was performed on pooled whole body zebrafish wild type and sox10 mutant larvae at 45 hpf 4 dpf and 7 dpf. Total of 18 samples. 45 hpf 3 replicates: controls n = 10 20 & 25; mutants n = 10 15 & 15 embryos 4 dpf 3 replicates: controls n = 10 15 & 12; mutants n = 10 11 & 12 embryos and 7 dpf 3 replicates: controls n = 12 30 & 18; mutants = 18 12 & 7 embryos", null, "pubmed:39791977", null, "Whole body 4 dpf wild type embryos biol rep 1", "GSM8655449", null, "source name:whole body|tissue:whole body|genotype:WT|time:4 dpf|geo loc name:missing|collection date:missing", "Whole body 4 dpf wild type embryos biol rep 1", "The data was processed through the Galaxy project using Trimmomatic version 0.39 Sequences were pseudoaligned and quantified at TPM values using Kallisto. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file includes TPM values for each transcript at 45 hpf 4 dpf and 7 dpf", "whole body", null, "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina\u2019s TruSeq\u00ae stranded mRNA library preparation kit.", null, "tissue:whole body|genotype:WT|time:4 dpf", "GSM8655449", "GSM8655449: Whole body 4 dpf wild type embryos biol rep 1; Danio rerio; RNA Seq", "GSM8655449 r1", "GSM8655449", "1", "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina's TruSeq\u00ae stranded mRNA library preparation kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP548139", null, null, "4 dpf_WT 1_R1.fastq.gz 4 dpf_WT 1_R2.fastq.gz", "fastq fastq", 15246602880.0, 50485440.0, "GSM8655449 r1", "0:151 1:151", "A:4017771448;C:3536729749;G:3495956173;T:4194910365;N:1235145", 151, 151, null, null, 4017771448, 3536729749, 3495956173, 4194910365, 1235145, "SRX26906744", "SRS23386330", null, null, "Barske Lab, Human Genetics, Cincinnati Children's Hospital", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-11-27", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [34218, "SRR31539743", "SRX26906743", "SRS23386329", "SRP548139", "PRJNA1191617", "Sox10 is required for systemic initiation of bone mineralization", "GSE283071", "Transcriptome Analysis", "Heterozygous variants in SOX10 cause syndromes affecting pigmentation digestion hearing and neural development primarily attributable to failed differentiation or loss of non skeletal neural crest derivatives. We report here an additional novel requirement for Sox10 in bone mineralization. Neither crest nor mesoderm derived bones initiate mineralization on time in zebrafish sox10 mutants despite normal osteoblast differentiation and matrix production. Mutants are deficient in the Trpv6+ ionocytes that take up calcium from the environment resulting in severe calcium deficiency. As these ionocytes derive from ectoderm not crest we hypothesized that the primary defect resides in a separate organ that systemically regulates ionocyte numbers. RNAseq revealed significantly elevated stanniocalcin Stc1a an anti hypercalcemic hormone in sox10 mutants. Stc1a inhibits calcium uptake in fish by repressing trpv6 expression and Trpv6+ ionocyte proliferation. Epistasis assays confirm excess Stc1a as the proximate cause of the calcium deficit. The pronephros derived glands that synthesize Stc1a interact with sox10+ cells but these cells are missing in mutants. We conclude that sox10+ crest derived cells non autonomously limit Stc1a production to allow the inaugural wave of calcium uptake necessary to initiate bone mineralization. Overall design: Bulk RNA seq was performed on pooled whole body zebrafish wild type and sox10 mutant larvae at 45 hpf 4 dpf and 7 dpf. Total of 18 samples. 45 hpf 3 replicates: controls n = 10 20 & 25; mutants n = 10 15 & 15 embryos 4 dpf 3 replicates: controls n = 10 15 & 12; mutants n = 10 11 & 12 embryos and 7 dpf 3 replicates: controls n = 12 30 & 18; mutants = 18 12 & 7 embryos", null, "pubmed:39791977", null, "Whole body 45 hpf sox10 mutant embryos biol rep 3", "GSM8655448", null, "source name:whole body|tissue:whole body|genotype:sox10 / |time:45 hpf|geo loc name:missing|collection date:missing", "Whole body 45 hpf sox10 mutant embryos biol rep 3", "The data was processed through the Galaxy project using Trimmomatic version 0.39 Sequences were pseudoaligned and quantified at TPM values using Kallisto. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file includes TPM values for each transcript at 45 hpf 4 dpf and 7 dpf", "whole body", null, "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina\u2019s TruSeq\u00ae stranded mRNA library preparation kit.", null, "tissue:whole body|genotype:sox10 / |time:45 hpf", "GSM8655448", "GSM8655448: Whole body 45 hpf sox10 mutant embryos biol rep 3; Danio rerio; RNA Seq", "GSM8655448 r1", "GSM8655448", "1", "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina's TruSeq\u00ae stranded mRNA library preparation kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP548139", null, null, "45 hpf_mut 3_R1.fastq.gz 45 hpf_mut 3_R2.fastq.gz", "fastq fastq", 14338321572.0, 47477886.0, "GSM8655448 r1", "0:151 1:151", "A:3808719246;C:3382555065;G:3212075099;T:3933758367;N:1213795", 151, 151, null, null, 3808719246, 3382555065, 3212075099, 3933758367, 1213795, "SRX26906743", "SRS23386329", null, null, "Barske Lab, Human Genetics, Cincinnati Children's Hospital", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-11-27", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [34219, "SRR31539744", "SRX26906742", "SRS23386326", "SRP548139", "PRJNA1191617", "Sox10 is required for systemic initiation of bone mineralization", "GSE283071", "Transcriptome Analysis", "Heterozygous variants in SOX10 cause syndromes affecting pigmentation digestion hearing and neural development primarily attributable to failed differentiation or loss of non skeletal neural crest derivatives. We report here an additional novel requirement for Sox10 in bone mineralization. Neither crest nor mesoderm derived bones initiate mineralization on time in zebrafish sox10 mutants despite normal osteoblast differentiation and matrix production. Mutants are deficient in the Trpv6+ ionocytes that take up calcium from the environment resulting in severe calcium deficiency. As these ionocytes derive from ectoderm not crest we hypothesized that the primary defect resides in a separate organ that systemically regulates ionocyte numbers. RNAseq revealed significantly elevated stanniocalcin Stc1a an anti hypercalcemic hormone in sox10 mutants. Stc1a inhibits calcium uptake in fish by repressing trpv6 expression and Trpv6+ ionocyte proliferation. Epistasis assays confirm excess Stc1a as the proximate cause of the calcium deficit. The pronephros derived glands that synthesize Stc1a interact with sox10+ cells but these cells are missing in mutants. We conclude that sox10+ crest derived cells non autonomously limit Stc1a production to allow the inaugural wave of calcium uptake necessary to initiate bone mineralization. Overall design: Bulk RNA seq was performed on pooled whole body zebrafish wild type and sox10 mutant larvae at 45 hpf 4 dpf and 7 dpf. Total of 18 samples. 45 hpf 3 replicates: controls n = 10 20 & 25; mutants n = 10 15 & 15 embryos 4 dpf 3 replicates: controls n = 10 15 & 12; mutants n = 10 11 & 12 embryos and 7 dpf 3 replicates: controls n = 12 30 & 18; mutants = 18 12 & 7 embryos", null, "pubmed:39791977", null, "Whole body 45 hpf sox10 mutant embryos biol rep 2", "GSM8655447", null, "source name:whole body|tissue:whole body|genotype:sox10 / |time:45 hpf|geo loc name:missing|collection date:missing", "Whole body 45 hpf sox10 mutant embryos biol rep 2", "The data was processed through the Galaxy project using Trimmomatic version 0.39 Sequences were pseudoaligned and quantified at TPM values using Kallisto. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file includes TPM values for each transcript at 45 hpf 4 dpf and 7 dpf", "whole body", null, "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina\u2019s TruSeq\u00ae stranded mRNA library preparation kit.", null, "tissue:whole body|genotype:sox10 / |time:45 hpf", "GSM8655447", "GSM8655447: Whole body 45 hpf sox10 mutant embryos biol rep 2; Danio rerio; RNA Seq", "GSM8655447 r1", "GSM8655447", "1", "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina's TruSeq\u00ae stranded mRNA library preparation kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP548139", null, null, "45 hpf_mut 2_R1.fastq.gz 45 hpf_mut 2_R2.fastq.gz", "fastq fastq", 15462167158.0, 51199229.0, "GSM8655447 r1", "0:151 1:151", "A:4089691508;C:3622289242;G:3495097207;T:4253826187;N:1263014", 151, 151, null, null, 4089691508, 3622289242, 3495097207, 4253826187, 1263014, "SRX26906742", "SRS23386326", null, null, "Barske Lab, Human Genetics, Cincinnati Children's Hospital", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-11-27", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [34220, "SRR31539745", "SRX26906741", "SRS23386327", "SRP548139", "PRJNA1191617", "Sox10 is required for systemic initiation of bone mineralization", "GSE283071", "Transcriptome Analysis", "Heterozygous variants in SOX10 cause syndromes affecting pigmentation digestion hearing and neural development primarily attributable to failed differentiation or loss of non skeletal neural crest derivatives. We report here an additional novel requirement for Sox10 in bone mineralization. Neither crest nor mesoderm derived bones initiate mineralization on time in zebrafish sox10 mutants despite normal osteoblast differentiation and matrix production. Mutants are deficient in the Trpv6+ ionocytes that take up calcium from the environment resulting in severe calcium deficiency. As these ionocytes derive from ectoderm not crest we hypothesized that the primary defect resides in a separate organ that systemically regulates ionocyte numbers. RNAseq revealed significantly elevated stanniocalcin Stc1a an anti hypercalcemic hormone in sox10 mutants. Stc1a inhibits calcium uptake in fish by repressing trpv6 expression and Trpv6+ ionocyte proliferation. Epistasis assays confirm excess Stc1a as the proximate cause of the calcium deficit. The pronephros derived glands that synthesize Stc1a interact with sox10+ cells but these cells are missing in mutants. We conclude that sox10+ crest derived cells non autonomously limit Stc1a production to allow the inaugural wave of calcium uptake necessary to initiate bone mineralization. Overall design: Bulk RNA seq was performed on pooled whole body zebrafish wild type and sox10 mutant larvae at 45 hpf 4 dpf and 7 dpf. Total of 18 samples. 45 hpf 3 replicates: controls n = 10 20 & 25; mutants n = 10 15 & 15 embryos 4 dpf 3 replicates: controls n = 10 15 & 12; mutants n = 10 11 & 12 embryos and 7 dpf 3 replicates: controls n = 12 30 & 18; mutants = 18 12 & 7 embryos", null, "pubmed:39791977", null, "Whole body 45 hpf sox10 mutant embryos biol rep 1", "GSM8655446", null, "source name:whole body|tissue:whole body|genotype:sox10 / |time:45 hpf|geo loc name:missing|collection date:missing", "Whole body 45 hpf sox10 mutant embryos biol rep 1", "The data was processed through the Galaxy project using Trimmomatic version 0.39 Sequences were pseudoaligned and quantified at TPM values using Kallisto. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file includes TPM values for each transcript at 45 hpf 4 dpf and 7 dpf", "whole body", null, "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina\u2019s TruSeq\u00ae stranded mRNA library preparation kit.", null, "tissue:whole body|genotype:sox10 / |time:45 hpf", "GSM8655446", "GSM8655446: Whole body 45 hpf sox10 mutant embryos biol rep 1; Danio rerio; RNA Seq", "GSM8655446 r1", "GSM8655446", "1", "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina's TruSeq\u00ae stranded mRNA library preparation kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP548139", null, null, "45 hpf_mut 1_R1.fastq.gz 45 hpf_mut 1_R2.fastq.gz", "fastq fastq", 15655817712.0, 51840456.0, "GSM8655446 r1", "0:151 1:151", "A:4157360171;C:3674570903;G:3484564544;T:4338002005;N:1320089", 151, 151, null, null, 4157360171, 3674570903, 3484564544, 4338002005, 1320089, "SRX26906741", "SRS23386327", null, null, "Barske Lab, Human Genetics, Cincinnati Children's Hospital", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-11-27", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [34221, "SRR31539746", "SRX26906740", "SRS23386328", "SRP548139", "PRJNA1191617", "Sox10 is required for systemic initiation of bone mineralization", "GSE283071", "Transcriptome Analysis", "Heterozygous variants in SOX10 cause syndromes affecting pigmentation digestion hearing and neural development primarily attributable to failed differentiation or loss of non skeletal neural crest derivatives. We report here an additional novel requirement for Sox10 in bone mineralization. Neither crest nor mesoderm derived bones initiate mineralization on time in zebrafish sox10 mutants despite normal osteoblast differentiation and matrix production. Mutants are deficient in the Trpv6+ ionocytes that take up calcium from the environment resulting in severe calcium deficiency. As these ionocytes derive from ectoderm not crest we hypothesized that the primary defect resides in a separate organ that systemically regulates ionocyte numbers. RNAseq revealed significantly elevated stanniocalcin Stc1a an anti hypercalcemic hormone in sox10 mutants. Stc1a inhibits calcium uptake in fish by repressing trpv6 expression and Trpv6+ ionocyte proliferation. Epistasis assays confirm excess Stc1a as the proximate cause of the calcium deficit. The pronephros derived glands that synthesize Stc1a interact with sox10+ cells but these cells are missing in mutants. We conclude that sox10+ crest derived cells non autonomously limit Stc1a production to allow the inaugural wave of calcium uptake necessary to initiate bone mineralization. Overall design: Bulk RNA seq was performed on pooled whole body zebrafish wild type and sox10 mutant larvae at 45 hpf 4 dpf and 7 dpf. Total of 18 samples. 45 hpf 3 replicates: controls n = 10 20 & 25; mutants n = 10 15 & 15 embryos 4 dpf 3 replicates: controls n = 10 15 & 12; mutants n = 10 11 & 12 embryos and 7 dpf 3 replicates: controls n = 12 30 & 18; mutants = 18 12 & 7 embryos", null, "pubmed:39791977", null, "Whole body 45 hpf wild type embryos biol rep 3", "GSM8655445", null, "source name:whole body|tissue:whole body|genotype:WT|time:45 hpf|geo loc name:missing|collection date:missing", "Whole body 45 hpf wild type embryos biol rep 3", "The data was processed through the Galaxy project using Trimmomatic version 0.39 Sequences were pseudoaligned and quantified at TPM values using Kallisto. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file includes TPM values for each transcript at 45 hpf 4 dpf and 7 dpf", "whole body", null, "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina\u2019s TruSeq\u00ae stranded mRNA library preparation kit.", null, "tissue:whole body|genotype:WT|time:45 hpf", "GSM8655445", "GSM8655445: Whole body 45 hpf wild type embryos biol rep 3; Danio rerio; RNA Seq", "GSM8655445 r1", "GSM8655445", "1", "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina's TruSeq\u00ae stranded mRNA library preparation kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP548139", null, null, "45 hpf_WT 3_R1.fastq.gz 45 hpf_WT 3_R2.fastq.gz", "fastq fastq", 14580346184.0, 48279292.0, "GSM8655445 r1", "0:151 1:151", "A:3858927638;C:3450290173;G:3271701209;T:3998202503;N:1224661", 151, 151, null, null, 3858927638, 3450290173, 3271701209, 3998202503, 1224661, "SRX26906740", "SRS23386328", null, null, "Barske Lab, Human Genetics, Cincinnati Children's Hospital", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-11-27", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [34222, "SRR31539747", "SRX26906739", "SRS23386325", "SRP548139", "PRJNA1191617", "Sox10 is required for systemic initiation of bone mineralization", "GSE283071", "Transcriptome Analysis", "Heterozygous variants in SOX10 cause syndromes affecting pigmentation digestion hearing and neural development primarily attributable to failed differentiation or loss of non skeletal neural crest derivatives. We report here an additional novel requirement for Sox10 in bone mineralization. Neither crest nor mesoderm derived bones initiate mineralization on time in zebrafish sox10 mutants despite normal osteoblast differentiation and matrix production. Mutants are deficient in the Trpv6+ ionocytes that take up calcium from the environment resulting in severe calcium deficiency. As these ionocytes derive from ectoderm not crest we hypothesized that the primary defect resides in a separate organ that systemically regulates ionocyte numbers. RNAseq revealed significantly elevated stanniocalcin Stc1a an anti hypercalcemic hormone in sox10 mutants. Stc1a inhibits calcium uptake in fish by repressing trpv6 expression and Trpv6+ ionocyte proliferation. Epistasis assays confirm excess Stc1a as the proximate cause of the calcium deficit. The pronephros derived glands that synthesize Stc1a interact with sox10+ cells but these cells are missing in mutants. We conclude that sox10+ crest derived cells non autonomously limit Stc1a production to allow the inaugural wave of calcium uptake necessary to initiate bone mineralization. Overall design: Bulk RNA seq was performed on pooled whole body zebrafish wild type and sox10 mutant larvae at 45 hpf 4 dpf and 7 dpf. Total of 18 samples. 45 hpf 3 replicates: controls n = 10 20 & 25; mutants n = 10 15 & 15 embryos 4 dpf 3 replicates: controls n = 10 15 & 12; mutants n = 10 11 & 12 embryos and 7 dpf 3 replicates: controls n = 12 30 & 18; mutants = 18 12 & 7 embryos", null, "pubmed:39791977", null, "Whole body 45 hpf wild type embryos biol rep 2", "GSM8655444", null, "source name:whole body|tissue:whole body|genotype:WT|time:45 hpf|geo loc name:missing|collection date:missing", "Whole body 45 hpf wild type embryos biol rep 2", "The data was processed through the Galaxy project using Trimmomatic version 0.39 Sequences were pseudoaligned and quantified at TPM values using Kallisto. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file includes TPM values for each transcript at 45 hpf 4 dpf and 7 dpf", "whole body", null, "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina\u2019s TruSeq\u00ae stranded mRNA library preparation kit.", null, "tissue:whole body|genotype:WT|time:45 hpf", "GSM8655444", "GSM8655444: Whole body 45 hpf wild type embryos biol rep 2; Danio rerio; RNA Seq", "GSM8655444 r1", "GSM8655444", "1", "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina's TruSeq\u00ae stranded mRNA library preparation kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP548139", null, null, "45 hpf_WT 2_R1.fastq.gz 45 hpf_WT_2_R2.fastq.gz", "fastq fastq", 15005198878.0, 49686089.0, "GSM8655444 r1", "0:151 1:151", "A:3950487195;C:3509517845;G:3418800225;T:4125159820;N:1233793", 151, 151, null, null, 3950487195, 3509517845, 3418800225, 4125159820, 1233793, "SRX26906739", "SRS23386325", null, null, "Barske Lab, Human Genetics, Cincinnati Children's Hospital", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-11-27", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [34223, "SRR31539748", "SRX26906738", "SRS23386324", "SRP548139", "PRJNA1191617", "Sox10 is required for systemic initiation of bone mineralization", "GSE283071", "Transcriptome Analysis", "Heterozygous variants in SOX10 cause syndromes affecting pigmentation digestion hearing and neural development primarily attributable to failed differentiation or loss of non skeletal neural crest derivatives. We report here an additional novel requirement for Sox10 in bone mineralization. Neither crest nor mesoderm derived bones initiate mineralization on time in zebrafish sox10 mutants despite normal osteoblast differentiation and matrix production. Mutants are deficient in the Trpv6+ ionocytes that take up calcium from the environment resulting in severe calcium deficiency. As these ionocytes derive from ectoderm not crest we hypothesized that the primary defect resides in a separate organ that systemically regulates ionocyte numbers. RNAseq revealed significantly elevated stanniocalcin Stc1a an anti hypercalcemic hormone in sox10 mutants. Stc1a inhibits calcium uptake in fish by repressing trpv6 expression and Trpv6+ ionocyte proliferation. Epistasis assays confirm excess Stc1a as the proximate cause of the calcium deficit. The pronephros derived glands that synthesize Stc1a interact with sox10+ cells but these cells are missing in mutants. We conclude that sox10+ crest derived cells non autonomously limit Stc1a production to allow the inaugural wave of calcium uptake necessary to initiate bone mineralization. Overall design: Bulk RNA seq was performed on pooled whole body zebrafish wild type and sox10 mutant larvae at 45 hpf 4 dpf and 7 dpf. Total of 18 samples. 45 hpf 3 replicates: controls n = 10 20 & 25; mutants n = 10 15 & 15 embryos 4 dpf 3 replicates: controls n = 10 15 & 12; mutants n = 10 11 & 12 embryos and 7 dpf 3 replicates: controls n = 12 30 & 18; mutants = 18 12 & 7 embryos", null, "pubmed:39791977", null, "Whole body 45 hpf wild type embryos biol rep 1", "GSM8655443", null, "source name:whole body|tissue:whole body|genotype:WT|time:45 hpf|geo loc name:missing|collection date:missing", "Whole body 45 hpf wild type embryos biol rep 1", "The data was processed through the Galaxy project using Trimmomatic version 0.39 Sequences were pseudoaligned and quantified at TPM values using Kallisto. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file includes TPM values for each transcript at 45 hpf 4 dpf and 7 dpf", "whole body", null, "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina\u2019s TruSeq\u00ae stranded mRNA library preparation kit.", null, "tissue:whole body|genotype:WT|time:45 hpf", "GSM8655443", "GSM8655443: Whole body 45 hpf wild type embryos biol rep 1; Danio rerio; RNA Seq", "GSM8655443 r1", "GSM8655443", "1", "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina's TruSeq\u00ae stranded mRNA library preparation kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP548139", null, null, "45 hpf_WT 1_R1.fastq.gz 45 hpf_WT 1_R2.fastq.gz", "fastq fastq", 14884992912.0, 49288056.0, "GSM8655443 r1", "0:151 1:151", "A:3878762924;C:3475070121;G:3485186845;T:4044768200;N:1204822", 151, 151, null, null, 3878762924, 3475070121, 3485186845, 4044768200, 1204822, "SRX26906738", "SRS23386324", null, null, "Barske Lab, Human Genetics, Cincinnati Children's Hospital", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-11-27", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [39771, "SRR2136297", "SRX1125768", "SRS1017739", "SRP061855", "PRJNA291531", "Identification of qkia/c target genes", "GSE71573", "Transcriptome Analysis", "Quaking are RNA binding proteins which are known to regulate the expression of different genes at the post transcriptional level. Genetic interference with quaking a qkia and quaking c qkic leads to major myofibril defects during zebrafish development without xxx early muscle differentiation. In order to understand how qkia and qkic jointly regulate myofibril formation we performed a comparative analysis of the transcriptome of qkia/qkic qkia mutant injected with qkic morpholino versus control embryos. We show that Quaking activity is required for accumulation of the muscle specific tropomyosin 3 transcript tpm3.1. Whereas interference with tmp3.1 function disrupts myofibril formation reintroducing tpm3.1 transcripts into embryos with reduced Quaking activity can restore structured myofibrils. Thus we identify tropomyosin as an essential component in the process of myofibril formation and as a relay downstream of the regulator proteins Quaking. Overall design: Transcriptome of control versus qkia/qkic embryos at 24 26hpf. Biological triplicate were prepared for both condition 3x2 samples.", null, "pubmed:28867488", null, "Qkiac 3", "GSM1838798", null, "tissue:trunk|Stage:embryo 24 26hpf|genotype:qkia / |injection:qkic morpholino", "Qkiac 3", "Before mapping poly N read tails were trimmed reads \u226440 bases were removed and reads with quality mean \u226430 were discarded. To obtain the counts on the exon features reads were then aligned against the genome using Bowtie version 0.12.9 with arguments n 2 l 34 e 70 k 2 best. To obtain the counts on the gene features reads were then aligned against the genome using STAR version 2.4.0j and Ensembl annotation v78. Alignments from reads matching more than once on the reference genome were removed using Java version of samtools. To compute gene expression Danio rerio Zv9 GFF3 genome annotation version 78 from Ensembl database was used. All overlapping regions between alignments and referenced exons were counted using HTSeq count 0.5.3. To obtain the counts on the exon features we used the bowtie alignments excluding the junction reads. HTSeq count was used with arguments: genomictype=exon attributeid=Name stranded=no overlapmode=union removeambiguouscases=false. To obtain the counts on the gene features we used the STAR alignments including the junction reads. HTSeq count was used with arguments: genomictype=exon stranded=no overlapmode=union removeambiguouscases=false and attributeid=Alias where Alias was the corresponding parent gene ID. The sample counts were normalized using DESeq 1.8.3. Statistical treatments and differential analyses were also performed using DESeq 1.8.3 with arguments: disp.est.method=pooled disp.est.sharing.mode=maximum disp.est.fit.type=parametric Genome build: Danio rerio Zv9 Supplementary files format and content: tab delimited text files include normalized reads counts for each Sample using DESeq 1.8.3 with arguments: disp.est.method=pooled disp.est.sharing.mode=maximum disp.est.fit.type=parametric.", "trunk", "Zebrafish trunks at 24 26hpf were dissected removal of head and yolk flash frozen on dry ice and stored at 80\u00b0C until RNA extraction.", "total RNA was extracted using the RNeasy Plus Universal Mini kit Qiagen and treated with Dnase. Messenger polyA+ RNAs were purified from 0.7 \u00b5g of total RNA using oligodT. Libraries were prepared using the strand non specific RNA Seq library preparation TruSeq RNA Sample Prep v2 kit Illumina. Libraries were multiplexed by 6 on 2 flowcell lanes. A 50 bp read sequencing was performed on a HiSeq 1500 device Illumina. A mean of 27459238 \u00b1 1611623 million passing Illumina quality filter reads was obtained for each of the 6 samples.", "Embryos resulting from crossing between qkia+/ fish were injected at a cell stage with qkic morpholino or control morpholino 0 6pmol. We let them develop until 24 26hpf stage where we could morphologically identify control embryos sibling qkia+/+ or qkia+/ with control morpholino and double qkia/c loss of function embryos qkia / with qkic morpholino.", "Stage:embryo 24 26hpf|genotype:qkia / |injection:qkic morpholino", "GSM1838798", "GSM1838798: Qkiac 3; Danio rerio; RNA Seq", "GSM1838798", null, "1", "total RNA was extracted using the RNeasy Plus Universal Mini kit Qiagen and treated with Dnase. Messenger polyA+ RNAs were purified from 0.7 \u00b5g of total RNA using oligodT. Libraries were prepared using the strand non specific RNA Seq library preparation TruSeq RNA Sample Prep v2 kit Illumina. Libraries were multiplexed by 6 on 2 flowcell lanes. A 50 bp read sequencing was performed on a HiSeq 1500 device Illumina. A mean of 27459238 \u00b1 1611623 million passing Illumina quality filter reads was obtained for each of the 6 samples.", "GEO Accession:GSM1838798", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 1500", null, "SRP061855", null, null, "Sample6_CTTGTA.fastq.bz2", "fastq", 2507001849.0, 49156899.0, "GSM1838798 r1", "0:51", "A:683306529;C:570965534;G:570449436;T:679826815;N:2453535", 51, null, null, null, 683306529, 570965534, 570449436, 679826815, 2453535, "SRX1125768", "SRS1017739", "SRA281148", "GEO", "Plateforme transcriptome, Biologie, Ecole Normale Sup\u00e9rieure", 1, 0.92678, null, 0.08779, null, 0.72892, null, 0.48795, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "France", "2015-07-30", "Pharyngula", "Embryo", "Trunk", "Surface Structure"], [39772, "SRR2136296", "SRX1125767", "SRS1017740", "SRP061855", "PRJNA291531", "Identification of qkia/c target genes", "GSE71573", "Transcriptome Analysis", "Quaking are RNA binding proteins which are known to regulate the expression of different genes at the post transcriptional level. Genetic interference with quaking a qkia and quaking c qkic leads to major myofibril defects during zebrafish development without xxx early muscle differentiation. In order to understand how qkia and qkic jointly regulate myofibril formation we performed a comparative analysis of the transcriptome of qkia/qkic qkia mutant injected with qkic morpholino versus control embryos. We show that Quaking activity is required for accumulation of the muscle specific tropomyosin 3 transcript tpm3.1. Whereas interference with tmp3.1 function disrupts myofibril formation reintroducing tpm3.1 transcripts into embryos with reduced Quaking activity can restore structured myofibrils. Thus we identify tropomyosin as an essential component in the process of myofibril formation and as a relay downstream of the regulator proteins Quaking. Overall design: Transcriptome of control versus qkia/qkic embryos at 24 26hpf. Biological triplicate were prepared for both condition 3x2 samples.", null, "pubmed:28867488", null, "Qkiac 2", "GSM1838797", null, "tissue:trunk|Stage:embryo 24 26hpf|genotype:qkia / |injection:qkic morpholino", "Qkiac 2", "Before mapping poly N read tails were trimmed reads \u226440 bases were removed and reads with quality mean \u226430 were discarded. To obtain the counts on the exon features reads were then aligned against the genome using Bowtie version 0.12.9 with arguments n 2 l 34 e 70 k 2 best. To obtain the counts on the gene features reads were then aligned against the genome using STAR version 2.4.0j and Ensembl annotation v78. Alignments from reads matching more than once on the reference genome were removed using Java version of samtools. To compute gene expression Danio rerio Zv9 GFF3 genome annotation version 78 from Ensembl database was used. All overlapping regions between alignments and referenced exons were counted using HTSeq count 0.5.3. To obtain the counts on the exon features we used the bowtie alignments excluding the junction reads. HTSeq count was used with arguments: genomictype=exon attributeid=Name stranded=no overlapmode=union removeambiguouscases=false. To obtain the counts on the gene features we used the STAR alignments including the junction reads. HTSeq count was used with arguments: genomictype=exon stranded=no overlapmode=union removeambiguouscases=false and attributeid=Alias where Alias was the corresponding parent gene ID. The sample counts were normalized using DESeq 1.8.3. Statistical treatments and differential analyses were also performed using DESeq 1.8.3 with arguments: disp.est.method=pooled disp.est.sharing.mode=maximum disp.est.fit.type=parametric Genome build: Danio rerio Zv9 Supplementary files format and content: tab delimited text files include normalized reads counts for each Sample using DESeq 1.8.3 with arguments: disp.est.method=pooled disp.est.sharing.mode=maximum disp.est.fit.type=parametric.", "trunk", "Zebrafish trunks at 24 26hpf were dissected removal of head and yolk flash frozen on dry ice and stored at 80\u00b0C until RNA extraction.", "total RNA was extracted using the RNeasy Plus Universal Mini kit Qiagen and treated with Dnase. Messenger polyA+ RNAs were purified from 0.7 \u00b5g of total RNA using oligodT. Libraries were prepared using the strand non specific RNA Seq library preparation TruSeq RNA Sample Prep v2 kit Illumina. Libraries were multiplexed by 6 on 2 flowcell lanes. A 50 bp read sequencing was performed on a HiSeq 1500 device Illumina. A mean of 27459238 \u00b1 1611623 million passing Illumina quality filter reads was obtained for each of the 6 samples.", "Embryos resulting from crossing between qkia+/ fish were injected at a cell stage with qkic morpholino or control morpholino 0 6pmol. We let them develop until 24 26hpf stage where we could morphologically identify control embryos sibling qkia+/+ or qkia+/ with control morpholino and double qkia/c loss of function embryos qkia / with qkic morpholino.", "Stage:embryo 24 26hpf|genotype:qkia / |injection:qkic morpholino", "GSM1838797", "GSM1838797: Qkiac 2; Danio rerio; RNA Seq", "GSM1838797", null, "1", "total RNA was extracted using the RNeasy Plus Universal Mini kit Qiagen and treated with Dnase. Messenger polyA+ RNAs were purified from 0.7 \u00b5g of total RNA using oligodT. Libraries were prepared using the strand non specific RNA Seq library preparation TruSeq RNA Sample Prep v2 kit Illumina. Libraries were multiplexed by 6 on 2 flowcell lanes. A 50 bp read sequencing was performed on a HiSeq 1500 device Illumina. A mean of 27459238 \u00b1 1611623 million passing Illumina quality filter reads was obtained for each of the 6 samples.", "GEO Accession:GSM1838797", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 1500", null, "SRP061855", null, null, "Sample5_CAGATC.fastq.bz2", "fastq", 2850272086.0, 55887688.0, "GSM1838797 r1", "0:51.00", "A:775475703;C:648531668;G:652753738;T:770730439;N:2780538", 51, null, null, null, 775475703, 648531668, 652753738, 770730439, 2780538, "SRX1125767", "SRS1017740", "SRA281148", "GEO", "Plateforme transcriptome, Biologie, Ecole Normale Sup\u00e9rieure", 1, 0.92802, null, 0.08465, null, 0.72744, null, 0.48656, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "France", "2015-07-30", "Pharyngula", "Embryo", "Trunk", "Surface Structure"], [39773, "SRR2136295", "SRX1125766", "SRS1017741", "SRP061855", "PRJNA291531", "Identification of qkia/c target genes", "GSE71573", "Transcriptome Analysis", "Quaking are RNA binding proteins which are known to regulate the expression of different genes at the post transcriptional level. Genetic interference with quaking a qkia and quaking c qkic leads to major myofibril defects during zebrafish development without xxx early muscle differentiation. In order to understand how qkia and qkic jointly regulate myofibril formation we performed a comparative analysis of the transcriptome of qkia/qkic qkia mutant injected with qkic morpholino versus control embryos. We show that Quaking activity is required for accumulation of the muscle specific tropomyosin 3 transcript tpm3.1. Whereas interference with tmp3.1 function disrupts myofibril formation reintroducing tpm3.1 transcripts into embryos with reduced Quaking activity can restore structured myofibrils. Thus we identify tropomyosin as an essential component in the process of myofibril formation and as a relay downstream of the regulator proteins Quaking. Overall design: Transcriptome of control versus qkia/qkic embryos at 24 26hpf. Biological triplicate were prepared for both condition 3x2 samples.", null, "pubmed:28867488", null, "Qkiac 1", "GSM1838796", null, "tissue:trunk|Stage:embryo 24 26hpf|genotype:qkia / |injection:qkic morpholino", "Qkiac 1", "Before mapping poly N read tails were trimmed reads \u226440 bases were removed and reads with quality mean \u226430 were discarded. To obtain the counts on the exon features reads were then aligned against the genome using Bowtie version 0.12.9 with arguments n 2 l 34 e 70 k 2 best. To obtain the counts on the gene features reads were then aligned against the genome using STAR version 2.4.0j and Ensembl annotation v78. Alignments from reads matching more than once on the reference genome were removed using Java version of samtools. To compute gene expression Danio rerio Zv9 GFF3 genome annotation version 78 from Ensembl database was used. All overlapping regions between alignments and referenced exons were counted using HTSeq count 0.5.3. To obtain the counts on the exon features we used the bowtie alignments excluding the junction reads. HTSeq count was used with arguments: genomictype=exon attributeid=Name stranded=no overlapmode=union removeambiguouscases=false. To obtain the counts on the gene features we used the STAR alignments including the junction reads. HTSeq count was used with arguments: genomictype=exon stranded=no overlapmode=union removeambiguouscases=false and attributeid=Alias where Alias was the corresponding parent gene ID. The sample counts were normalized using DESeq 1.8.3. Statistical treatments and differential analyses were also performed using DESeq 1.8.3 with arguments: disp.est.method=pooled disp.est.sharing.mode=maximum disp.est.fit.type=parametric Genome build: Danio rerio Zv9 Supplementary files format and content: tab delimited text files include normalized reads counts for each Sample using DESeq 1.8.3 with arguments: disp.est.method=pooled disp.est.sharing.mode=maximum disp.est.fit.type=parametric.", "trunk", "Zebrafish trunks at 24 26hpf were dissected removal of head and yolk flash frozen on dry ice and stored at 80\u00b0C until RNA extraction.", "total RNA was extracted using the RNeasy Plus Universal Mini kit Qiagen and treated with Dnase. Messenger polyA+ RNAs were purified from 0.7 \u00b5g of total RNA using oligodT. Libraries were prepared using the strand non specific RNA Seq library preparation TruSeq RNA Sample Prep v2 kit Illumina. Libraries were multiplexed by 6 on 2 flowcell lanes. A 50 bp read sequencing was performed on a HiSeq 1500 device Illumina. A mean of 27459238 \u00b1 1611623 million passing Illumina quality filter reads was obtained for each of the 6 samples.", "Embryos resulting from crossing between qkia+/ fish were injected at a cell stage with qkic morpholino or control morpholino 0 6pmol. We let them develop until 24 26hpf stage where we could morphologically identify control embryos sibling qkia+/+ or qkia+/ with control morpholino and double qkia/c loss of function embryos qkia / with qkic morpholino.", "Stage:embryo 24 26hpf|genotype:qkia / |injection:qkic morpholino", "GSM1838796", "GSM1838796: Qkiac 1; Danio rerio; RNA Seq", "GSM1838796", null, "1", "total RNA was extracted using the RNeasy Plus Universal Mini kit Qiagen and treated with Dnase. Messenger polyA+ RNAs were purified from 0.7 \u00b5g of total RNA using oligodT. Libraries were prepared using the strand non specific RNA Seq library preparation TruSeq RNA Sample Prep v2 kit Illumina. Libraries were multiplexed by 6 on 2 flowcell lanes. A 50 bp read sequencing was performed on a HiSeq 1500 device Illumina. A mean of 27459238 \u00b1 1611623 million passing Illumina quality filter reads was obtained for each of the 6 samples.", "GEO Accession:GSM1838796", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 1500", null, "SRP061855", null, null, "Sample4_GCCAAT.fastq.bz2", "fastq", 2881827420.0, 56506420.0, "GSM1838796 r1", "0:51", "A:782512581;C:658453854;G:659856487;T:778195522;N:2808976", 51, null, null, null, 782512581, 658453854, 659856487, 778195522, 2808976, "SRX1125766", "SRS1017741", "SRA281148", "GEO", "Plateforme transcriptome, Biologie, Ecole Normale Sup\u00e9rieure", 1, 0.92629, null, 0.08316, null, 0.7276, null, 0.47801, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "France", "2015-07-30", "Pharyngula", "Embryo", "Trunk", "Surface Structure"], [39774, "SRR2136294", "SRX1125765", "SRS1017742", "SRP061855", "PRJNA291531", "Identification of qkia/c target genes", "GSE71573", "Transcriptome Analysis", "Quaking are RNA binding proteins which are known to regulate the expression of different genes at the post transcriptional level. Genetic interference with quaking a qkia and quaking c qkic leads to major myofibril defects during zebrafish development without xxx early muscle differentiation. In order to understand how qkia and qkic jointly regulate myofibril formation we performed a comparative analysis of the transcriptome of qkia/qkic qkia mutant injected with qkic morpholino versus control embryos. We show that Quaking activity is required for accumulation of the muscle specific tropomyosin 3 transcript tpm3.1. Whereas interference with tmp3.1 function disrupts myofibril formation reintroducing tpm3.1 transcripts into embryos with reduced Quaking activity can restore structured myofibrils. Thus we identify tropomyosin as an essential component in the process of myofibril formation and as a relay downstream of the regulator proteins Quaking. Overall design: Transcriptome of control versus qkia/qkic embryos at 24 26hpf. Biological triplicate were prepared for both condition 3x2 samples.", null, "pubmed:28867488", null, "Control 3", "GSM1838795", null, "tissue:trunk|Stage:embryo 24 26hpf|genotype:qkia+/+ or qkia+/ |injection:control morpholino", "Control 3", "Before mapping poly N read tails were trimmed reads \u226440 bases were removed and reads with quality mean \u226430 were discarded. To obtain the counts on the exon features reads were then aligned against the genome using Bowtie version 0.12.9 with arguments n 2 l 34 e 70 k 2 best. To obtain the counts on the gene features reads were then aligned against the genome using STAR version 2.4.0j and Ensembl annotation v78. Alignments from reads matching more than once on the reference genome were removed using Java version of samtools. To compute gene expression Danio rerio Zv9 GFF3 genome annotation version 78 from Ensembl database was used. All overlapping regions between alignments and referenced exons were counted using HTSeq count 0.5.3. To obtain the counts on the exon features we used the bowtie alignments excluding the junction reads. HTSeq count was used with arguments: genomictype=exon attributeid=Name stranded=no overlapmode=union removeambiguouscases=false. To obtain the counts on the gene features we used the STAR alignments including the junction reads. HTSeq count was used with arguments: genomictype=exon stranded=no overlapmode=union removeambiguouscases=false and attributeid=Alias where Alias was the corresponding parent gene ID. The sample counts were normalized using DESeq 1.8.3. Statistical treatments and differential analyses were also performed using DESeq 1.8.3 with arguments: disp.est.method=pooled disp.est.sharing.mode=maximum disp.est.fit.type=parametric Genome build: Danio rerio Zv9 Supplementary files format and content: tab delimited text files include normalized reads counts for each Sample using DESeq 1.8.3 with arguments: disp.est.method=pooled disp.est.sharing.mode=maximum disp.est.fit.type=parametric.", "trunk", "Zebrafish trunks at 24 26hpf were dissected removal of head and yolk flash frozen on dry ice and stored at 80\u00b0C until RNA extraction.", "total RNA was extracted using the RNeasy Plus Universal Mini kit Qiagen and treated with Dnase. Messenger polyA+ RNAs were purified from 0.7 \u00b5g of total RNA using oligodT. Libraries were prepared using the strand non specific RNA Seq library preparation TruSeq RNA Sample Prep v2 kit Illumina. Libraries were multiplexed by 6 on 2 flowcell lanes. A 50 bp read sequencing was performed on a HiSeq 1500 device Illumina. A mean of 27459238 \u00b1 1611623 million passing Illumina quality filter reads was obtained for each of the 6 samples.", "Embryos resulting from crossing between qkia+/ fish were injected at a cell stage with qkic morpholino or control morpholino 0 6pmol. We let them develop until 24 26hpf stage where we could morphologically identify control embryos sibling qkia+/+ or qkia+/ with control morpholino and double qkia/c loss of function embryos qkia / with qkic morpholino.", "Stage:embryo 24 26hpf|genotype:qkia+/+ or qkia+/ |injection:control morpholino", "GSM1838795", "GSM1838795: Control 3; Danio rerio; RNA Seq", "GSM1838795", null, "1", "total RNA was extracted using the RNeasy Plus Universal Mini kit Qiagen and treated with Dnase. Messenger polyA+ RNAs were purified from 0.7 \u00b5g of total RNA using oligodT. Libraries were prepared using the strand non specific RNA Seq library preparation TruSeq RNA Sample Prep v2 kit Illumina. Libraries were multiplexed by 6 on 2 flowcell lanes. A 50 bp read sequencing was performed on a HiSeq 1500 device Illumina. A mean of 27459238 \u00b1 1611623 million passing Illumina quality filter reads was obtained for each of the 6 samples.", "GEO Accession:GSM1838795", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 1500", null, "SRP061855", null, null, "Sample3_ACAGTG.fastq.bz2", "fastq", 2611892782.0, 51213584.0, "GSM1838795 r1", "0:51.00", "A:707525221;C:599202602;G:597562199;T:705047589;N:2555171", 51, null, null, null, 707525221, 599202602, 597562199, 705047589, 2555171, "SRX1125765", "SRS1017742", "SRA281148", "GEO", "Plateforme transcriptome, Biologie, Ecole Normale Sup\u00e9rieure", 1, 0.9282, null, 0.09007, null, 0.72147, null, 0.47387, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "France", "2015-07-30", "Pharyngula", "Embryo", "Trunk", "Surface Structure"], [39775, "SRR2136293", "SRX1125764", "SRS1017743", "SRP061855", "PRJNA291531", "Identification of qkia/c target genes", "GSE71573", "Transcriptome Analysis", "Quaking are RNA binding proteins which are known to regulate the expression of different genes at the post transcriptional level. Genetic interference with quaking a qkia and quaking c qkic leads to major myofibril defects during zebrafish development without xxx early muscle differentiation. In order to understand how qkia and qkic jointly regulate myofibril formation we performed a comparative analysis of the transcriptome of qkia/qkic qkia mutant injected with qkic morpholino versus control embryos. We show that Quaking activity is required for accumulation of the muscle specific tropomyosin 3 transcript tpm3.1. Whereas interference with tmp3.1 function disrupts myofibril formation reintroducing tpm3.1 transcripts into embryos with reduced Quaking activity can restore structured myofibrils. Thus we identify tropomyosin as an essential component in the process of myofibril formation and as a relay downstream of the regulator proteins Quaking. Overall design: Transcriptome of control versus qkia/qkic embryos at 24 26hpf. Biological triplicate were prepared for both condition 3x2 samples.", null, "pubmed:28867488", null, "Control 2", "GSM1838794", null, "tissue:trunk|Stage:embryo 24 26hpf|genotype:qkia+/+ or qkia+/ |injection:control morpholino", "Control 2", "Before mapping poly N read tails were trimmed reads \u226440 bases were removed and reads with quality mean \u226430 were discarded. To obtain the counts on the exon features reads were then aligned against the genome using Bowtie version 0.12.9 with arguments n 2 l 34 e 70 k 2 best. To obtain the counts on the gene features reads were then aligned against the genome using STAR version 2.4.0j and Ensembl annotation v78. Alignments from reads matching more than once on the reference genome were removed using Java version of samtools. To compute gene expression Danio rerio Zv9 GFF3 genome annotation version 78 from Ensembl database was used. All overlapping regions between alignments and referenced exons were counted using HTSeq count 0.5.3. To obtain the counts on the exon features we used the bowtie alignments excluding the junction reads. HTSeq count was used with arguments: genomictype=exon attributeid=Name stranded=no overlapmode=union removeambiguouscases=false. To obtain the counts on the gene features we used the STAR alignments including the junction reads. HTSeq count was used with arguments: genomictype=exon stranded=no overlapmode=union removeambiguouscases=false and attributeid=Alias where Alias was the corresponding parent gene ID. The sample counts were normalized using DESeq 1.8.3. Statistical treatments and differential analyses were also performed using DESeq 1.8.3 with arguments: disp.est.method=pooled disp.est.sharing.mode=maximum disp.est.fit.type=parametric Genome build: Danio rerio Zv9 Supplementary files format and content: tab delimited text files include normalized reads counts for each Sample using DESeq 1.8.3 with arguments: disp.est.method=pooled disp.est.sharing.mode=maximum disp.est.fit.type=parametric.", "trunk", "Zebrafish trunks at 24 26hpf were dissected removal of head and yolk flash frozen on dry ice and stored at 80\u00b0C until RNA extraction.", "total RNA was extracted using the RNeasy Plus Universal Mini kit Qiagen and treated with Dnase. Messenger polyA+ RNAs were purified from 0.7 \u00b5g of total RNA using oligodT. Libraries were prepared using the strand non specific RNA Seq library preparation TruSeq RNA Sample Prep v2 kit Illumina. Libraries were multiplexed by 6 on 2 flowcell lanes. A 50 bp read sequencing was performed on a HiSeq 1500 device Illumina. A mean of 27459238 \u00b1 1611623 million passing Illumina quality filter reads was obtained for each of the 6 samples.", "Embryos resulting from crossing between qkia+/ fish were injected at a cell stage with qkic morpholino or control morpholino 0 6pmol. We let them develop until 24 26hpf stage where we could morphologically identify control embryos sibling qkia+/+ or qkia+/ with control morpholino and double qkia/c loss of function embryos qkia / with qkic morpholino.", "Stage:embryo 24 26hpf|genotype:qkia+/+ or qkia+/ |injection:control morpholino", "GSM1838794", "GSM1838794: Control 2; Danio rerio; RNA Seq", "GSM1838794", null, "1", "total RNA was extracted using the RNeasy Plus Universal Mini kit Qiagen and treated with Dnase. Messenger polyA+ RNAs were purified from 0.7 \u00b5g of total RNA using oligodT. Libraries were prepared using the strand non specific RNA Seq library preparation TruSeq RNA Sample Prep v2 kit Illumina. Libraries were multiplexed by 6 on 2 flowcell lanes. A 50 bp read sequencing was performed on a HiSeq 1500 device Illumina. A mean of 27459238 \u00b1 1611623 million passing Illumina quality filter reads was obtained for each of the 6 samples.", "GEO Accession:GSM1838794", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 1500", null, "SRP061855", null, null, "Sample2_TGACCA.fastq.bz2", "fastq", 2686989417.0, 52686067.0, "GSM1838794 r1", "0:51", "A:728607816;C:615847292;G:614033432;T:725881768;N:2619109", 51, null, null, null, 728607816, 615847292, 614033432, 725881768, 2619109, "SRX1125764", "SRS1017743", "SRA281148", "GEO", "Plateforme transcriptome, Biologie, Ecole Normale Sup\u00e9rieure", 1, 0.92483, null, 0.09787, null, 0.7203, null, 0.45884, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "France", "2015-07-30", "Pharyngula", "Embryo", "Trunk", "Surface Structure"], [39776, "SRR2136292", "SRX1125763", "SRS1017744", "SRP061855", "PRJNA291531", "Identification of qkia/c target genes", "GSE71573", "Transcriptome Analysis", "Quaking are RNA binding proteins which are known to regulate the expression of different genes at the post transcriptional level. Genetic interference with quaking a qkia and quaking c qkic leads to major myofibril defects during zebrafish development without xxx early muscle differentiation. In order to understand how qkia and qkic jointly regulate myofibril formation we performed a comparative analysis of the transcriptome of qkia/qkic qkia mutant injected with qkic morpholino versus control embryos. We show that Quaking activity is required for accumulation of the muscle specific tropomyosin 3 transcript tpm3.1. Whereas interference with tmp3.1 function disrupts myofibril formation reintroducing tpm3.1 transcripts into embryos with reduced Quaking activity can restore structured myofibrils. Thus we identify tropomyosin as an essential component in the process of myofibril formation and as a relay downstream of the regulator proteins Quaking. Overall design: Transcriptome of control versus qkia/qkic embryos at 24 26hpf. Biological triplicate were prepared for both condition 3x2 samples.", null, "pubmed:28867488", null, "Control 1", "GSM1838793", null, "tissue:trunk|Stage:embryo 24 26hpf|genotype:qkia+/+ or qkia+/ |injection:control morpholino", "Control 1", "Before mapping poly N read tails were trimmed reads \u226440 bases were removed and reads with quality mean \u226430 were discarded. To obtain the counts on the exon features reads were then aligned against the genome using Bowtie version 0.12.9 with arguments n 2 l 34 e 70 k 2 best. To obtain the counts on the gene features reads were then aligned against the genome using STAR version 2.4.0j and Ensembl annotation v78. Alignments from reads matching more than once on the reference genome were removed using Java version of samtools. To compute gene expression Danio rerio Zv9 GFF3 genome annotation version 78 from Ensembl database was used. All overlapping regions between alignments and referenced exons were counted using HTSeq count 0.5.3. To obtain the counts on the exon features we used the bowtie alignments excluding the junction reads. HTSeq count was used with arguments: genomictype=exon attributeid=Name stranded=no overlapmode=union removeambiguouscases=false. To obtain the counts on the gene features we used the STAR alignments including the junction reads. HTSeq count was used with arguments: genomictype=exon stranded=no overlapmode=union removeambiguouscases=false and attributeid=Alias where Alias was the corresponding parent gene ID. The sample counts were normalized using DESeq 1.8.3. Statistical treatments and differential analyses were also performed using DESeq 1.8.3 with arguments: disp.est.method=pooled disp.est.sharing.mode=maximum disp.est.fit.type=parametric Genome build: Danio rerio Zv9 Supplementary files format and content: tab delimited text files include normalized reads counts for each Sample using DESeq 1.8.3 with arguments: disp.est.method=pooled disp.est.sharing.mode=maximum disp.est.fit.type=parametric.", "trunk", "Zebrafish trunks at 24 26hpf were dissected removal of head and yolk flash frozen on dry ice and stored at 80\u00b0C until RNA extraction.", "total RNA was extracted using the RNeasy Plus Universal Mini kit Qiagen and treated with Dnase. Messenger polyA+ RNAs were purified from 0.7 \u00b5g of total RNA using oligodT. Libraries were prepared using the strand non specific RNA Seq library preparation TruSeq RNA Sample Prep v2 kit Illumina. Libraries were multiplexed by 6 on 2 flowcell lanes. A 50 bp read sequencing was performed on a HiSeq 1500 device Illumina. A mean of 27459238 \u00b1 1611623 million passing Illumina quality filter reads was obtained for each of the 6 samples.", "Embryos resulting from crossing between qkia+/ fish were injected at a cell stage with qkic morpholino or control morpholino 0 6pmol. We let them develop until 24 26hpf stage where we could morphologically identify control embryos sibling qkia+/+ or qkia+/ with control morpholino and double qkia/c loss of function embryos qkia / with qkic morpholino.", "Stage:embryo 24 26hpf|genotype:qkia+/+ or qkia+/ |injection:control morpholino", "GSM1838793", "GSM1838793: Control 1; Danio rerio; RNA Seq", "GSM1838793", null, "1", "total RNA was extracted using the RNeasy Plus Universal Mini kit Qiagen and treated with Dnase. Messenger polyA+ RNAs were purified from 0.7 \u00b5g of total RNA using oligodT. Libraries were prepared using the strand non specific RNA Seq library preparation TruSeq RNA Sample Prep v2 kit Illumina. Libraries were multiplexed by 6 on 2 flowcell lanes. A 50 bp read sequencing was performed on a HiSeq 1500 device Illumina. A mean of 27459238 \u00b1 1611623 million passing Illumina quality filter reads was obtained for each of the 6 samples.", "GEO Accession:GSM1838793", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 1500", null, "SRP061855", null, null, "Sample1_CGATGT.fastq.bz2", "fastq", 2920348075.0, 57261727.0, "GSM1838793 r1", "0:51.00", "A:788971393;C:671861209;G:669575375;T:787095383;N:2844715", 51, null, null, null, 788971393, 671861209, 669575375, 787095383, 2844715, "SRX1125763", "SRS1017744", "SRA281148", "GEO", "Plateforme transcriptome, Biologie, Ecole Normale Sup\u00e9rieure", 1, 0.92794, null, 0.09884, null, 0.71711, null, 0.4721, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "France", "2015-07-30", "Pharyngula", "Embryo", "Trunk", "Surface Structure"], [41511, "SRR5004963", "SRX2336797", "SRS1790193", "SRP092907", "PRJNA352850", "Transcriptomics analysis of gene expressions m6A enrichment levels and ythdf2 binding targets in control and mettl3 or ythdf2 morphants zebrafish embryos", "GSE89655", "Other", "RNA was isolated from control and mettl3 or ythdf2 morphants zebrafish cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. All samples showed a RIN RNA integrity number of higher than 9. Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq2500 or HiSeq 3000 Illumina in paired read mode creating reads with a length of 101 or 151 bp. Sequencing chemistry v2 Illumina was used. Overall design: Examination of gene expressive levels m6A enrichment levels m6A single uncleotide sites and ythdf2 binding targets in normal and mettl3 or ythdf2 morphants zebrafish cells", null, "pubmed:28869969", null, "zebrafish embryos ythdf2 RIP rep2", "GSM2386192", null, "source name:zebrafish embryos|genotype/variation:normal|cell type:embryos cells|age:28hpf|tissue:trunk", "zebrafish embryos ythdf2 RIP rep2", "Reads were aligned to the zv9 genome assembly using TopHat v2.0.9 For each sample reads counts of all genes were computed using HTSeq v0.5.3p9 Genome build: zv9 Supplementary files format and content: reads count HTSeq.xls: Reads count for each gene of all samples Supplementary files format and content: ythdf2 binding target.xls: ythdf2 binding targets identified by macs2 software", "zebrafish embryos", null, "For RIP seq RNA was isolate from ythdf2 Flag mRNA injected zebrafish embryos and the RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode creating reads with a length of 101 bp.", null, "genotype/variation:normal|cell type:embryos cells|age:28hpf|tissue:trunk", "GSM2386192", "GSM2386192: zebrafish embryos ythdf2 RIP rep2; Danio rerio; RIP Seq", "GSM2386192", null, "1", "For RIP seq RNA was isolate from ythdf2 Flag mRNA injected zebrafish embryos and the RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode creating reads with a length of 101 bp.", "GEO Accession:GSM2386192", "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP092907", null, null, "ythdf2_RIP_rep2_1.fastq.gz ythdf2_RIP_rep2_2.fastq.gz", "fastq fastq", 4007024510.0, 19836755.0, "GSM2386192 r1", "0:101 1:101", "A:769487104;C:1245093129;G:1251328145;T:740377823;N:738309", 101, 101, null, null, 769487104, 1245093129, 1251328145, 740377823, 738309, "SRX2336797", "SRS1790193", "SRA491654", "GEO", "Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)", 2, 0.97768, 0.97802, 0.22786, 0.21743, 0.89885, 0.89968, 0.77584, 0.83808, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "other", "trueseq", "bulk", "bulk", "bulk", null, "China", "2016-11-08", "Pharyngula", "Embryo", "Trunk", "Surface Structure"], [41512, "SRR5004962", "SRX2336796", "SRS1790194", "SRP092907", "PRJNA352850", "Transcriptomics analysis of gene expressions m6A enrichment levels and ythdf2 binding targets in control and mettl3 or ythdf2 morphants zebrafish embryos", "GSE89655", "Other", "RNA was isolated from control and mettl3 or ythdf2 morphants zebrafish cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. All samples showed a RIN RNA integrity number of higher than 9. Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq2500 or HiSeq 3000 Illumina in paired read mode creating reads with a length of 101 or 151 bp. Sequencing chemistry v2 Illumina was used. Overall design: Examination of gene expressive levels m6A enrichment levels m6A single uncleotide sites and ythdf2 binding targets in normal and mettl3 or ythdf2 morphants zebrafish cells", null, "pubmed:28869969", null, "zebrafish embryos ythdf2 RIP rep1", "GSM2386191", null, "source name:zebrafish embryos|genotype/variation:normal|cell type:embryos cells|age:28hpf|tissue:trunk", "zebrafish embryos ythdf2 RIP rep1", "Reads were aligned to the zv9 genome assembly using TopHat v2.0.9 For each sample reads counts of all genes were computed using HTSeq v0.5.3p9 Genome build: zv9 Supplementary files format and content: reads count HTSeq.xls: Reads count for each gene of all samples Supplementary files format and content: ythdf2 binding target.xls: ythdf2 binding targets identified by macs2 software", "zebrafish embryos", null, "For RIP seq RNA was isolate from ythdf2 Flag mRNA injected zebrafish embryos and the RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode creating reads with a length of 101 bp.", null, "genotype/variation:normal|cell type:embryos cells|age:28hpf|tissue:trunk", "GSM2386191", "GSM2386191: zebrafish embryos ythdf2 RIP rep1; Danio rerio; RIP Seq", "GSM2386191", null, "1", "For RIP seq RNA was isolate from ythdf2 Flag mRNA injected zebrafish embryos and the RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode creating reads with a length of 101 bp.", "GEO Accession:GSM2386191", "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP092907", null, null, "ythdf2_RIP_rep1_1.fastq.gz ythdf2_RIP_rep1_2.fastq.gz", "fastq fastq", 6144583662.0, 30418731.0, "GSM2386191 r1", "0:101 1:101", "A:1227614258;C:1869131844;G:1825793436;T:1220118819;N:1925305", 101, 101, null, null, 1227614258, 1869131844, 1825793436, 1220118819, 1925305, "SRX2336796", "SRS1790194", "SRA491654", "GEO", "Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)", 2, 0.96857, 0.96917, 0.23397, 0.22377, 0.89832, 0.90147, 0.78619, 0.8258, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "other", "trueseq", "bulk", "bulk", "bulk", null, "China", "2016-11-08", "Pharyngula", "Embryo", "Trunk", "Surface Structure"], [41513, "SRR5004961", "SRX2336795", "SRS1790192", "SRP092907", "PRJNA352850", "Transcriptomics analysis of gene expressions m6A enrichment levels and ythdf2 binding targets in control and mettl3 or ythdf2 morphants zebrafish embryos", "GSE89655", "Other", "RNA was isolated from control and mettl3 or ythdf2 morphants zebrafish cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. All samples showed a RIN RNA integrity number of higher than 9. Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq2500 or HiSeq 3000 Illumina in paired read mode creating reads with a length of 101 or 151 bp. Sequencing chemistry v2 Illumina was used. Overall design: Examination of gene expressive levels m6A enrichment levels m6A single uncleotide sites and ythdf2 binding targets in normal and mettl3 or ythdf2 morphants zebrafish cells", null, "pubmed:28869969", null, "ythdf2 morphant zebrafish endothelial cells rep2", "GSM2386190", null, "source name:zebrafish embryos|genotype/variation:ythdf2|cell type:endothelial cells|age:28hpf|tissue:trunk", "ythdf2 morphant zebrafish endothelial cells rep2", "Reads were aligned to the zv9 genome assembly using TopHat v2.0.9 For each sample reads counts of all genes were computed using HTSeq v0.5.3p9 Genome build: zv9 Supplementary files format and content: reads count HTSeq.xls: Reads count for each gene of all samples", "zebrafish embryos", null, "For RNA seq RNA was isolated from endothelial cells of control mettl3 and ythdf2 morphant zebrafish embryos using the QIAGEN RNeasy Micro kit by following the company manual and the RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq2500 Illumina in paired read mode creating reads with a length of 101 bp.", null, "genotype/variation:ythdf2|cell type:endothelial cells|age:28hpf|tissue:trunk", "GSM2386190", "GSM2386190: ythdf2 morphant zebrafish endothelial cells rep2; Danio rerio; RNA Seq", "GSM2386190", null, "1", "For RNA seq RNA was isolated from endothelial cells of control mettl3 and ythdf2 morphant zebrafish embryos using the QIAGEN RNeasy Micro kit by following the company manual and the RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq2500 Illumina in paired read mode creating reads with a length of 101 bp.", "GEO Accession:GSM2386190", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP092907", null, null, "endothelial_cell_ythdf2-mo_rep2_1.fastq.gz endothelial_cell_ythdf2-mo_rep2_2.fastq.gz", "fastq fastq", 1751180420.0, 8669210.0, "GSM2386190 r1", "0:101 1:101", "A:462178757;C:379825322;G:386498872;T:522589780;N:87689", 101, 101, null, null, 462178757, 379825322, 386498872, 522589780, 87689, "SRX2336795", "SRS1790192", "SRA491654", "GEO", "Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)", 2, 0.81757, 0.85227, 0.07405, 0.08, 0.80115, 0.79109, 0.53025, 0.54273, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "China", "2016-11-08", "Pharyngula", "Embryo", "Trunk", "Surface Structure"], [41514, "SRR5004960", "SRX2336794", "SRS1790191", "SRP092907", "PRJNA352850", "Transcriptomics analysis of gene expressions m6A enrichment levels and ythdf2 binding targets in control and mettl3 or ythdf2 morphants zebrafish embryos", "GSE89655", "Other", "RNA was isolated from control and mettl3 or ythdf2 morphants zebrafish cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. All samples showed a RIN RNA integrity number of higher than 9. Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq2500 or HiSeq 3000 Illumina in paired read mode creating reads with a length of 101 or 151 bp. Sequencing chemistry v2 Illumina was used. Overall design: Examination of gene expressive levels m6A enrichment levels m6A single uncleotide sites and ythdf2 binding targets in normal and mettl3 or ythdf2 morphants zebrafish cells", null, "pubmed:28869969", null, "ythdf2 morphant zebrafish endothelial cells rep1", "GSM2386189", null, "source name:zebrafish embryos|genotype/variation:ythdf2|cell type:endothelial cells|age:28hpf|tissue:trunk", "ythdf2 morphant zebrafish endothelial cells rep1", "Reads were aligned to the zv9 genome assembly using TopHat v2.0.9 For each sample reads counts of all genes were computed using HTSeq v0.5.3p9 Genome build: zv9 Supplementary files format and content: reads count HTSeq.xls: Reads count for each gene of all samples", "zebrafish embryos", null, "For RNA seq RNA was isolated from endothelial cells of control mettl3 and ythdf2 morphant zebrafish embryos using the QIAGEN RNeasy Micro kit by following the company manual and the RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq2500 Illumina in paired read mode creating reads with a length of 101 bp.", null, "genotype/variation:ythdf2|cell type:endothelial cells|age:28hpf|tissue:trunk", "GSM2386189", "GSM2386189: ythdf2 morphant zebrafish endothelial cells rep1; Danio rerio; RNA Seq", "GSM2386189", null, "1", "For RNA seq RNA was isolated from endothelial cells of control mettl3 and ythdf2 morphant zebrafish embryos using the QIAGEN RNeasy Micro kit by following the company manual and the RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq2500 Illumina in paired read mode creating reads with a length of 101 bp.", "GEO Accession:GSM2386189", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP092907", null, null, "endothelial_cell_ythdf2-mo_rep1_1.fastq.gz endothelial_cell_ythdf2-mo_rep1_2.fastq.gz", "fastq fastq", 1742328376.0, 8625388.0, "GSM2386189 r1", "0:101 1:101", "A:459756903;C:377963663;G:384414298;T:520124358;N:69154", 101, 101, null, null, 459756903, 377963663, 384414298, 520124358, 69154, "SRX2336794", "SRS1790191", "SRA491654", "GEO", "Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)", 2, 0.8172, 0.85221, 0.07451, 0.08095, 0.80257, 0.79279, 0.53287, 0.54215, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "China", "2016-11-08", "Pharyngula", "Embryo", "Trunk", "Surface Structure"], [41515, "SRR5004959", "SRX2336793", "SRS1790190", "SRP092907", "PRJNA352850", "Transcriptomics analysis of gene expressions m6A enrichment levels and ythdf2 binding targets in control and mettl3 or ythdf2 morphants zebrafish embryos", "GSE89655", "Other", "RNA was isolated from control and mettl3 or ythdf2 morphants zebrafish cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. All samples showed a RIN RNA integrity number of higher than 9. Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq2500 or HiSeq 3000 Illumina in paired read mode creating reads with a length of 101 or 151 bp. Sequencing chemistry v2 Illumina was used. Overall design: Examination of gene expressive levels m6A enrichment levels m6A single uncleotide sites and ythdf2 binding targets in normal and mettl3 or ythdf2 morphants zebrafish cells", null, "pubmed:28869969", null, "mettl3 morphant zebrafish endothelial cells rep2", "GSM2386188", null, "source name:zebrafish embryos|genotype/variation:mettl3|cell type:endothelial cells|age:28hpf|tissue:trunk", "mettl3 morphant zebrafish endothelial cells rep2", "Reads were aligned to the zv9 genome assembly using TopHat v2.0.9 For each sample reads counts of all genes were computed using HTSeq v0.5.3p9 Genome build: zv9 Supplementary files format and content: reads count HTSeq.xls: Reads count for each gene of all samples", "zebrafish embryos", null, "For RNA seq RNA was isolated from endothelial cells of control mettl3 and ythdf2 morphant zebrafish embryos using the QIAGEN RNeasy Micro kit by following the company manual and the RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq2500 Illumina in paired read mode creating reads with a length of 101 bp.", null, "genotype/variation:mettl3|cell type:endothelial cells|age:28hpf|tissue:trunk", "GSM2386188", "GSM2386188: mettl3 morphant zebrafish endothelial cells rep2; Danio rerio; RNA Seq", "GSM2386188", null, "1", "For RNA seq RNA was isolated from endothelial cells of control mettl3 and ythdf2 morphant zebrafish embryos using the QIAGEN RNeasy Micro kit by following the company manual and the RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq2500 Illumina in paired read mode creating reads with a length of 101 bp.", "GEO Accession:GSM2386188", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP092907", null, null, "endothelial_cell_mettl3-mo_rep2_1.fastq.gz endothelial_cell_mettl3-mo_rep2_2.fastq.gz", "fastq fastq", 2165990854.0, 10722727.0, "GSM2386188 r1", "0:101 1:101", "A:574707709;C:455284651;G:465998545;T:669891099;N:108850", 101, 101, null, null, 574707709, 455284651, 465998545, 669891099, 108850, "SRX2336793", "SRS1790190", "SRA491654", "GEO", "Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)", 2, 0.80096, 0.82938, 0.06333, 0.06431, 0.80649, 0.79653, 0.51689, 0.52452, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "China", "2016-11-08", "Pharyngula", "Embryo", "Trunk", "Surface Structure"], [41516, "SRR5004958", "SRX2336792", "SRS1790188", "SRP092907", "PRJNA352850", "Transcriptomics analysis of gene expressions m6A enrichment levels and ythdf2 binding targets in control and mettl3 or ythdf2 morphants zebrafish embryos", "GSE89655", "Other", "RNA was isolated from control and mettl3 or ythdf2 morphants zebrafish cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. All samples showed a RIN RNA integrity number of higher than 9. Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq2500 or HiSeq 3000 Illumina in paired read mode creating reads with a length of 101 or 151 bp. Sequencing chemistry v2 Illumina was used. Overall design: Examination of gene expressive levels m6A enrichment levels m6A single uncleotide sites and ythdf2 binding targets in normal and mettl3 or ythdf2 morphants zebrafish cells", null, "pubmed:28869969", null, "mettl3 morphant zebrafish endothelial cells rep1", "GSM2386187", null, "source name:zebrafish embryos|genotype/variation:mettl3|cell type:endothelial cells|age:28hpf|tissue:trunk", "mettl3 morphant zebrafish endothelial cells rep1", "Reads were aligned to the zv9 genome assembly using TopHat v2.0.9 For each sample reads counts of all genes were computed using HTSeq v0.5.3p9 Genome build: zv9 Supplementary files format and content: reads count HTSeq.xls: Reads count for each gene of all samples", "zebrafish embryos", null, "For RNA seq RNA was isolated from endothelial cells of control mettl3 and ythdf2 morphant zebrafish embryos using the QIAGEN RNeasy Micro kit by following the company manual and the RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq2500 Illumina in paired read mode creating reads with a length of 101 bp.", null, "genotype/variation:mettl3|cell type:endothelial cells|age:28hpf|tissue:trunk", "GSM2386187", "GSM2386187: mettl3 morphant zebrafish endothelial cells rep1; Danio rerio; RNA Seq", "GSM2386187", null, "1", "For RNA seq RNA was isolated from endothelial cells of control mettl3 and ythdf2 morphant zebrafish embryos using the QIAGEN RNeasy Micro kit by following the company manual and the RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq2500 Illumina in paired read mode creating reads with a length of 101 bp.", "GEO Accession:GSM2386187", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP092907", null, null, "endothelial_cell_mettl3-mo_rep1_2.fastq.gz endothelial_cell_mettl3-mo_rep1_1.fastq.gz", "fastq fastq", 2157926004.0, 10682802.0, "GSM2386187 r1", "0:101 1:101", "A:572319424;C:453720885;G:464068962;T:667731381;N:85352", 101, 101, null, null, 572319424, 453720885, 464068962, 667731381, 85352, "SRX2336792", "SRS1790188", "SRA491654", "GEO", "Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)", 2, 0.79868, 0.82933, 0.06247, 0.06426, 0.80833, 0.79784, 0.4946, 0.52498, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "China", "2016-11-08", "Pharyngula", "Embryo", "Trunk", "Surface Structure"], [41517, "SRR5004957", "SRX2336791", "SRS1790189", "SRP092907", "PRJNA352850", "Transcriptomics analysis of gene expressions m6A enrichment levels and ythdf2 binding targets in control and mettl3 or ythdf2 morphants zebrafish embryos", "GSE89655", "Other", "RNA was isolated from control and mettl3 or ythdf2 morphants zebrafish cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. All samples showed a RIN RNA integrity number of higher than 9. Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq2500 or HiSeq 3000 Illumina in paired read mode creating reads with a length of 101 or 151 bp. Sequencing chemistry v2 Illumina was used. Overall design: Examination of gene expressive levels m6A enrichment levels m6A single uncleotide sites and ythdf2 binding targets in normal and mettl3 or ythdf2 morphants zebrafish cells", null, "pubmed:28869969", null, "control zebrafish endothelial cells rep2", "GSM2386186", null, "source name:zebrafish embryos|genotype/variation:normal|cell type:endothelial cells|age:28hpf|tissue:trunk", "control zebrafish endothelial cells rep2", "Reads were aligned to the zv9 genome assembly using TopHat v2.0.9 For each sample reads counts of all genes were computed using HTSeq v0.5.3p9 Genome build: zv9 Supplementary files format and content: reads count HTSeq.xls: Reads count for each gene of all samples", "zebrafish embryos", null, "For RNA seq RNA was isolated from endothelial cells of control mettl3 and ythdf2 morphant zebrafish embryos using the QIAGEN RNeasy Micro kit by following the company manual and the RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq2500 Illumina in paired read mode creating reads with a length of 101 bp.", null, "genotype/variation:normal|cell type:endothelial cells|age:28hpf|tissue:trunk", "GSM2386186", "GSM2386186: control zebrafish endothelial cells rep2; Danio rerio; RNA Seq", "GSM2386186", null, "1", "For RNA seq RNA was isolated from endothelial cells of control mettl3 and ythdf2 morphant zebrafish embryos using the QIAGEN RNeasy Micro kit by following the company manual and the RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq2500 Illumina in paired read mode creating reads with a length of 101 bp.", "GEO Accession:GSM2386186", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP092907", null, null, "endothelial_cell_control_rep2_1.fastq.gz endothelial_cell_control_rep2_2.fastq.gz", "fastq fastq", 2763563414.0, 13681007.0, "GSM2386186 r1", "0:101 1:101", "A:716446089;C:573695371;G:579488720;T:889637572;N:4295662", 101, 101, null, null, 716446089, 573695371, 579488720, 889637572, 4295662, "SRX2336791", "SRS1790189", "SRA491654", "GEO", "Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)", 2, 0.90371, 0.93106, 0.07354, 0.0772, 0.79642, 0.78547, 0.50661, 0.51809, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "China", "2016-11-08", "Pharyngula", "Embryo", "Trunk", "Surface Structure"], [41518, "SRR5004956", "SRX2336790", "SRS1790187", "SRP092907", "PRJNA352850", "Transcriptomics analysis of gene expressions m6A enrichment levels and ythdf2 binding targets in control and mettl3 or ythdf2 morphants zebrafish embryos", "GSE89655", "Other", "RNA was isolated from control and mettl3 or ythdf2 morphants zebrafish cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. All samples showed a RIN RNA integrity number of higher than 9. Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq2500 or HiSeq 3000 Illumina in paired read mode creating reads with a length of 101 or 151 bp. Sequencing chemistry v2 Illumina was used. Overall design: Examination of gene expressive levels m6A enrichment levels m6A single uncleotide sites and ythdf2 binding targets in normal and mettl3 or ythdf2 morphants zebrafish cells", null, "pubmed:28869969", null, "control zebrafish endothelial cells rep1", "GSM2386185", null, "source name:zebrafish embryos|genotype/variation:normal|cell type:endothelial cells|age:28hpf|tissue:trunk", "control zebrafish endothelial cells rep1", "Reads were aligned to the zv9 genome assembly using TopHat v2.0.9 For each sample reads counts of all genes were computed using HTSeq v0.5.3p9 Genome build: zv9 Supplementary files format and content: reads count HTSeq.xls: Reads count for each gene of all samples", "zebrafish embryos", null, "For RNA seq RNA was isolated from endothelial cells of control mettl3 and ythdf2 morphant zebrafish embryos using the QIAGEN RNeasy Micro kit by following the company manual and the RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq2500 Illumina in paired read mode creating reads with a length of 101 bp.", null, "genotype/variation:normal|cell type:endothelial cells|age:28hpf|tissue:trunk", "GSM2386185", "GSM2386185: control zebrafish endothelial cells rep1; Danio rerio; RNA Seq", "GSM2386185", null, "1", "For RNA seq RNA was isolated from endothelial cells of control mettl3 and ythdf2 morphant zebrafish embryos using the QIAGEN RNeasy Micro kit by following the company manual and the RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq2500 Illumina in paired read mode creating reads with a length of 101 bp.", "GEO Accession:GSM2386185", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP092907", null, null, "endothelial_cell_control_rep1_1.fastq.gz endothelial_cell_control_rep1_2.fastq.gz", "fastq fastq", 2779305880.0, 13758940.0, "GSM2386185 r1", "0:101 1:101", "A:720581765;C:576943159;G:582516380;T:894833915;N:4430661", 101, 101, null, null, 720581765, 576943159, 582516380, 894833915, 4430661, "SRX2336790", "SRS1790187", "SRA491654", "GEO", "Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)", 2, 0.90685, 0.93205, 0.0759, 0.07759, 0.79614, 0.78541, 0.50727, 0.51529, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "China", "2016-11-08", "Pharyngula", "Embryo", "Trunk", "Surface Structure"], [41519, "SRR5004955", "SRX2336789", "SRS1790186", "SRP092907", "PRJNA352850", "Transcriptomics analysis of gene expressions m6A enrichment levels and ythdf2 binding targets in control and mettl3 or ythdf2 morphants zebrafish embryos", "GSE89655", "Other", "RNA was isolated from control and mettl3 or ythdf2 morphants zebrafish cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. All samples showed a RIN RNA integrity number of higher than 9. Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq2500 or HiSeq 3000 Illumina in paired read mode creating reads with a length of 101 or 151 bp. Sequencing chemistry v2 Illumina was used. Overall design: Examination of gene expressive levels m6A enrichment levels m6A single uncleotide sites and ythdf2 binding targets in normal and mettl3 or ythdf2 morphants zebrafish cells", null, "pubmed:28869969", null, "mettl3 morphant zebrafish embryos input rep2", "GSM2386184", null, "source name:zebrafish embryos|genotype/variation:mettl3|cell type:embryos cells|age:28hpf|tissue:trunk", "mettl3 morphant zebrafish embryos input rep2", "Library strategy: MeRIP seq Reads were aligned to the zv9 genome assembly using TopHat v2.0.9 Genome build: zv9 Supplementary files format and content: reads count HTSeq.xls: Reads count for each gene of all samples", "zebrafish embryos", null, "For MeRIP seq mRNA was isolated from the trunck region of zebrafish embryos at 28hpf. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. The RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode creating reads with a length of 101 bp.", null, "genotype/variation:mettl3|cell type:embryos cells|age:28hpf|tissue:trunk", "GSM2386184", "GSM2386184: mettl3 morphant zebrafish embryos input rep2; Danio rerio; RNA Seq", "GSM2386184", null, "1", "For MeRIP seq mRNA was isolated from the trunck region of zebrafish embryos at 28hpf. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. The RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode creating reads with a length of 101 bp.", "GEO Accession:GSM2386184", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP092907", null, null, "mettl3-mo_input_rep2_1.fastq.gz mettl3-mo_input_rep2_2.fastq.gz", "fastq fastq", 15677274742.0, 77610271.0, "GSM2386184 r1", "0:101 1:101", "A:4349575028;C:3553088246;G:3444690573;T:4326018819;N:3902076", 101, 101, null, null, 4349575028, 3553088246, 3444690573, 4326018819, 3902076, "SRX2336789", "SRS1790186", "SRA491654", "GEO", "Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)", 2, 0.9442, 0.94896, 0.12173, 0.11299, 0.70891, 0.70094, 0.52438, 0.50498, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "China", "2016-11-08", "Pharyngula", "Embryo", "Trunk", "Surface Structure"], [41520, "SRR5004954", "SRX2336788", "SRS1790185", "SRP092907", "PRJNA352850", "Transcriptomics analysis of gene expressions m6A enrichment levels and ythdf2 binding targets in control and mettl3 or ythdf2 morphants zebrafish embryos", "GSE89655", "Other", "RNA was isolated from control and mettl3 or ythdf2 morphants zebrafish cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. All samples showed a RIN RNA integrity number of higher than 9. Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq2500 or HiSeq 3000 Illumina in paired read mode creating reads with a length of 101 or 151 bp. Sequencing chemistry v2 Illumina was used. Overall design: Examination of gene expressive levels m6A enrichment levels m6A single uncleotide sites and ythdf2 binding targets in normal and mettl3 or ythdf2 morphants zebrafish cells", null, "pubmed:28869969", null, "mettl3 morphant zebrafish embryos input rep1", "GSM2386183", null, "source name:zebrafish embryos|genotype/variation:mettl3|cell type:embryos cells|age:28hpf|tissue:trunk", "mettl3 morphant zebrafish embryos input rep1", "Library strategy: MeRIP seq Reads were aligned to the zv9 genome assembly using TopHat v2.0.9 Genome build: zv9 Supplementary files format and content: reads count HTSeq.xls: Reads count for each gene of all samples", "zebrafish embryos", null, "For MeRIP seq mRNA was isolated from the trunck region of zebrafish embryos at 28hpf. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. The RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode creating reads with a length of 151 bp.", null, "genotype/variation:mettl3|cell type:embryos cells|age:28hpf|tissue:trunk", "GSM2386183", "GSM2386183: mettl3 morphant zebrafish embryos input rep1; Danio rerio; RNA Seq", "GSM2386183", null, "1", "For MeRIP seq mRNA was isolated from the trunck region of zebrafish embryos at 28hpf. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. The RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode creating reads with a length of 151 bp.", "GEO Accession:GSM2386183", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP092907", null, null, "mettl3-mo_input_rep1_1.fastq.gz mettl3-mo_input_rep1_2.fastq.gz", "fastq fastq", 15652948712.0, 51830956.0, "GSM2386183 r1", "0:151 1:151", "A:4232005872;C:3610891744;G:3588831417;T:4218453808;N:2765871", 151, 151, null, null, 4232005872, 3610891744, 3588831417, 4218453808, 2765871, "SRX2336788", "SRS1790185", "SRA491654", "GEO", "Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)", 2, 0.9522, 0.95324, 0.10697, 0.10191, 0.7176, 0.72328, 0.56867, 0.5644, 151, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "China", "2016-11-08", "Pharyngula", "Embryo", "Trunk", "Surface Structure"], [41521, "SRR5004953", "SRX2336787", "SRS1790184", "SRP092907", "PRJNA352850", "Transcriptomics analysis of gene expressions m6A enrichment levels and ythdf2 binding targets in control and mettl3 or ythdf2 morphants zebrafish embryos", "GSE89655", "Other", "RNA was isolated from control and mettl3 or ythdf2 morphants zebrafish cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. All samples showed a RIN RNA integrity number of higher than 9. Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq2500 or HiSeq 3000 Illumina in paired read mode creating reads with a length of 101 or 151 bp. Sequencing chemistry v2 Illumina was used. Overall design: Examination of gene expressive levels m6A enrichment levels m6A single uncleotide sites and ythdf2 binding targets in normal and mettl3 or ythdf2 morphants zebrafish cells", null, "pubmed:28869969", null, "mettl3 morphant zebrafish embryos m6A IP rep2", "GSM2386182", null, "source name:zebrafish embryos|genotype/variation:mettl3|cell type:embryos cells|age:28hpf|tissue:trunk|enrichment antibody vendor:Synaptic Systems", "mettl3 morphant zebrafish embryos m6A IP rep2", "Library strategy: MeRIP seq Reads were aligned to the zv9 genome assembly using TopHat v2.0.9 Genome build: zv9 Supplementary files format and content: m6A peak locus.xls: m6A peaks indentified by macs2 software Supplementary files format and content: reads count HTSeq.xls: Reads count for each gene of all samples", "zebrafish embryos", null, "For MeRIP seq mRNA was isolated from the trunck region of zebrafish embryos at 28hpf. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. The RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode creating reads with a length of 101 bp.", null, "genotype/variation:mettl3|cell type:embryos cells|age:28hpf|tissue:trunk|enrichment antibody vendor:Synaptic Systems", "GSM2386182", "GSM2386182: mettl3 morphant zebrafish embryos m6A IP rep2; Danio rerio; OTHER", "GSM2386182", null, "1", "For MeRIP seq mRNA was isolated from the trunck region of zebrafish embryos at 28hpf. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. The RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode creating reads with a length of 101 bp.", "GEO Accession:GSM2386182", "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP092907", null, null, "mettl3-mo_IP_rep2_1.fastq.gz mettl3-mo_IP_rep2_2.fastq.gz", "fastq fastq", 12246129204.0, 60624402.0, "GSM2386182 r1", "0:101 1:101", "A:3253814653;C:2887966071;G:2921051332;T:3179545005;N:3752143", 101, 101, null, null, 3253814653, 2887966071, 2921051332, 3179545005, 3752143, "SRX2336787", "SRS1790184", "SRA491654", "GEO", "Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)", 2, 0.93906, 0.94462, 0.08073, 0.07972, 0.69148, 0.69394, 0.43224, 0.48778, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "other", "trueseq", "bulk", "bulk", "bulk", null, "China", "2016-11-08", "Pharyngula", "Embryo", "Trunk", "Surface Structure"], [41522, "SRR5004952", "SRX2336785", "SRS1790183", "SRP092907", "PRJNA352850", "Transcriptomics analysis of gene expressions m6A enrichment levels and ythdf2 binding targets in control and mettl3 or ythdf2 morphants zebrafish embryos", "GSE89655", "Other", "RNA was isolated from control and mettl3 or ythdf2 morphants zebrafish cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. All samples showed a RIN RNA integrity number of higher than 9. Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq2500 or HiSeq 3000 Illumina in paired read mode creating reads with a length of 101 or 151 bp. Sequencing chemistry v2 Illumina was used. Overall design: Examination of gene expressive levels m6A enrichment levels m6A single uncleotide sites and ythdf2 binding targets in normal and mettl3 or ythdf2 morphants zebrafish cells", null, "pubmed:28869969", null, "mettl3 morphant zebrafish embryos m6A IP rep1", "GSM2386181", null, "source name:zebrafish embryos|genotype/variation:mettl3|cell type:embryos cells|age:28hpf|tissue:trunk|enrichment antibody vendor:Synaptic Systems", "mettl3 morphant zebrafish embryos m6A IP rep1", "Library strategy: MeRIP seq Reads were aligned to the zv9 genome assembly using TopHat v2.0.9 Genome build: zv9 Supplementary files format and content: m6A peak locus.xls: m6A peaks indentified by macs2 software Supplementary files format and content: reads count HTSeq.xls: Reads count for each gene of all samples", "zebrafish embryos", null, "For MeRIP seq mRNA was isolated from the trunck region of zebrafish embryos at 28hpf. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. The RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode creating reads with a length of 151 bp.", null, "genotype/variation:mettl3|cell type:embryos cells|age:28hpf|tissue:trunk|enrichment antibody vendor:Synaptic Systems", "GSM2386181", "GSM2386181: mettl3 morphant zebrafish embryos m6A IP rep1; Danio rerio; OTHER", "GSM2386181", null, "1", "For MeRIP seq mRNA was isolated from the trunck region of zebrafish embryos at 28hpf. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. The RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode creating reads with a length of 151 bp.", "GEO Accession:GSM2386181", "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP092907", null, null, "mettl3-mo_IP_rep1_1.fastq.gz mettl3-mo_IP_rep1_2.fastq.gz", "fastq fastq", 22767872412.0, 75390306.0, "GSM2386181 r1", "0:151 1:151", "A:6356270201;C:5175380564;G:5545741592;T:5686194578;N:4285477", 151, 151, null, null, 6356270201, 5175380564, 5545741592, 5686194578, 4285477, "SRX2336785", "SRS1790183", "SRA491654", "GEO", "Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)", 2, 0.94647, 0.95162, 0.07314, 0.07248, 0.70796, 0.71021, 0.54859, 0.54624, 151, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "other", "trueseq", "bulk", "bulk", "bulk", null, "China", "2016-11-08", "Pharyngula", "Embryo", "Trunk", "Surface Structure"], [41523, "SRR5004951", "SRX2336784", "SRS1790182", "SRP092907", "PRJNA352850", "Transcriptomics analysis of gene expressions m6A enrichment levels and ythdf2 binding targets in control and mettl3 or ythdf2 morphants zebrafish embryos", "GSE89655", "Other", "RNA was isolated from control and mettl3 or ythdf2 morphants zebrafish cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. All samples showed a RIN RNA integrity number of higher than 9. Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq2500 or HiSeq 3000 Illumina in paired read mode creating reads with a length of 101 or 151 bp. Sequencing chemistry v2 Illumina was used. Overall design: Examination of gene expressive levels m6A enrichment levels m6A single uncleotide sites and ythdf2 binding targets in normal and mettl3 or ythdf2 morphants zebrafish cells", null, "pubmed:28869969", null, "control zebrafish embryos input rep2", "GSM2386180", null, "source name:zebrafish embryos|genotype/variation:normal|cell type:embryos cells|age:28hpf|tissue:trunk", "control zebrafish embryos input rep2", "Library strategy: MeRIP seq Reads were aligned to the zv9 genome assembly using TopHat v2.0.9 Genome build: zv9 Supplementary files format and content: reads count HTSeq.xls: Reads count for each gene of all samples", "zebrafish embryos", null, "For MeRIP seq mRNA was isolated from the trunck region of zebrafish embryos at 28hpf. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. The RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode creating reads with a length of 101 bp.", null, "genotype/variation:normal|cell type:embryos cells|age:28hpf|tissue:trunk", "GSM2386180", "GSM2386180: control zebrafish embryos input rep2; Danio rerio; OTHER", "GSM2386180", null, "1", "For MeRIP seq mRNA was isolated from the trunck region of zebrafish embryos at 28hpf. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. The RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode creating reads with a length of 101 bp.", "GEO Accession:GSM2386180", "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP092907", null, null, "control_input_rep2_1.fastq.gz control_input_rep2_2.fastq.gz", "fastq fastq", 20629042748.0, 102123974.0, "GSM2386180 r1", "0:101 1:101", "A:5541548211;C:4810650367;G:4699999124;T:5571342766;N:5502280", 101, 101, null, null, 5541548211, 4810650367, 4699999124, 5571342766, 5502280, "SRX2336784", "SRS1790182", "SRA491654", "GEO", "Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)", 2, 0.94898, 0.9511, 0.10842, 0.10266, 0.70465, 0.70481, 0.4986, 0.48915, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "other", "trueseq", "bulk", "bulk", "bulk", null, "China", "2016-11-08", "Pharyngula", "Embryo", "Trunk", "Surface Structure"], [41524, "SRR5004950", "SRX2336783", "SRS1790181", "SRP092907", "PRJNA352850", "Transcriptomics analysis of gene expressions m6A enrichment levels and ythdf2 binding targets in control and mettl3 or ythdf2 morphants zebrafish embryos", "GSE89655", "Other", "RNA was isolated from control and mettl3 or ythdf2 morphants zebrafish cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. All samples showed a RIN RNA integrity number of higher than 9. Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq2500 or HiSeq 3000 Illumina in paired read mode creating reads with a length of 101 or 151 bp. Sequencing chemistry v2 Illumina was used. Overall design: Examination of gene expressive levels m6A enrichment levels m6A single uncleotide sites and ythdf2 binding targets in normal and mettl3 or ythdf2 morphants zebrafish cells", null, "pubmed:28869969", null, "control zebrafish embryos input rep1", "GSM2386179", null, "source name:zebrafish embryos|genotype/variation:normal|cell type:embryos cells|age:28hpf|tissue:trunk", "control zebrafish embryos input rep1", "Library strategy: MeRIP seq Reads were aligned to the zv9 genome assembly using TopHat v2.0.9 Genome build: zv9 Supplementary files format and content: reads count HTSeq.xls: Reads count for each gene of all samples", "zebrafish embryos", null, "For MeRIP seq mRNA was isolated from the trunck region of zebrafish embryos at 28hpf. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. The RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode creating reads with a length of 151 bp.", null, "genotype/variation:normal|cell type:embryos cells|age:28hpf|tissue:trunk", "GSM2386179", "GSM2386179: control zebrafish embryos input rep1; Danio rerio; OTHER", "GSM2386179", null, "1", "For MeRIP seq mRNA was isolated from the trunck region of zebrafish embryos at 28hpf. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. The RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode creating reads with a length of 151 bp.", "GEO Accession:GSM2386179", "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP092907", null, null, "control_input_rep1_1.fastq.gz control_input_rep1_2.fastq.gz", "fastq fastq", 27776308060.0, 91974530.0, "GSM2386179 r1", "0:151 1:151", "A:7467418896;C:6517753701;G:6333567394;T:7452805069;N:4763000", 151, 151, null, null, 7467418896, 6517753701, 6333567394, 7452805069, 4763000, "SRX2336783", "SRS1790181", "SRA491654", "GEO", "Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)", 2, 0.95616, 0.95939, 0.10401, 0.09776, 0.72263, 0.73637, 0.57906, 0.58185, 151, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "other", "trueseq", "bulk", "bulk", "bulk", null, "China", "2016-11-08", "Pharyngula", "Embryo", "Trunk", "Surface Structure"], [41525, "SRR5004949", "SRX2336782", "SRS1790180", "SRP092907", "PRJNA352850", "Transcriptomics analysis of gene expressions m6A enrichment levels and ythdf2 binding targets in control and mettl3 or ythdf2 morphants zebrafish embryos", "GSE89655", "Other", "RNA was isolated from control and mettl3 or ythdf2 morphants zebrafish cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. All samples showed a RIN RNA integrity number of higher than 9. Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq2500 or HiSeq 3000 Illumina in paired read mode creating reads with a length of 101 or 151 bp. Sequencing chemistry v2 Illumina was used. Overall design: Examination of gene expressive levels m6A enrichment levels m6A single uncleotide sites and ythdf2 binding targets in normal and mettl3 or ythdf2 morphants zebrafish cells", null, "pubmed:28869969", null, "control zebrafish embryos m6A IP rep2", "GSM2386178", null, "source name:zebrafish embryos|genotype/variation:normal|cell type:embryos cells|age:28hpf|tissue:trunk|enrichment antibody vendor:Synaptic Systems", "control zebrafish embryos m6A IP rep2", "Library strategy: MeRIP seq Reads were aligned to the zv9 genome assembly using TopHat v2.0.9 Genome build: zv9 Supplementary files format and content: m6A peak locus.xls: m6A peaks indentified by macs2 software Supplementary files format and content: reads count HTSeq.xls: Reads count for each gene of all samples", "zebrafish embryos", null, "For MeRIP seq mRNA was isolated from the trunck region of zebrafish embryos at 28hpf. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. The RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode creating reads with a length of 101 bp.", null, "genotype/variation:normal|cell type:embryos cells|age:28hpf|tissue:trunk|enrichment antibody vendor:Synaptic Systems", "GSM2386178", "GSM2386178: control zebrafish embryos m6A IP rep2; Danio rerio; OTHER", "GSM2386178", null, "1", "For MeRIP seq mRNA was isolated from the trunck region of zebrafish embryos at 28hpf. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. The RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode creating reads with a length of 101 bp.", "GEO Accession:GSM2386178", "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP092907", null, null, "control_IP_rep2_1.fastq.gz control_IP_rep2_2.fastq.gz", "fastq fastq", 11899573964.0, 58908782.0, "GSM2386178 r1", "0:101 1:101", "A:3146907590;C:2817914269;G:2838718195;T:3092392965;N:3640945", 101, 101, null, null, 3146907590, 2817914269, 2838718195, 3092392965, 3640945, "SRX2336782", "SRS1790180", "SRA491654", "GEO", "Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)", 2, 0.93821, 0.94281, 0.08361, 0.08174, 0.69676, 0.69816, 0.4628, 0.46386, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "other", "trueseq", "bulk", "bulk", "bulk", null, "China", "2016-11-08", "Pharyngula", "Embryo", "Trunk", "Surface Structure"], [41526, "SRR5004948", "SRX2336781", "SRS1790179", "SRP092907", "PRJNA352850", "Transcriptomics analysis of gene expressions m6A enrichment levels and ythdf2 binding targets in control and mettl3 or ythdf2 morphants zebrafish embryos", "GSE89655", "Other", "RNA was isolated from control and mettl3 or ythdf2 morphants zebrafish cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. All samples showed a RIN RNA integrity number of higher than 9. Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq2500 or HiSeq 3000 Illumina in paired read mode creating reads with a length of 101 or 151 bp. Sequencing chemistry v2 Illumina was used. Overall design: Examination of gene expressive levels m6A enrichment levels m6A single uncleotide sites and ythdf2 binding targets in normal and mettl3 or ythdf2 morphants zebrafish cells", null, "pubmed:28869969", null, "control zebrafish embryos m6A IP rep1", "GSM2386177", null, "source name:zebrafish embryos|genotype/variation:normal|cell type:embryos cells|age:28hpf|tissue:trunk|enrichment antibody vendor:Synaptic Systems", "control zebrafish embryos m6A IP rep1", "Library strategy: MeRIP seq Reads were aligned to the zv9 genome assembly using TopHat v2.0.9 Genome build: zv9 Supplementary files format and content: m6A peak locus.xls: m6A peaks indentified by macs2 software Supplementary files format and content: reads count HTSeq.xls: Reads count for each gene of all samples", "zebrafish embryos", null, "For MeRIP seq mRNA was isolated from the trunck region of zebrafish embryos at 28hpf. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. The RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode creating reads with a length of 151 bp.", null, "genotype/variation:normal|cell type:embryos cells|age:28hpf|tissue:trunk|enrichment antibody vendor:Synaptic Systems", "GSM2386177", "GSM2386177: control zebrafish embryos m6A IP rep1; Danio rerio; OTHER", "GSM2386177", null, "1", "For MeRIP seq mRNA was isolated from the trunck region of zebrafish embryos at 28hpf. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. The RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode creating reads with a length of 151 bp.", "GEO Accession:GSM2386177", "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP092907", null, null, "control_IP_rep1_1.fastq.gz control_IP_rep1_2.fastq.gz", "fastq fastq", 16582066208.0, 54907504.0, "GSM2386177 r1", "0:151 1:151", "A:4529890968;C:3812739433;G:4031512714;T:4204817283;N:3105810", 151, 151, null, null, 4529890968, 3812739433, 4031512714, 4204817283, 3105810, "SRX2336781", "SRS1790179", "SRA491654", "GEO", "Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)", 2, 0.93701, 0.95377, 0.07009, 0.07008, 0.70972, 0.71173, 0.54711, 0.54995, 151, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "other", "trueseq", "bulk", "bulk", "bulk", null, "China", "2016-11-08", "Pharyngula", "Embryo", "Trunk", "Surface Structure"], [48109, "SRR7049633", "SRX3981086", "SRS3205925", "SRP141415", "PRJNA451191", "RNA seq of zebrafish ptk7 mutants with severe spinal curvature and heterozygous straight siblings", "PRJNA451191", "Other", "To identify molecular mechanisms underlying scoliosis spine curvature we performed next generation RNA sequencing on ptk7 mutant vs. ptk7/+ sibling fish at an age correlating with severe scoliosis progression 1 cm length. Because the tissue of idiopathic scoliosis origin remains unknown RNA Seq was performed on bulk RNA samples collected from the entire trunk and tail heads were removed at the level of the gill to eliminate signals associated with abnormal Ptk7 function in the brain.", null, null, null, null, "ptk7/+ 13", null, "isolate:fish #13|age:21 dpf|sex:NA|tissue:trunk|genotype:ptk7/+|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA sequencing of Danio rerio: scoliosis trunk", "ptk7 het 13", "ptk7 het 13", "Total RNA extraction was preformed using the Qiagen RNeasy kit following the manufacturer's instructions Qiagen. RNA sample quality was assessed using an Agilent Bioanalyzer. Library prep and subsequent sequencing was performed by The Centre for Applied Genomics at The Hospital for Sick Children SickKids using the NEBNext stranded RNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP141415", null, null, "Ptk7_het_straight_13_R1.fastq.gz Ptk7_het_straight_13_R2.fastq.gz", "fastq fastq", 10525455360.0, 41767680.0, "Ptk7 het straight 13 R1.fastq.gz", "0:126 1:126", "A:2642906925;C:2610985400;G:2703570608;T:2566247621;N:1744806", 126, 126, null, null, 2642906925, 2610985400, 2703570608, 2566247621, 1744806, "SRX3981086", "SRS3205925", "SRA693409", "The Hospital for Sick Children|Developmental and Stem Cell Biology", "The Hospital for Sick Children", 2, 0.8399, 0.83879, 0.10378, 0.1035, 0.73746, 0.73864, 0.48562, 0.52042, 126, 126, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "Canada", "2018-04-20", "Larval", "Larval", "Trunk", "Surface Structure"], [48110, "SRR7049634", "SRX3981085", "SRS3205926", "SRP141415", "PRJNA451191", "RNA seq of zebrafish ptk7 mutants with severe spinal curvature and heterozygous straight siblings", "PRJNA451191", "Other", "To identify molecular mechanisms underlying scoliosis spine curvature we performed next generation RNA sequencing on ptk7 mutant vs. ptk7/+ sibling fish at an age correlating with severe scoliosis progression 1 cm length. Because the tissue of idiopathic scoliosis origin remains unknown RNA Seq was performed on bulk RNA samples collected from the entire trunk and tail heads were removed at the level of the gill to eliminate signals associated with abnormal Ptk7 function in the brain.", null, null, null, null, "ptk7/+ 11", null, "isolate:fish #11|age:21 dpf|sex:NA|tissue:trunk|genotype:ptk7/+|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA sequencing of Danio rerio: scoliosis trunk", "ptk7 het 11", "ptk7 het 11", "Total RNA extraction was preformed using the Qiagen RNeasy kit following the manufacturer's instructions Qiagen. RNA sample quality was assessed using an Agilent Bioanalyzer. Library prep and subsequent sequencing was performed by The Centre for Applied Genomics at The Hospital for Sick Children SickKids using the NEBNext stranded RNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP141415", null, "loader:fastq load.py", "Ptk7_het_straight_11_R2.fastq.gz Ptk7_het_straight_11_R1.fastq", "fastq fastq", 10112242392.0, 40127946.0, "Ptk7 het straight 11 R2.fastq.gz", "0:126 1:126", "A:2526420409;C:2531445826;G:2613534392;T:2439160326;N:1681439", 126, 126, null, null, 2526420409, 2531445826, 2613534392, 2439160326, 1681439, "SRX3981085", "SRS3205926", "SRA693409", "The Hospital for Sick Children|Developmental and Stem Cell Biology", "The Hospital for Sick Children", 2, 0.83476, 0.83453, 0.10235, 0.10313, 0.73614, 0.73799, 0.46442, 0.52808, 126, 126, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "Canada", "2018-05-16", "Larval", "Larval", "Trunk", "Surface Structure"], [48111, "SRR7049635", "SRX3981084", "SRS3205923", "SRP141415", "PRJNA451191", "RNA seq of zebrafish ptk7 mutants with severe spinal curvature and heterozygous straight siblings", "PRJNA451191", "Other", "To identify molecular mechanisms underlying scoliosis spine curvature we performed next generation RNA sequencing on ptk7 mutant vs. ptk7/+ sibling fish at an age correlating with severe scoliosis progression 1 cm length. Because the tissue of idiopathic scoliosis origin remains unknown RNA Seq was performed on bulk RNA samples collected from the entire trunk and tail heads were removed at the level of the gill to eliminate signals associated with abnormal Ptk7 function in the brain.", null, null, null, null, "ptk7 4", null, "isolate:fish #4|age:21 dpf|sex:NA|tissue:trunk|disease:idiopathic scoliosis|disease stg:severe|genotype:ptk7|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA sequencing of Danio rerio: scoliosis trunk", "ptk7 mutant 4", "ptk7 mutant 4", "Total RNA extraction was preformed using the Qiagen RNeasy kit following the manufacturer's instructions Qiagen. RNA sample quality was assessed using an Agilent Bioanalyzer. Library prep and subsequent sequencing was performed by The Centre for Applied Genomics at The Hospital for Sick Children SickKids using the NEBNext stranded RNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP141415", null, null, "Ptk7_mut_3d_4_R2.fastq.gz Ptk7_mut_3d_4_R1.fastq.gz", "fastq fastq", 10725732108.0, 42562429.0, "Ptk7 mut 3d 4 R1.fastq.gz", "0:126 1:126", "A:2712076087;C:2650097574;G:2715648916;T:2646147621;N:1761910", 126, 126, null, null, 2712076087, 2650097574, 2715648916, 2646147621, 1761910, "SRX3981084", "SRS3205923", "SRA693409", "The Hospital for Sick Children|Developmental and Stem Cell Biology", "The Hospital for Sick Children", 2, 0.828, 0.8269, 0.10307, 0.10332, 0.72886, 0.73008, 0.4646, 0.51847, 126, 126, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "Canada", "2019-11-26", "Larval", "Larval", "Trunk", "Surface Structure"], [48112, "SRR7049636", "SRX3981083", "SRS3205921", "SRP141415", "PRJNA451191", "RNA seq of zebrafish ptk7 mutants with severe spinal curvature and heterozygous straight siblings", "PRJNA451191", "Other", "To identify molecular mechanisms underlying scoliosis spine curvature we performed next generation RNA sequencing on ptk7 mutant vs. ptk7/+ sibling fish at an age correlating with severe scoliosis progression 1 cm length. Because the tissue of idiopathic scoliosis origin remains unknown RNA Seq was performed on bulk RNA samples collected from the entire trunk and tail heads were removed at the level of the gill to eliminate signals associated with abnormal Ptk7 function in the brain.", null, null, null, null, "ptk7/+ 16", null, "isolate:fish #16|age:21 dpf|sex:NA|tissue:trunk|genotype:ptk7/+|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA sequencing of Danio rerio: scoliosis trunk", "ptk7 het 16", "ptk7 het 16", "Total RNA extraction was preformed using the Qiagen RNeasy kit following the manufacturer's instructions Qiagen. RNA sample quality was assessed using an Agilent Bioanalyzer. Library prep and subsequent sequencing was performed by The Centre for Applied Genomics at The Hospital for Sick Children SickKids using the NEBNext stranded RNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP141415", null, null, "Ptk7_het_straight_16_R2.fastq.gz Ptk7_het_straight_16_R1.fastq.gz", "fastq fastq", 11320148448.0, 44921224.0, "Ptk7 het straight 16 R2.fastq.gz", "0:126 1:126", "A:2864005270;C:2791952997;G:2861078925;T:2801270066;N:1841190", 126, 126, null, null, 2864005270, 2791952997, 2861078925, 2801270066, 1841190, "SRX3981083", "SRS3205921", "SRA693409", "The Hospital for Sick Children|Developmental and Stem Cell Biology", "The Hospital for Sick Children", 2, 0.90868, 0.90876, 0.10214, 0.10215, 0.72366, 0.72204, 0.54602, 0.52494, 126, 126, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "Canada", "2018-04-20", "Larval", "Larval", "Trunk", "Surface Structure"], [48113, "SRR7049637", "SRX3981082", "SRS3205920", "SRP141415", "PRJNA451191", "RNA seq of zebrafish ptk7 mutants with severe spinal curvature and heterozygous straight siblings", "PRJNA451191", "Other", "To identify molecular mechanisms underlying scoliosis spine curvature we performed next generation RNA sequencing on ptk7 mutant vs. ptk7/+ sibling fish at an age correlating with severe scoliosis progression 1 cm length. Because the tissue of idiopathic scoliosis origin remains unknown RNA Seq was performed on bulk RNA samples collected from the entire trunk and tail heads were removed at the level of the gill to eliminate signals associated with abnormal Ptk7 function in the brain.", null, null, null, null, "ptk7 26", null, "isolate:fish #26|age:21 dpf|sex:NA|tissue:trunk|disease:idiopathic scoliosis|disease stg:severe|genotype:ptk7|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA sequencing of Danio rerio: scoliosis trunk", "ptk7 mutant 26", "ptk7 mutant 26", "Total RNA extraction was preformed using the Qiagen RNeasy kit following the manufacturer's instructions Qiagen. RNA sample quality was assessed using an Agilent Bioanalyzer. Library prep and subsequent sequencing was performed by The Centre for Applied Genomics at The Hospital for Sick Children SickKids using the NEBNext stranded RNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP141415", null, null, "Ptk7_mut_3d_26_R1.fastq.gz Ptk7_mut_3d_26_R2.fastq.gz", "fastq fastq", 11687835600.0, 46380300.0, "Ptk7 mut 3d 26 R1.fastq.gz", "0:126 1:126", "A:2952483656;C:2895878965;G:2958079390;T:2879469880;N:1923709", 126, 126, null, null, 2952483656, 2895878965, 2958079390, 2879469880, 1923709, "SRX3981082", "SRS3205920", "SRA693409", "The Hospital for Sick Children|Developmental and Stem Cell Biology", "The Hospital for Sick Children", 2, 0.93611, 0.93546, 0.10565, 0.10647, 0.71348, 0.71429, 0.541, 0.50001, 126, 126, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "Canada", "2019-11-26", "Larval", "Larval", "Trunk", "Surface Structure"], [48114, "SRR7049638", "SRX3981081", "SRS3205922", "SRP141415", "PRJNA451191", "RNA seq of zebrafish ptk7 mutants with severe spinal curvature and heterozygous straight siblings", "PRJNA451191", "Other", "To identify molecular mechanisms underlying scoliosis spine curvature we performed next generation RNA sequencing on ptk7 mutant vs. ptk7/+ sibling fish at an age correlating with severe scoliosis progression 1 cm length. Because the tissue of idiopathic scoliosis origin remains unknown RNA Seq was performed on bulk RNA samples collected from the entire trunk and tail heads were removed at the level of the gill to eliminate signals associated with abnormal Ptk7 function in the brain.", null, null, null, null, "ptk7 24", null, "isolate:fish #24|age:21 dpf|sex:NA|tissue:trunk|disease:idiopathic scoliosis|disease stg:severe|genotype:ptk7|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA sequencing of Danio rerio: scoliosis trunk", "ptk7 mutant 24", "ptk7 mutant 24", "Total RNA extraction was preformed using the Qiagen RNeasy kit following the manufacturer's instructions Qiagen. RNA sample quality was assessed using an Agilent Bioanalyzer. Library prep and subsequent sequencing was performed by The Centre for Applied Genomics at The Hospital for Sick Children SickKids using the NEBNext stranded RNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP141415", null, null, "Ptk7_mut_3d_24_R2.fastq.gz Ptk7_mut_3d_24_R1.fastq.gz", "fastq fastq", 9730052136.0, 38611318.0, "Ptk7 mut 3d 24 R1.fastq.gz", "0:126 1:126", "A:2423031974;C:2443352528;G:2499840379;T:2362201530;N:1625725", 126, 126, null, null, 2423031974, 2443352528, 2499840379, 2362201530, 1625725, "SRX3981081", "SRS3205922", "SRA693409", "The Hospital for Sick Children|Developmental and Stem Cell Biology", "The Hospital for Sick Children", 2, 0.9256, 0.9243, 0.1058, 0.10658, 0.71849, 0.72034, 0.54398, 0.54002, 126, 126, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "Canada", "2019-11-26", "Larval", "Larval", "Trunk", "Surface Structure"], [48117, "SRR7061291", "SRX3992234", "SRS3216613", "SRP142542", "PRJNA453405", "RNA seq of zebrafish ptk7 mutants at beginning of curve onset and ptk7+Tgfoxj1a:ptk7 straight siblings", "PRJNA453405", "Other", "To identify molecular mechanisms underlying scoliosis spine curvature we performed next generation RNA sequencing on ptk7 mutant vs. ptk7+Tgfoxj1a:ptk7 sibling fish at an age correlating with onset of scoliosis progression 0.5 cm length. Because the tissue of idiopathic scoliosis origin remains unknown RNA Seq was performed on bulk RNA samples collected from the entire trunk and tail heads were removed at the level of the gill to eliminate signals associated with abnormal Ptk7 function in the brain.", null, null, null, null, "tg ptk7 beginning 16", null, "isolate:fish #16|age:16 dpf|sex:NA|tissue:trunk|genotype:ptk7 + Tgfoxj1a::ptk7|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of zebrafish at beginning of scoliosis onset: trunk", "tg ptk7 bc 16", "tg ptk7 bc 16", "Total RNA extraction was preformed using the Qiagen RNeasy kit following the manufacturer's instructions Qiagen. RNA sample quality was assessed using an Agilent Bioanalyzer. Library prep and subsequent sequencing was performed by The Centre for Applied Genomics at The Hospital for Sick Children SickKids using the NEBNext stranded RNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP142542", null, null, "Tg_Mut_Ptk7_body_BC_16_R1.fastq.gz Tg_Mut_Ptk7_body_BC_16_R2.fastq.gz", "fastq fastq", 18230004576.0, 72341288.0, "Tg Mut Ptk7 body BC 16 R2.fastq.gz", "0:126 1:126", "A:4770738872;C:4501308359;G:4154385312;T:4786197250;N:17374783", 126, 126, null, null, 4770738872, 4501308359, 4154385312, 4786197250, 17374783, "SRX3992234", "SRS3216613", "SRA694974", "The Hospital for Sick Children|Developmental and Stem Cell Biology", "The Hospital for Sick Children", 2, 0.89667, 0.89511, 0.03831, 0.03776, 0.77082, 0.76911, 0.4238, 0.458, 126, 126, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "Canada", "2019-11-26", "Larval", "Larval", "Trunk", "Surface Structure"], [48118, "SRR7061292", "SRX3992233", "SRS3216612", "SRP142542", "PRJNA453405", "RNA seq of zebrafish ptk7 mutants at beginning of curve onset and ptk7+Tgfoxj1a:ptk7 straight siblings", "PRJNA453405", "Other", "To identify molecular mechanisms underlying scoliosis spine curvature we performed next generation RNA sequencing on ptk7 mutant vs. ptk7+Tgfoxj1a:ptk7 sibling fish at an age correlating with onset of scoliosis progression 0.5 cm length. Because the tissue of idiopathic scoliosis origin remains unknown RNA Seq was performed on bulk RNA samples collected from the entire trunk and tail heads were removed at the level of the gill to eliminate signals associated with abnormal Ptk7 function in the brain.", null, null, null, null, "tg ptk7 beginning 17", null, "isolate:fish #17|age:16 dpf|sex:NA|tissue:trunk|genotype:ptk7 + Tgfoxj1a::ptk7|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of zebrafish at beginning of scoliosis onset: trunk", "tg ptk7 bc 17", "tg ptk7 bc 17", "Total RNA extraction was preformed using the Qiagen RNeasy kit following the manufacturer's instructions Qiagen. RNA sample quality was assessed using an Agilent Bioanalyzer. Library prep and subsequent sequencing was performed by The Centre for Applied Genomics at The Hospital for Sick Children SickKids using the NEBNext stranded RNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP142542", null, null, "Tg_Mut_Ptk7_body_BC_17_R1.fastq.gz Tg_Mut_Ptk7_body_BC_17_R2.fastq.gz", "fastq fastq", 15963544800.0, 63347400.0, "Tg Mut Ptk7 body BC 17 R2.fastq.gz", "0:126 1:126", "A:4152387061;C:3876914533;G:3743807198;T:4174617764;N:15818244", 126, 126, null, null, 4152387061, 3876914533, 3743807198, 4174617764, 15818244, "SRX3992233", "SRS3216612", "SRA694974", "The Hospital for Sick Children|Developmental and Stem Cell Biology", "The Hospital for Sick Children", 2, 0.9524, 0.95134, 0.04376, 0.04268, 0.74556, 0.74014, 0.46096, 0.43976, 126, 126, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "Canada", "2019-11-26", "Larval", "Larval", "Trunk", "Surface Structure"], [48119, "SRR7061293", "SRX3992232", "SRS3216611", "SRP142542", "PRJNA453405", "RNA seq of zebrafish ptk7 mutants at beginning of curve onset and ptk7+Tgfoxj1a:ptk7 straight siblings", "PRJNA453405", "Other", "To identify molecular mechanisms underlying scoliosis spine curvature we performed next generation RNA sequencing on ptk7 mutant vs. ptk7+Tgfoxj1a:ptk7 sibling fish at an age correlating with onset of scoliosis progression 0.5 cm length. Because the tissue of idiopathic scoliosis origin remains unknown RNA Seq was performed on bulk RNA samples collected from the entire trunk and tail heads were removed at the level of the gill to eliminate signals associated with abnormal Ptk7 function in the brain.", null, null, null, null, "ptk7 beginning 5", null, "isolate:fish #5|age:16 dpf|sex:NA|tissue:trunk|disease:idiopathic scoliosis|disease stg:onset of curve|genotype:ptk7|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of zebrafish at beginning of scoliosis onset: trunk", "ptk7 bc 5", "ptk7 bc 5", "Total RNA extraction was preformed using the Qiagen RNeasy kit following the manufacturer's instructions Qiagen. RNA sample quality was assessed using an Agilent Bioanalyzer. Library prep and subsequent sequencing was performed by The Centre for Applied Genomics at The Hospital for Sick Children SickKids using the NEBNext stranded RNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP142542", null, null, "Mut_Ptk7_body_BC_5_R1.fastq.gz Mut_Ptk7_body_BC_5_R2.fastq.gz", "fastq fastq", 19542002508.0, 77547629.0, "Mut Ptk7 body BC 5 R1.fastq.gz", "0:126 1:126", "A:5239466803;C:4599632249;G:4496980222;T:5182933554;N:22989680", 126, 126, null, null, 5239466803, 4599632249, 4496980222, 5182933554, 22989680, "SRX3992232", "SRS3216611", "SRA694974", "The Hospital for Sick Children|Developmental and Stem Cell Biology", "The Hospital for Sick Children", 2, 0.94155, 0.94116, 0.08675, 0.08906, 0.71384, 0.72025, 0.45722, 0.46471, 126, 126, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "Canada", "2018-04-24", "Larval", "Larval", "Trunk", "Surface Structure"], [48120, "SRR7061294", "SRX3992231", "SRS3216610", "SRP142542", "PRJNA453405", "RNA seq of zebrafish ptk7 mutants at beginning of curve onset and ptk7+Tgfoxj1a:ptk7 straight siblings", "PRJNA453405", "Other", "To identify molecular mechanisms underlying scoliosis spine curvature we performed next generation RNA sequencing on ptk7 mutant vs. ptk7+Tgfoxj1a:ptk7 sibling fish at an age correlating with onset of scoliosis progression 0.5 cm length. Because the tissue of idiopathic scoliosis origin remains unknown RNA Seq was performed on bulk RNA samples collected from the entire trunk and tail heads were removed at the level of the gill to eliminate signals associated with abnormal Ptk7 function in the brain.", null, null, null, null, "ptk7 beginning 6", null, "isolate:fish #6|age:16 dpf|sex:NA|tissue:trunk|disease:idiopathic scoliosis|disease stg:onset of curve|genotype:ptk7|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of zebrafish at beginning of scoliosis onset: trunk", "ptk7 bc 6", "ptk7 bc 6", "Total RNA extraction was preformed using the Qiagen RNeasy kit following the manufacturer's instructions Qiagen. RNA sample quality was assessed using an Agilent Bioanalyzer. Library prep and subsequent sequencing was performed by The Centre for Applied Genomics at The Hospital for Sick Children SickKids using the NEBNext stranded RNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP142542", null, null, "Mut_Ptk7_body_BC_6_R1.fastq.gz Mut_Ptk7_body_BC_6_R2.fastq.gz", "fastq fastq", 15025670100.0, 59625675.0, "Mut Ptk7 body BC 6 R1.fastq.gz", "0:126 1:126", "A:4008673912;C:3530336734;G:3479093779;T:3991560475;N:16005200", 126, 126, null, null, 4008673912, 3530336734, 3479093779, 3991560475, 16005200, "SRX3992231", "SRS3216610", "SRA694974", "The Hospital for Sick Children|Developmental and Stem Cell Biology", "The Hospital for Sick Children", 2, 0.94076, 0.94186, 0.08203, 0.08457, 0.71693, 0.72188, 0.45758, 0.46903, 126, 126, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "Canada", "2019-11-26", "Larval", "Larval", "Trunk", "Surface Structure"], [48121, "SRR7061295", "SRX3992230", "SRS3216609", "SRP142542", "PRJNA453405", "RNA seq of zebrafish ptk7 mutants at beginning of curve onset and ptk7+Tgfoxj1a:ptk7 straight siblings", "PRJNA453405", "Other", "To identify molecular mechanisms underlying scoliosis spine curvature we performed next generation RNA sequencing on ptk7 mutant vs. ptk7+Tgfoxj1a:ptk7 sibling fish at an age correlating with onset of scoliosis progression 0.5 cm length. Because the tissue of idiopathic scoliosis origin remains unknown RNA Seq was performed on bulk RNA samples collected from the entire trunk and tail heads were removed at the level of the gill to eliminate signals associated with abnormal Ptk7 function in the brain.", null, null, null, null, "ptk7 beginning 3", null, "isolate:fish #3|age:16 dpf|sex:NA|tissue:trunk|disease:idiopathic scoliosis|disease stg:onset of curve|genotype:ptk7|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of zebrafish at beginning of scoliosis onset: trunk", "ptk7 bc 3", "ptk7 bc 3", "Total RNA extraction was preformed using the Qiagen RNeasy kit following the manufacturer's instructions Qiagen. RNA sample quality was assessed using an Agilent Bioanalyzer. Library prep and subsequent sequencing was performed by The Centre for Applied Genomics at The Hospital for Sick Children SickKids using the NEBNext stranded RNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP142542", null, null, "Mut_Ptk7_body_BC_3_R1.fastq.gz Mut_Ptk7_body_BC_3_R2.fastq.gz", "fastq fastq", 13349261772.0, 52973261.0, "Mut Ptk7 body BC 3 R1.fastq.gz", "0:126 1:126", "A:3468695285;C:3240330681;G:3133095510;T:3496115282;N:11025014", 126, 126, null, null, 3468695285, 3240330681, 3133095510, 3496115282, 11025014, "SRX3992230", "SRS3216609", "SRA694974", "The Hospital for Sick Children|Developmental and Stem Cell Biology", "The Hospital for Sick Children", 2, 0.95269, 0.95384, 0.0542, 0.05571, 0.72502, 0.7293, 0.4481, 0.45593, 126, 126, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "Canada", "2019-11-26", "Larval", "Larval", "Trunk", "Surface Structure"], [48122, "SRR7061296", "SRX3992229", "SRS3216608", "SRP142542", "PRJNA453405", "RNA seq of zebrafish ptk7 mutants at beginning of curve onset and ptk7+Tgfoxj1a:ptk7 straight siblings", "PRJNA453405", "Other", "To identify molecular mechanisms underlying scoliosis spine curvature we performed next generation RNA sequencing on ptk7 mutant vs. ptk7+Tgfoxj1a:ptk7 sibling fish at an age correlating with onset of scoliosis progression 0.5 cm length. Because the tissue of idiopathic scoliosis origin remains unknown RNA Seq was performed on bulk RNA samples collected from the entire trunk and tail heads were removed at the level of the gill to eliminate signals associated with abnormal Ptk7 function in the brain.", null, null, null, null, "ptk7 beginning 4", null, "isolate:fish #4|age:16 dpf|sex:NA|tissue:trunk|disease:idiopathic scoliosis|disease stg:onset of curve|genotype:ptk7|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of zebrafish at beginning of scoliosis onset: trunk", "ptk7 bc 4", "ptk7 bc 4", "Total RNA extraction was preformed using the Qiagen RNeasy kit following the manufacturer's instructions Qiagen. RNA sample quality was assessed using an Agilent Bioanalyzer. Library prep and subsequent sequencing was performed by The Centre for Applied Genomics at The Hospital for Sick Children SickKids using the NEBNext stranded RNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP142542", null, null, "Mut_Ptk7_body_BC_4_R1.fastq.gz Mut_Ptk7_body_BC_4_R2.fastq.gz", "fastq fastq", 15955541532.0, 63315641.0, "Mut Ptk7 body BC 4 R1.fastq.gz", "0:126 1:126", "A:4194932443;C:3801291346;G:3733150757;T:4208258150;N:17908836", 126, 126, null, null, 4194932443, 3801291346, 3733150757, 4208258150, 17908836, "SRX3992229", "SRS3216608", "SRA694974", "The Hospital for Sick Children|Developmental and Stem Cell Biology", "The Hospital for Sick Children", 2, 0.94726, 0.94809, 0.0624, 0.06365, 0.71965, 0.72537, 0.47355, 0.47537, 126, 126, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "Canada", "2019-11-26", "Larval", "Larval", "Trunk", "Surface Structure"], [48123, "SRR7061297", "SRX3992228", "SRS3216607", "SRP142542", "PRJNA453405", "RNA seq of zebrafish ptk7 mutants at beginning of curve onset and ptk7+Tgfoxj1a:ptk7 straight siblings", "PRJNA453405", "Other", "To identify molecular mechanisms underlying scoliosis spine curvature we performed next generation RNA sequencing on ptk7 mutant vs. ptk7+Tgfoxj1a:ptk7 sibling fish at an age correlating with onset of scoliosis progression 0.5 cm length. Because the tissue of idiopathic scoliosis origin remains unknown RNA Seq was performed on bulk RNA samples collected from the entire trunk and tail heads were removed at the level of the gill to eliminate signals associated with abnormal Ptk7 function in the brain.", null, null, null, null, "ptk7 beginning 1", null, "isolate:fish #1|age:16 dpf|sex:NA|tissue:trunk|disease:idiopathic scoliosis|disease stg:onset of curve|genotype:ptk7|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of zebrafish at beginning of scoliosis onset: trunk", "ptk7 bc 1", "ptk7 bc 1", "Total RNA extraction was preformed using the Qiagen RNeasy kit following the manufacturer's instructions Qiagen. RNA sample quality was assessed using an Agilent Bioanalyzer. Library prep and subsequent sequencing was performed by The Centre for Applied Genomics at The Hospital for Sick Children SickKids using the NEBNext stranded RNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP142542", null, null, "Mut_Ptk7_body_BC_1_R1.fastq.gz Mut_Ptk7_body_BC_1_R2.fastq.gz", "fastq fastq", 16619171688.0, 65949094.0, "Mut Ptk7 body BC 1 R1.fastq.gz", "0:126 1:126", "A:4312352521;C:4041193834;G:3953363168;T:4294491628;N:17770537", 126, 126, null, null, 4312352521, 4041193834, 3953363168, 4294491628, 17770537, "SRX3992228", "SRS3216607", "SRA694974", "The Hospital for Sick Children|Developmental and Stem Cell Biology", "The Hospital for Sick Children", 2, 0.96015, 0.9616, 0.04222, 0.04353, 0.7303, 0.73647, 0.45408, 0.46116, 126, 126, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "Canada", "2019-11-26", "Larval", "Larval", "Trunk", "Surface Structure"], [48124, "SRR7061298", "SRX3992227", "SRS3216606", "SRP142542", "PRJNA453405", "RNA seq of zebrafish ptk7 mutants at beginning of curve onset and ptk7+Tgfoxj1a:ptk7 straight siblings", "PRJNA453405", "Other", "To identify molecular mechanisms underlying scoliosis spine curvature we performed next generation RNA sequencing on ptk7 mutant vs. ptk7+Tgfoxj1a:ptk7 sibling fish at an age correlating with onset of scoliosis progression 0.5 cm length. Because the tissue of idiopathic scoliosis origin remains unknown RNA Seq was performed on bulk RNA samples collected from the entire trunk and tail heads were removed at the level of the gill to eliminate signals associated with abnormal Ptk7 function in the brain.", null, null, null, null, "ptk7 beginning 2", null, "isolate:fish #2|age:16 dpf|sex:NA|tissue:trunk|disease:idiopathic scoliosis|disease stg:onset of curve|genotype:ptk7|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of zebrafish at beginning of scoliosis onset: trunk", "ptk7 bc 2", "ptk7 bc 2", "Total RNA extraction was preformed using the Qiagen RNeasy kit following the manufacturer's instructions Qiagen. RNA sample quality was assessed using an Agilent Bioanalyzer. Library prep and subsequent sequencing was performed by The Centre for Applied Genomics at The Hospital for Sick Children SickKids using the NEBNext stranded RNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP142542", null, null, "Mut_Ptk7_body_BC_2_R1.fastq.gz Mut_Ptk7_body_BC_2_R2.fastq.gz", "fastq fastq", 14799609216.0, 58728608.0, "Mut Ptk7 body BC 2 R2.fastq.gz", "0:126 1:126", "A:3874071255;C:3562796142;G:3473537895;T:3874207407;N:14996517", 126, 126, null, null, 3874071255, 3562796142, 3473537895, 3874207407, 14996517, "SRX3992227", "SRS3216606", "SRA694974", "The Hospital for Sick Children|Developmental and Stem Cell Biology", "The Hospital for Sick Children", 2, 0.94642, 0.9446, 0.09548, 0.09301, 0.72882, 0.72133, 0.44805, 0.44195, 126, 126, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "Canada", "2019-11-26", "Larval", "Larval", "Trunk", "Surface Structure"], [48125, "SRR7061299", "SRX3992226", "SRS3216603", "SRP142542", "PRJNA453405", "RNA seq of zebrafish ptk7 mutants at beginning of curve onset and ptk7+Tgfoxj1a:ptk7 straight siblings", "PRJNA453405", "Other", "To identify molecular mechanisms underlying scoliosis spine curvature we performed next generation RNA sequencing on ptk7 mutant vs. ptk7+Tgfoxj1a:ptk7 sibling fish at an age correlating with onset of scoliosis progression 0.5 cm length. Because the tissue of idiopathic scoliosis origin remains unknown RNA Seq was performed on bulk RNA samples collected from the entire trunk and tail heads were removed at the level of the gill to eliminate signals associated with abnormal Ptk7 function in the brain.", null, null, null, null, "tg ptk7 beginning 24", null, "isolate:fish #24|age:16 dpf|sex:NA|tissue:trunk|genotype:ptk7 + Tgfoxj1a::ptk7|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of zebrafish at beginning of scoliosis onset: trunk", "tg ptk7 bc 24", "tg ptk7 bc 24", "Total RNA extraction was preformed using the Qiagen RNeasy kit following the manufacturer's instructions Qiagen. RNA sample quality was assessed using an Agilent Bioanalyzer. Library prep and subsequent sequencing was performed by The Centre for Applied Genomics at The Hospital for Sick Children SickKids using the NEBNext stranded RNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP142542", null, null, "Tg_Mut_Ptk7_body_BC_24_R1.fastq.gz Tg_Mut_Ptk7_body_BC_24_R2.fastq.gz", "fastq fastq", 15451786224.0, 61316612.0, "Tg Mut Ptk7 body BC 24 R1.fastq.gz", "0:126 1:126", "A:4033286339;C:3744828094;G:3591368414;T:4066188504;N:16114873", 126, 126, null, null, 4033286339, 3744828094, 3591368414, 4066188504, 16114873, "SRX3992226", "SRS3216603", "SRA694974", "The Hospital for Sick Children|Developmental and Stem Cell Biology", "The Hospital for Sick Children", 2, 0.94809, 0.95045, 0.06395, 0.06563, 0.74696, 0.75221, 0.46965, 0.4482, 126, 126, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "Canada", "2019-11-26", "Larval", "Larval", "Trunk", "Surface Structure"], [48126, "SRR7061300", "SRX3992225", "SRS3216604", "SRP142542", "PRJNA453405", "RNA seq of zebrafish ptk7 mutants at beginning of curve onset and ptk7+Tgfoxj1a:ptk7 straight siblings", "PRJNA453405", "Other", "To identify molecular mechanisms underlying scoliosis spine curvature we performed next generation RNA sequencing on ptk7 mutant vs. ptk7+Tgfoxj1a:ptk7 sibling fish at an age correlating with onset of scoliosis progression 0.5 cm length. Because the tissue of idiopathic scoliosis origin remains unknown RNA Seq was performed on bulk RNA samples collected from the entire trunk and tail heads were removed at the level of the gill to eliminate signals associated with abnormal Ptk7 function in the brain.", null, null, null, null, "tg ptk7 beginning 25", null, "isolate:fish #25|age:16 dpf|sex:NA|tissue:trunk|genotype:ptk7 + Tgfoxj1a::ptk7|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of zebrafish at beginning of scoliosis onset: trunk", "tg ptk7 bc 25", "tg ptk7 bc 25", "Total RNA extraction was preformed using the Qiagen RNeasy kit following the manufacturer's instructions Qiagen. RNA sample quality was assessed using an Agilent Bioanalyzer. Library prep and subsequent sequencing was performed by The Centre for Applied Genomics at The Hospital for Sick Children SickKids using the NEBNext stranded RNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP142542", null, null, "Tg_Mut_Ptk7_body_BC_25_R1.fastq.gz Tg_Mut_Ptk7_body_BC_25_R2.fastq.gz", "fastq fastq", 19414976112.0, 77043556.0, "Tg Mut Ptk7 body BC 25 R2.fastq.gz", "0:126 1:126", "A:5068881331;C:4706060760;G:4550013699;T:5065895399;N:24124923", 126, 126, null, null, 5068881331, 4706060760, 4550013699, 5065895399, 24124923, "SRX3992225", "SRS3216604", "SRA694974", "The Hospital for Sick Children|Developmental and Stem Cell Biology", "The Hospital for Sick Children", 2, 0.93933, 0.93774, 0.05308, 0.05225, 0.75221, 0.74844, 0.45336, 0.45649, 126, 126, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "Canada", "2019-11-26", "Larval", "Larval", "Trunk", "Surface Structure"], [48127, "SRR7061301", "SRX3992224", "SRS3216605", "SRP142542", "PRJNA453405", "RNA seq of zebrafish ptk7 mutants at beginning of curve onset and ptk7+Tgfoxj1a:ptk7 straight siblings", "PRJNA453405", "Other", "To identify molecular mechanisms underlying scoliosis spine curvature we performed next generation RNA sequencing on ptk7 mutant vs. ptk7+Tgfoxj1a:ptk7 sibling fish at an age correlating with onset of scoliosis progression 0.5 cm length. Because the tissue of idiopathic scoliosis origin remains unknown RNA Seq was performed on bulk RNA samples collected from the entire trunk and tail heads were removed at the level of the gill to eliminate signals associated with abnormal Ptk7 function in the brain.", null, null, null, null, "tg ptk7 beginning 26", null, "isolate:fish #26|age:16 dpf|sex:NA|tissue:trunk|genotype:ptk7 + Tgfoxj1a::ptk7|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of zebrafish at beginning of scoliosis onset: trunk", "tg ptk7 bc 26", "tg ptk7 bc 26", "Total RNA extraction was preformed using the Qiagen RNeasy kit following the manufacturer's instructions Qiagen. RNA sample quality was assessed using an Agilent Bioanalyzer. Library prep and subsequent sequencing was performed by The Centre for Applied Genomics at The Hospital for Sick Children SickKids using the NEBNext stranded RNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP142542", null, null, "Tg_Mut_Ptk7_body_BC_26_R1.fastq.gz Tg_Mut_Ptk7_body_BC_26_R2.fastq.gz", "fastq fastq", 14629258476.0, 58052613.0, "Tg Mut Ptk7 body BC 26 R1.fastq.gz", "0:126 1:126", "A:3823786035;C:3525708876;G:3400152685;T:3865868094;N:13742786", 126, 126, null, null, 3823786035, 3525708876, 3400152685, 3865868094, 13742786, "SRX3992224", "SRS3216605", "SRA694974", "The Hospital for Sick Children|Developmental and Stem Cell Biology", "The Hospital for Sick Children", 2, 0.95443, 0.95502, 0.04566, 0.04676, 0.73882, 0.7441, 0.43821, 0.44797, 126, 126, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "Canada", "2019-11-26", "Larval", "Larval", "Trunk", "Surface Structure"], [48128, "SRR7061302", "SRX3992223", "SRS3216602", "SRP142542", "PRJNA453405", "RNA seq of zebrafish ptk7 mutants at beginning of curve onset and ptk7+Tgfoxj1a:ptk7 straight siblings", "PRJNA453405", "Other", "To identify molecular mechanisms underlying scoliosis spine curvature we performed next generation RNA sequencing on ptk7 mutant vs. ptk7+Tgfoxj1a:ptk7 sibling fish at an age correlating with onset of scoliosis progression 0.5 cm length. Because the tissue of idiopathic scoliosis origin remains unknown RNA Seq was performed on bulk RNA samples collected from the entire trunk and tail heads were removed at the level of the gill to eliminate signals associated with abnormal Ptk7 function in the brain.", null, null, null, null, "tg ptk7 beginning 27", null, "isolate:fish #27|age:16 dpf|sex:NA|tissue:trunk|genotype:ptk7 + Tgfoxj1a::ptk7|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of zebrafish at beginning of scoliosis onset: trunk", "tg ptk7 bc 27", "tg ptk7 bc 27", "Total RNA extraction was preformed using the Qiagen RNeasy kit following the manufacturer's instructions Qiagen. RNA sample quality was assessed using an Agilent Bioanalyzer. Library prep and subsequent sequencing was performed by The Centre for Applied Genomics at The Hospital for Sick Children SickKids using the NEBNext stranded RNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP142542", null, null, "Tg_Mut_Ptk7_body_BC_27_R1.fastq.gz Tg_Mut_Ptk7_body_BC_27_R2.fastq.gz", "fastq fastq", 15118499592.0, 59994046.0, "Tg Mut Ptk7 body BC 27 R1.fastq.gz", "0:126 1:126", "A:3988013765;C:3602884642;G:3492600730;T:4018560745;N:16439710", 126, 126, null, null, 3988013765, 3602884642, 3492600730, 4018560745, 16439710, "SRX3992223", "SRS3216602", "SRA694974", "The Hospital for Sick Children|Developmental and Stem Cell Biology", "The Hospital for Sick Children", 2, 0.94992, 0.94984, 0.05417, 0.05542, 0.73249, 0.73813, 0.46542, 0.4591, 126, 126, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "Canada", "2019-11-26", "Larval", "Larval", "Trunk", "Surface Structure"], [48178, "SRR7089628", "SRX4018604", "SRS3239991", "SRP144228", "PRJNA454503", "RNA seq of zebrafish ptk7 mutants with mild and severe scoliosis and ptk7+Tgfoxj1a:ptk7 straight siblings", "PRJNA454503", "Other", "To identify molecular mechanisms underlying scoliosis spine curvature we performed next generation RNA sequencing on ptk7 mutant vs. ptk7+Tgfoxj1a:ptk7 sibling fish at an age correlating with mild scoliosis and severe scoliosis 0.8 cm length. Because the tissue of idiopathic scoliosis origin remains unknown RNA Seq was performed on bulk RNA samples collected from the entire trunk and tail heads were removed at the level of the gill to eliminate signals associated with abnormal Ptk7 function in the brain.", null, null, null, null, "ptk7 + Tgfoxj1a::ptk7 sm 49", null, "isolate:fish #49|age:21 dpf|sex:NA|tissue:trunk|genotype:ptk7 + Tgfoxj1a::ptk7|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA sequencing of Danio rerio: mild and severe scoliosis trunk", "tg ptk7 sm 49", "tg ptk7 sm 49", "Total RNA extraction was preformed using the Qiagen RNeasy kit following the manufacturer's instructions Qiagen. RNA sample quality was assessed using an Agilent Bioanalyzer. 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