{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_source = \"TRANSCRIPTOMIC\", technology = \"bulk\" and tissue_curation_coarse = \"Surface Structure\"", "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. 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, "sibCGFP4", "GSM7749557", 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", "sibCGFP4", "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", "GSM7749557", "GSM7749557: sibCGFP4; Danio rerio; RNA Seq", "GSM7749557 r1", "GSM7749557", "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-sibCGFP4_S46_L002_R1_001.fastq.gz WA-3548-sibCGFP4_S46_L002_R2_001.fastq.gz", "fastq fastq", 11996252984.0, 39722692.0, "GSM7749557 r1", "0:151 1:151", "A:3208564840;C:2791941387;G:2921724669;T:3073456372;N:565716", 151, 151, null, null, 3208564840, 2791941387, 2921724669, 3073456372, 565716, "SRX21589492", "SRS18767065", "SRA1703879", "Ume\u00e5 Univeristy", "Ume\u00e5 Univeristy", 2, 0.96224, 0.96334, 0.07442, 0.07372, 0.70595, 0.70688, 0.47053, 0.46853, 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"], [25330, "SRR25868072", "SRX21589491", "SRS18767064", "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, "sibCGFP3", "GSM7749556", 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", "sibCGFP3", "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", "GSM7749556", "GSM7749556: sibCGFP3; Danio rerio; RNA Seq", "GSM7749556 r1", "GSM7749556", "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-sibCGFP3_S45_L002_R1_001.fastq.gz WA-3548-sibCGFP3_S45_L002_R2_001.fastq.gz", "fastq fastq", 10113421300.0, 33488150.0, "GSM7749556 r1", "0:151 1:151", "A:2677217319;C:2366433560;G:2481164832;T:2588131881;N:473708", 151, 151, null, null, 2677217319, 2366433560, 2481164832, 2588131881, 473708, "SRX21589491", "SRS18767064", "SRA1703879", "Ume\u00e5 Univeristy", "Ume\u00e5 Univeristy", 2, 0.96295, 0.96335, 0.07275, 0.07118, 0.70654, 0.7092, 0.45672, 0.44027, 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"], [25331, "SRR25868073", "SRX21589490", "SRS18767063", "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, "sibCGFP2", "GSM7749555", 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", "sibCGFP2", "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", "GSM7749555", "GSM7749555: sibCGFP2; Danio rerio; RNA Seq", "GSM7749555 r1", "GSM7749555", "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-sibCGFP2_S44_L002_R1_001.fastq.gz WA-3548-sibCGFP2_S44_L002_R2_001.fastq.gz", "fastq fastq", 10142198578.0, 33583439.0, "GSM7749555 r1", "0:151 1:151", "A:2687719512;C:2375571494;G:2493046337;T:2585391111;N:470124", 151, 151, null, null, 2687719512, 2375571494, 2493046337, 2585391111, 470124, "SRX21589490", "SRS18767063", "SRA1703879", "Ume\u00e5 Univeristy", "Ume\u00e5 Univeristy", 2, 0.96241, 0.96294, 0.07398, 0.07262, 0.70524, 0.70589, 0.45777, 0.46014, 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"], [25332, "SRR25868074", "SRX21589489", "SRS18767062", "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, "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. 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", "GSM7749554", "GSM7749554: sibCGFP1; Danio rerio; RNA Seq", "GSM7749554 r1", "GSM7749554", "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-sibCGFP1_S43_L002_R1_001.fastq.gz WA-3548-sibCGFP1_S43_L002_R2_001.fastq.gz", "fastq fastq", 10994030650.0, 36404075.0, "GSM7749554 r1", "0:151 1:151", "A:2911908895;C:2573164804;G:2700790583;T:2807654156;N:512212", 151, 151, null, null, 2911908895, 2573164804, 2700790583, 2807654156, 512212, "SRX21589489", "SRS18767062", "SRA1703879", "Ume\u00e5 Univeristy", "Ume\u00e5 Univeristy", 2, 0.96119, 0.96215, 0.07361, 0.07253, 0.70632, 0.7069, 0.45503, 0.45981, 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"], [25333, "SRR25868075", "SRX21589488", "SRS18767059", "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, "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. 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-sibC4_S42_L002_R1_001.fastq.gz WA-3548-sibC4_S42_L002_R2_001.fastq.gz", "fastq fastq", 11107320816.0, 36779208.0, "GSM7749553 r1", "0:151 1:151", "A:2945889871;C:2588267204;G:2719520712;T:2853118433;N:524596", 151, 151, null, null, 2945889871, 2588267204, 2719520712, 2853118433, 524596, "SRX21589488", "SRS18767059", "SRA1703879", "Ume\u00e5 Univeristy", "Ume\u00e5 Univeristy", 2, 0.96098, 0.96213, 0.07535, 0.07463, 0.70623, 0.70749, 0.42034, 0.43255, 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"], [25334, "SRR25868076", "SRX21589487", "SRS18767060", "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, "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. 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-sibC3_S41_L002_R1_001.fastq.gz WA-3548-sibC3_S41_L002_R2_001.fastq.gz", "fastq fastq", 12566811014.0, 41611957.0, "GSM7749552 r1", "0:151 1:151", "A:3330340903;C:2960050871;G:3087690864;T:3188143295;N:585081", 151, 151, null, null, 3330340903, 2960050871, 3087690864, 3188143295, 585081, "SRX21589487", "SRS18767060", "SRA1703879", "Ume\u00e5 Univeristy", "Ume\u00e5 Univeristy", 2, 0.9619, 0.96201, 0.08592, 0.08414, 0.69581, 0.69637, 0.47091, 0.47561, 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"], [25335, "SRR25868077", "SRX21589486", "SRS18767057", "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, "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"], [33894, "SRR30866028", "SRX26263941", "SRS22803195", "SRP536275", "PRJNA1168148", "Mgat4b mediated selective N glycosyl modification regulates melanocyte development and melanoma progression [bulk RNA seq]", "GSE278653", "Transcriptome Analysis", "Dysregulated melanocyte state transitions are a pivotal driver of melanoma development  highlighting the need to identify key regulators of these processes. Understanding these factors is key to know how normal melanocyte functions and shift towards initiation of melanoma. Our study identifies Mgat4b  a glycosyl transferase involved in selective N glycan branching enriched in pigment progenitors  as a key regulator of directional melanocyte migration and establishment of Melanocyte stem cell McSC pool during early development in zebrafish and mammalian melanocytes. Single cell RNA sequencing analysis in zebrafish upon targeted disruption of Mgat4b reveals that a subset of melanocytes marked by aberrant galectin expression are impaired in migration and are lost. Lectin binding proteomic analysis reveals the glycosylation of key melanocyte proteins Gpnmb  Kit  and Tyrp1 to be under the control of Mgat4b. Additionally  mislocalization of Gamma catenin Jup explains the observed defects in cell adhesion and migration to be regulated by mgat4b but not its isozyme mgat4a. Our meta analysis further revealed that melanoma patients with both the BrafV600E mutation and elevated Mgat4b levels have significantly worse survival outcomes compared to those with only the BrafV600E mutation. By leveraging the MAZERATI platform to model BrafV600E driver mutation in vivo  we show that Mgat4b mutant cells fail to aggregate and initiate tumors. Our study underscores the importance of selective N glycan branching in both melanocyte development and melanoma initiation  suggesting a Mitf controlled Mgat4b as a promising therapeutic target for melanoma treatment. Overall design: To investigate the mechanisms that inhibit mutant cells from initiating melanoma in the absence of mgat4b  we utilized mature melanophores and melanoma cells from the skin of five zebrafish  including both MAZERATI wild type and  MAZERATI zebrafish carrying mgat4b mutations. We then performed gene expression profiling analysis using data obtained from RNA seq of melanophores and melanoma cells from both the zebrafish wild type and m4b mut. Comparative gene expression analysis was performed for wild type melanoma and melanophores  m4b mut melanoma and melanophores  wild type and m4b mut melanoma.", null, null, null, "m4b mut melanoma  biol rep 2", "GSM8552314", null, "source name:skin|tissue:skin|cell type:melanoma|genotype:mgat4b mutant|treatment:MAZERATI|geo loc name:missing|collection date:missing", "m4b mut melanoma  biol rep 2", "Raw fastq files were trimmed using trimmomatic to remove adaptors and retain high quality reads. The reads were then aligned with zebrafish reference assembly GRCz11 using STAR. Featurecounts was used to calculate raw counts from the aligned reads. Assembly: GRCz11 Supplementary files format and content: tab delimited text file including raw counts for each sample", "skin", null, "The cell isolation process involved density gradient centrifugation  followed by RNA extraction using Trizol method. Illumina standard total RNA prep kit was used for library construction", null, "tissue:skin|cell type:melanoma|genotype:mgat4b mutant|treatment:MAZERATI", "GSM8552314", "GSM8552314: m4b mut melanoma  biol rep 2; Danio rerio; RNA Seq", "GSM8552314 r1", "GSM8552314", "1", "The cell isolation process involved density gradient centrifugation  followed by RNA extraction using Trizol method. Illumina standard total RNA prep kit was used for library construction", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP536275", null, null, "MKO2_S39_R1_001.fastq.gz MKO2_S39_R2_001.fastq.gz", "fastq fastq", 3705364625.0, 14164066.0, "GSM8552314 r1", "0:126.72 1:134.89", "A:785806700;C:949078797;G:1178279032;T:784972987;N:7227109", 126, 134, null, null, 785806700, 949078797, 1178279032, 784972987, 7227109, "SRX26263941", "SRS22803195", "SRA1984938", "Pigment Cell Biology Lab, CSIR-IGIB", "Pigment Cell Biology Lab, CSIR-IGIB", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "trueseq", "sc_generic", "bulk", "bulk", null, "India", "2024-10-02", "Undetermined", "Undetermined", "Skin", "Surface Structure"], [33895, "SRR30866029", "SRX26263940", "SRS22803194", "SRP536275", "PRJNA1168148", "Mgat4b mediated selective N glycosyl modification regulates melanocyte development and melanoma progression [bulk RNA seq]", "GSE278653", "Transcriptome Analysis", "Dysregulated melanocyte state transitions are a pivotal driver of melanoma development  highlighting the need to identify key regulators of these processes. Understanding these factors is key to know how normal melanocyte functions and shift towards initiation of melanoma. Our study identifies Mgat4b  a glycosyl transferase involved in selective N glycan branching enriched in pigment progenitors  as a key regulator of directional melanocyte migration and establishment of Melanocyte stem cell McSC pool during early development in zebrafish and mammalian melanocytes. Single cell RNA sequencing analysis in zebrafish upon targeted disruption of Mgat4b reveals that a subset of melanocytes marked by aberrant galectin expression are impaired in migration and are lost. Lectin binding proteomic analysis reveals the glycosylation of key melanocyte proteins Gpnmb  Kit  and Tyrp1 to be under the control of Mgat4b. Additionally  mislocalization of Gamma catenin Jup explains the observed defects in cell adhesion and migration to be regulated by mgat4b but not its isozyme mgat4a. Our meta analysis further revealed that melanoma patients with both the BrafV600E mutation and elevated Mgat4b levels have significantly worse survival outcomes compared to those with only the BrafV600E mutation. By leveraging the MAZERATI platform to model BrafV600E driver mutation in vivo  we show that Mgat4b mutant cells fail to aggregate and initiate tumors. Our study underscores the importance of selective N glycan branching in both melanocyte development and melanoma initiation  suggesting a Mitf controlled Mgat4b as a promising therapeutic target for melanoma treatment. Overall design: To investigate the mechanisms that inhibit mutant cells from initiating melanoma in the absence of mgat4b  we utilized mature melanophores and melanoma cells from the skin of five zebrafish  including both MAZERATI wild type and  MAZERATI zebrafish carrying mgat4b mutations. We then performed gene expression profiling analysis using data obtained from RNA seq of melanophores and melanoma cells from both the zebrafish wild type and m4b mut. Comparative gene expression analysis was performed for wild type melanoma and melanophores  m4b mut melanoma and melanophores  wild type and m4b mut melanoma.", null, null, null, "m4b mut melanoma  biol rep 1", "GSM8552313", null, "source name:skin|tissue:skin|cell type:melanoma|genotype:mgat4b mutant|treatment:MAZERATI|geo loc name:missing|collection date:missing", "m4b mut melanoma  biol rep 1", "Raw fastq files were trimmed using trimmomatic to remove adaptors and retain high quality reads. The reads were then aligned with zebrafish reference assembly GRCz11 using STAR. Featurecounts was used to calculate raw counts from the aligned reads. Assembly: GRCz11 Supplementary files format and content: tab delimited text file including raw counts for each sample", "skin", null, "The cell isolation process involved density gradient centrifugation  followed by RNA extraction using Trizol method. Illumina standard total RNA prep kit was used for library construction", null, "tissue:skin|cell type:melanoma|genotype:mgat4b mutant|treatment:MAZERATI", "GSM8552313", "GSM8552313: m4b mut melanoma  biol rep 1; Danio rerio; RNA Seq", "GSM8552313 r1", "GSM8552313", "1", "The cell isolation process involved density gradient centrifugation  followed by RNA extraction using Trizol method. Illumina standard total RNA prep kit was used for library construction", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP536275", null, null, "MKO1_S38_R1_001.fastq.gz MKO1_S38_R2_001.fastq.gz", "fastq fastq", 4779377372.0, 18058294.0, "GSM8552313 r1", "0:128.72 1:135.94", "A:1016908920;C:1236613888;G:1502465334;T:1018053808;N:5335422", 128, 135, null, null, 1016908920, 1236613888, 1502465334, 1018053808, 5335422, "SRX26263940", "SRS22803194", "SRA1984938", "Pigment Cell Biology Lab, CSIR-IGIB", "Pigment Cell Biology Lab, CSIR-IGIB", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "trueseq", "sc_generic", "bulk", "bulk", null, "India", "2024-10-02", "Undetermined", "Undetermined", "Skin", "Surface Structure"], [33896, "SRR30866030", "SRX26263939", "SRS22803193", "SRP536275", "PRJNA1168148", "Mgat4b mediated selective N glycosyl modification regulates melanocyte development and melanoma progression [bulk RNA seq]", "GSE278653", "Transcriptome Analysis", "Dysregulated melanocyte state transitions are a pivotal driver of melanoma development  highlighting the need to identify key regulators of these processes. Understanding these factors is key to know how normal melanocyte functions and shift towards initiation of melanoma. Our study identifies Mgat4b  a glycosyl transferase involved in selective N glycan branching enriched in pigment progenitors  as a key regulator of directional melanocyte migration and establishment of Melanocyte stem cell McSC pool during early development in zebrafish and mammalian melanocytes. Single cell RNA sequencing analysis in zebrafish upon targeted disruption of Mgat4b reveals that a subset of melanocytes marked by aberrant galectin expression are impaired in migration and are lost. Lectin binding proteomic analysis reveals the glycosylation of key melanocyte proteins Gpnmb  Kit  and Tyrp1 to be under the control of Mgat4b. Additionally  mislocalization of Gamma catenin Jup explains the observed defects in cell adhesion and migration to be regulated by mgat4b but not its isozyme mgat4a. Our meta analysis further revealed that melanoma patients with both the BrafV600E mutation and elevated Mgat4b levels have significantly worse survival outcomes compared to those with only the BrafV600E mutation. By leveraging the MAZERATI platform to model BrafV600E driver mutation in vivo  we show that Mgat4b mutant cells fail to aggregate and initiate tumors. Our study underscores the importance of selective N glycan branching in both melanocyte development and melanoma initiation  suggesting a Mitf controlled Mgat4b as a promising therapeutic target for melanoma treatment. Overall design: To investigate the mechanisms that inhibit mutant cells from initiating melanoma in the absence of mgat4b  we utilized mature melanophores and melanoma cells from the skin of five zebrafish  including both MAZERATI wild type and  MAZERATI zebrafish carrying mgat4b mutations. We then performed gene expression profiling analysis using data obtained from RNA seq of melanophores and melanoma cells from both the zebrafish wild type and m4b mut. Comparative gene expression analysis was performed for wild type melanoma and melanophores  m4b mut melanoma and melanophores  wild type and m4b mut melanoma.", null, null, null, "wild type melanoma control  biol rep 2", "GSM8552312", null, "source name:skin|tissue:skin|cell type:melanoma|genotype:WT|treatment:MAZERATI|geo loc name:missing|collection date:missing", "wild type melanoma control  biol rep 2", "Raw fastq files were trimmed using trimmomatic to remove adaptors and retain high quality reads. The reads were then aligned with zebrafish reference assembly GRCz11 using STAR. Featurecounts was used to calculate raw counts from the aligned reads. Assembly: GRCz11 Supplementary files format and content: tab delimited text file including raw counts for each sample", "skin", null, "The cell isolation process involved density gradient centrifugation  followed by RNA extraction using Trizol method. Illumina standard total RNA prep kit was used for library construction", null, "tissue:skin|cell type:melanoma|genotype:WT|treatment:MAZERATI", "GSM8552312", "GSM8552312: wild type melanoma control  biol rep 2; Danio rerio; RNA Seq", "GSM8552312 r1", "GSM8552312", "1", "The cell isolation process involved density gradient centrifugation  followed by RNA extraction using Trizol method. Illumina standard total RNA prep kit was used for library construction", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP536275", null, null, "EV2_S37_R1_001.fastq.gz EV2_S37_R2_001.fastq.gz", "fastq fastq", 5427379509.0, 19981504.0, "GSM8552312 r1", "0:133.16 1:138.46", "A:1136639418;C:1414638483;G:1736492639;T:1137614638;N:1994331", 133, 138, null, null, 1136639418, 1414638483, 1736492639, 1137614638, 1994331, "SRX26263939", "SRS22803193", "SRA1984938", "Pigment Cell Biology Lab, CSIR-IGIB", "Pigment Cell Biology Lab, CSIR-IGIB", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "trueseq", "sc_generic", "bulk", "bulk", null, "India", "2024-10-02", "Undetermined", "Undetermined", "Skin", "Surface Structure"], [33897, "SRR30866031", "SRX26263938", "SRS22803192", "SRP536275", "PRJNA1168148", "Mgat4b mediated selective N glycosyl modification regulates melanocyte development and melanoma progression [bulk RNA seq]", "GSE278653", "Transcriptome Analysis", "Dysregulated melanocyte state transitions are a pivotal driver of melanoma development  highlighting the need to identify key regulators of these processes. Understanding these factors is key to know how normal melanocyte functions and shift towards initiation of melanoma. Our study identifies Mgat4b  a glycosyl transferase involved in selective N glycan branching enriched in pigment progenitors  as a key regulator of directional melanocyte migration and establishment of Melanocyte stem cell McSC pool during early development in zebrafish and mammalian melanocytes. Single cell RNA sequencing analysis in zebrafish upon targeted disruption of Mgat4b reveals that a subset of melanocytes marked by aberrant galectin expression are impaired in migration and are lost. Lectin binding proteomic analysis reveals the glycosylation of key melanocyte proteins Gpnmb  Kit  and Tyrp1 to be under the control of Mgat4b. Additionally  mislocalization of Gamma catenin Jup explains the observed defects in cell adhesion and migration to be regulated by mgat4b but not its isozyme mgat4a. Our meta analysis further revealed that melanoma patients with both the BrafV600E mutation and elevated Mgat4b levels have significantly worse survival outcomes compared to those with only the BrafV600E mutation. By leveraging the MAZERATI platform to model BrafV600E driver mutation in vivo  we show that Mgat4b mutant cells fail to aggregate and initiate tumors. Our study underscores the importance of selective N glycan branching in both melanocyte development and melanoma initiation  suggesting a Mitf controlled Mgat4b as a promising therapeutic target for melanoma treatment. Overall design: To investigate the mechanisms that inhibit mutant cells from initiating melanoma in the absence of mgat4b  we utilized mature melanophores and melanoma cells from the skin of five zebrafish  including both MAZERATI wild type and  MAZERATI zebrafish carrying mgat4b mutations. We then performed gene expression profiling analysis using data obtained from RNA seq of melanophores and melanoma cells from both the zebrafish wild type and m4b mut. Comparative gene expression analysis was performed for wild type melanoma and melanophores  m4b mut melanoma and melanophores  wild type and m4b mut melanoma.", null, null, null, "wild type melanoma control  biol rep 1", "GSM8552311", null, "source name:skin|tissue:skin|cell type:melanoma|genotype:WT|treatment:MAZERATI|geo loc name:missing|collection date:missing", "wild type melanoma control  biol rep 1", "Raw fastq files were trimmed using trimmomatic to remove adaptors and retain high quality reads. The reads were then aligned with zebrafish reference assembly GRCz11 using STAR. Featurecounts was used to calculate raw counts from the aligned reads. Assembly: GRCz11 Supplementary files format and content: tab delimited text file including raw counts for each sample", "skin", null, "The cell isolation process involved density gradient centrifugation  followed by RNA extraction using Trizol method. Illumina standard total RNA prep kit was used for library construction", null, "tissue:skin|cell type:melanoma|genotype:WT|treatment:MAZERATI", "GSM8552311", "GSM8552311: wild type melanoma control  biol rep 1; Danio rerio; RNA Seq", "GSM8552311 r1", "GSM8552311", "1", "The cell isolation process involved density gradient centrifugation  followed by RNA extraction using Trizol method. Illumina standard total RNA prep kit was used for library construction", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP536275", null, null, "EV1_S36_R1_001.fastq.gz EV1_S36_R2_001.fastq.gz", "fastq fastq", 5248108957.0, 19087024.0, "GSM8552311 r1", "0:135.12 1:139.84", "A:1112163842;C:1354895660;G:1658732932;T:1120342985;N:1973538", 135, 139, null, null, 1112163842, 1354895660, 1658732932, 1120342985, 1973538, "SRX26263938", "SRS22803192", "SRA1984938", "Pigment Cell Biology Lab, CSIR-IGIB", "Pigment Cell Biology Lab, CSIR-IGIB", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "trueseq", "sc_generic", "bulk", "bulk", null, "India", "2024-10-02", "Undetermined", "Undetermined", "Skin", "Surface Structure"], [33898, "SRR30866032", "SRX26263937", "SRS22803191", "SRP536275", "PRJNA1168148", "Mgat4b mediated selective N glycosyl modification regulates melanocyte development and melanoma progression [bulk RNA seq]", "GSE278653", "Transcriptome Analysis", "Dysregulated melanocyte state transitions are a pivotal driver of melanoma development  highlighting the need to identify key regulators of these processes. Understanding these factors is key to know how normal melanocyte functions and shift towards initiation of melanoma. Our study identifies Mgat4b  a glycosyl transferase involved in selective N glycan branching enriched in pigment progenitors  as a key regulator of directional melanocyte migration and establishment of Melanocyte stem cell McSC pool during early development in zebrafish and mammalian melanocytes. Single cell RNA sequencing analysis in zebrafish upon targeted disruption of Mgat4b reveals that a subset of melanocytes marked by aberrant galectin expression are impaired in migration and are lost. Lectin binding proteomic analysis reveals the glycosylation of key melanocyte proteins Gpnmb  Kit  and Tyrp1 to be under the control of Mgat4b. Additionally  mislocalization of Gamma catenin Jup explains the observed defects in cell adhesion and migration to be regulated by mgat4b but not its isozyme mgat4a. Our meta analysis further revealed that melanoma patients with both the BrafV600E mutation and elevated Mgat4b levels have significantly worse survival outcomes compared to those with only the BrafV600E mutation. By leveraging the MAZERATI platform to model BrafV600E driver mutation in vivo  we show that Mgat4b mutant cells fail to aggregate and initiate tumors. Our study underscores the importance of selective N glycan branching in both melanocyte development and melanoma initiation  suggesting a Mitf controlled Mgat4b as a promising therapeutic target for melanoma treatment. Overall design: To investigate the mechanisms that inhibit mutant cells from initiating melanoma in the absence of mgat4b  we utilized mature melanophores and melanoma cells from the skin of five zebrafish  including both MAZERATI wild type and  MAZERATI zebrafish carrying mgat4b mutations. We then performed gene expression profiling analysis using data obtained from RNA seq of melanophores and melanoma cells from both the zebrafish wild type and m4b mut. Comparative gene expression analysis was performed for wild type melanoma and melanophores  m4b mut melanoma and melanophores  wild type and m4b mut melanoma.", null, null, null, "melanophore  biol rep 2", "GSM8552310", null, "source name:skin|tissue:skin|cell type:melanophore|genotype:WT|treatment:No|geo loc name:missing|collection date:missing", "melanophore  biol rep 2", "Raw fastq files were trimmed using trimmomatic to remove adaptors and retain high quality reads. The reads were then aligned with zebrafish reference assembly GRCz11 using STAR. Featurecounts was used to calculate raw counts from the aligned reads. Assembly: GRCz11 Supplementary files format and content: tab delimited text file including raw counts for each sample", "skin", null, "The cell isolation process involved density gradient centrifugation  followed by RNA extraction using Trizol method. Illumina standard total RNA prep kit was used for library construction", null, "tissue:skin|cell type:melanophore|genotype:WT|treatment:No", "GSM8552310", "GSM8552310: melanophore  biol rep 2; Danio rerio; RNA Seq", "GSM8552310 r1", "GSM8552310", "1", "The cell isolation process involved density gradient centrifugation  followed by RNA extraction using Trizol method. Illumina standard total RNA prep kit was used for library construction", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP536275", null, null, "WT2_S41_R1_001.fastq.gz WT2_S41_R2_001.fastq.gz", "fastq fastq", 4636631881.0, 16340506.0, "GSM8552310 r1", "0:140.47 1:143.28", "A:1114533149;C:1104066636;G:1293649625;T:1122672029;N:1710442", 140, 143, null, null, 1114533149, 1104066636, 1293649625, 1122672029, 1710442, "SRX26263937", "SRS22803191", "SRA1984938", "Pigment Cell Biology Lab, CSIR-IGIB", "Pigment Cell Biology Lab, CSIR-IGIB", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "trueseq", "sc_generic", "bulk", "bulk", null, "India", "2024-10-02", "Undetermined", "Undetermined", "Skin", "Surface Structure"], [33899, "SRR30866033", "SRX26263936", "SRS22803190", "SRP536275", "PRJNA1168148", "Mgat4b mediated selective N glycosyl modification regulates melanocyte development and melanoma progression [bulk RNA seq]", "GSE278653", "Transcriptome Analysis", "Dysregulated melanocyte state transitions are a pivotal driver of melanoma development  highlighting the need to identify key regulators of these processes. Understanding these factors is key to know how normal melanocyte functions and shift towards initiation of melanoma. Our study identifies Mgat4b  a glycosyl transferase involved in selective N glycan branching enriched in pigment progenitors  as a key regulator of directional melanocyte migration and establishment of Melanocyte stem cell McSC pool during early development in zebrafish and mammalian melanocytes. Single cell RNA sequencing analysis in zebrafish upon targeted disruption of Mgat4b reveals that a subset of melanocytes marked by aberrant galectin expression are impaired in migration and are lost. Lectin binding proteomic analysis reveals the glycosylation of key melanocyte proteins Gpnmb  Kit  and Tyrp1 to be under the control of Mgat4b. Additionally  mislocalization of Gamma catenin Jup explains the observed defects in cell adhesion and migration to be regulated by mgat4b but not its isozyme mgat4a. Our meta analysis further revealed that melanoma patients with both the BrafV600E mutation and elevated Mgat4b levels have significantly worse survival outcomes compared to those with only the BrafV600E mutation. By leveraging the MAZERATI platform to model BrafV600E driver mutation in vivo  we show that Mgat4b mutant cells fail to aggregate and initiate tumors. Our study underscores the importance of selective N glycan branching in both melanocyte development and melanoma initiation  suggesting a Mitf controlled Mgat4b as a promising therapeutic target for melanoma treatment. Overall design: To investigate the mechanisms that inhibit mutant cells from initiating melanoma in the absence of mgat4b  we utilized mature melanophores and melanoma cells from the skin of five zebrafish  including both MAZERATI wild type and  MAZERATI zebrafish carrying mgat4b mutations. We then performed gene expression profiling analysis using data obtained from RNA seq of melanophores and melanoma cells from both the zebrafish wild type and m4b mut. Comparative gene expression analysis was performed for wild type melanoma and melanophores  m4b mut melanoma and melanophores  wild type and m4b mut melanoma.", null, null, null, "melanophore  biol rep 1", "GSM8552309", null, "source name:skin|tissue:skin|cell type:melanophore|genotype:WT|treatment:No|geo loc name:missing|collection date:missing", "melanophore  biol rep 1", "Raw fastq files were trimmed using trimmomatic to remove adaptors and retain high quality reads. The reads were then aligned with zebrafish reference assembly GRCz11 using STAR. Featurecounts was used to calculate raw counts from the aligned reads. Assembly: GRCz11 Supplementary files format and content: tab delimited text file including raw counts for each sample", "skin", null, "The cell isolation process involved density gradient centrifugation  followed by RNA extraction using Trizol method. Illumina standard total RNA prep kit was used for library construction", null, "tissue:skin|cell type:melanophore|genotype:WT|treatment:No", "GSM8552309", "GSM8552309: melanophore  biol rep 1; Danio rerio; RNA Seq", "GSM8552309 r1", "GSM8552309", "1", "The cell isolation process involved density gradient centrifugation  followed by RNA extraction using Trizol method. Illumina standard total RNA prep kit was used for library construction", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP536275", null, null, "WT1_S40_R1_001.fastq.gz WT1_S40_R2_001.fastq.gz", "fastq fastq", 5185761246.0, 18118534.0, "GSM8552309 r1", "0:141.81 1:144.40", "A:1231235669;C:1235759770;G:1476864583;T:1240636871;N:1264353", 141, 144, null, null, 1231235669, 1235759770, 1476864583, 1240636871, 1264353, "SRX26263936", "SRS22803190", "SRA1984938", "Pigment Cell Biology Lab, CSIR-IGIB", "Pigment Cell Biology Lab, CSIR-IGIB", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "trueseq", "sc_generic", "bulk", "bulk", null, "India", "2024-10-02", "Undetermined", "Undetermined", "Skin", "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"], [36741, "SRR850608", "SRX277695", "SRS420758", "SRP022612", "PRJNA203029", "RNA seq of Danio rerio and Mus musculus skin for three different age groups", "GSE46916", "Other", "Background: Comparison of temporal gene expression profiles. The RNA seq data comprises 3 age groups: 2  15 month and 30 month for mouse skin; 5  24 month and 42 month for zebrafish skin. Illumina 50bp single stranded single read RNA sequencing Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 15 samples for mouse: 5 biological replicates for 2 month  6 biological replicates for 15 month and 4 biological replicates for 30 month; 20 samples for zebrafish: 9 biological replicates for 5 month  6 biological replicates for 24 month and 5 biological replicates for 42 month", null, "pubmed:26620638", null, "Nr18 danrer skin 42months rep5", "GSM1141118", null, "source name:total RNA extracted from skin|strain:TuAB|age:42 month|tissue:skin", "Nr18 danrer skin 42months rep5", "Illumina Casava software used for extraction of FASTQ files FASTQ files were mapped using Bowtie vs. the respective genomic sequence and a splice site data set created using UCSC's RefSeq annotation for each species Counting of uniquely mapped reads and assignment to RefSeq transcripts/genes using R Statistical Language and Bioconductor Calculation of RPKM values for each transcript and gene from the corresponding RefSeq annotation Genome build: D.\u00a0rerio: danRer7; M. musculus: mm9 Supplementary files format and content: Excel file include raw counts and RPKM values for each sample", "total RNA extracted from skin", null, "D.\u00a0rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen  Hilden  Germany at 80 \u00b0C. Total RNA was isolated with TRIzol Life Technologies  Darmstadt  Germany according to the instructions of the manufacturer. M.\u00a0musculus: The isolated skin was homogenized in 500\u00a0\u03bcl QIAzol Qiagen by subsequently adding 100\u00a0\u03bcl chloroform. Following phase separation  the aqueous phase was transferred into a fresh tube  then 0.16 volume NaAc 2\u00a0M  pH\u00a04.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20\u00a0\u03bcl water GIBCO and stored at \u201380\u00b0C until use. D.\u00a0rerio: 5\u00a0\u00b5g of total RNA was used for preparation of libraries using Illumina\u2019s mRNA Seq sample prep kit Illumina  San Diego  CA  USA following the manufacturer\u2019s instruction. M.\u00a0musculus: 2.5\u00a0\u00b5g of total RNA was used with Illumina\u2019s TruSeq RNA sample prep kit.", null, "strain:TuAB|age:42 month|tissue:skin", "GSM1141118", "GSM1141118: Nr18 danrer skin 42months rep5; Danio rerio; RNA Seq", "GSM1141118 1", null, "1", "D.\u00a0rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen  Hilden  Germany at 80 \u00b0C. Total RNA was isolated with TRIzol Life Technologies  Darmstadt  Germany according to the instructions of the manufacturer. M.\u00a0musculus: The isolated skin was homogenized in 500\u00a0\u03bcl QIAzol Qiagen by subsequently adding 100\u00a0\u03bcl chloroform. Following phase separation  the aqueous phase was transferred into a fresh tube  then 0.16 volume NaAc 2\u00a0M  pH\u00a04.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20\u00a0\u03bcl water GIBCO and stored at \u201380\u00b0C until use. D.\u00a0rerio: 5\u00a0\u00b5g of total RNA was used for preparation of libraries using Illumina\u2019s mRNA Seq sample prep kit Illumina  San Diego  CA  USA following the manufacturer\u2019s instruction. M.\u00a0musculus: 2.5\u00a0\u00b5g of total RNA was used with Illumina\u2019s TruSeq RNA sample prep kit.", "GEO Accession:GSM1141118", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", null, "SRP022612", null, null, "Nr18_3.5y_l3_export.fq.gz", "fastq", 3269418540.0, 43018665.0, "GSM1141118 r1", "0:76", "A:892486836;C:744426899;G:749230539;T:883114979;N:159287", 76, null, null, null, 892486836, 744426899, 749230539, 883114979, 159287, "SRX277695", "SRS420758", "SRA076297", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.91402, null, 0.1106, null, 0.73436, null, 0.4911, null, 76, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "Germany", "2013-05-14", "Adult", "Adult", "Skin", "Surface Structure"], [36742, "SRR850607", "SRX277694", "SRS420757", "SRP022612", "PRJNA203029", "RNA seq of Danio rerio and Mus musculus skin for three different age groups", "GSE46916", "Other", "Background: Comparison of temporal gene expression profiles. The RNA seq data comprises 3 age groups: 2  15 month and 30 month for mouse skin; 5  24 month and 42 month for zebrafish skin. Illumina 50bp single stranded single read RNA sequencing Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 15 samples for mouse: 5 biological replicates for 2 month  6 biological replicates for 15 month and 4 biological replicates for 30 month; 20 samples for zebrafish: 9 biological replicates for 5 month  6 biological replicates for 24 month and 5 biological replicates for 42 month", null, "pubmed:26620638", null, "Nr14 danrer skin 42months rep4", "GSM1141117", null, "source name:total RNA extracted from skin|strain:TuAB|age:42 month|tissue:skin", "Nr14 danrer skin 42months rep4", "Illumina Casava software used for extraction of FASTQ files FASTQ files were mapped using Bowtie vs. the respective genomic sequence and a splice site data set created using UCSC's RefSeq annotation for each species Counting of uniquely mapped reads and assignment to RefSeq transcripts/genes using R Statistical Language and Bioconductor Calculation of RPKM values for each transcript and gene from the corresponding RefSeq annotation Genome build: D.\u00a0rerio: danRer7; M. musculus: mm9 Supplementary files format and content: Excel file include raw counts and RPKM values for each sample", "total RNA extracted from skin", null, "D.\u00a0rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen  Hilden  Germany at 80 \u00b0C. Total RNA was isolated with TRIzol Life Technologies  Darmstadt  Germany according to the instructions of the manufacturer. M.\u00a0musculus: The isolated skin was homogenized in 500\u00a0\u03bcl QIAzol Qiagen by subsequently adding 100\u00a0\u03bcl chloroform. Following phase separation  the aqueous phase was transferred into a fresh tube  then 0.16 volume NaAc 2\u00a0M  pH\u00a04.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20\u00a0\u03bcl water GIBCO and stored at \u201380\u00b0C until use. D.\u00a0rerio: 5\u00a0\u00b5g of total RNA was used for preparation of libraries using Illumina\u2019s mRNA Seq sample prep kit Illumina  San Diego  CA  USA following the manufacturer\u2019s instruction. M.\u00a0musculus: 2.5\u00a0\u00b5g of total RNA was used with Illumina\u2019s TruSeq RNA sample prep kit.", null, "strain:TuAB|age:42 month|tissue:skin", "GSM1141117", "GSM1141117: Nr14 danrer skin 42months rep4; Danio rerio; RNA Seq", "GSM1141117 1", null, "1", "D.\u00a0rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen  Hilden  Germany at 80 \u00b0C. Total RNA was isolated with TRIzol Life Technologies  Darmstadt  Germany according to the instructions of the manufacturer. M.\u00a0musculus: The isolated skin was homogenized in 500\u00a0\u03bcl QIAzol Qiagen by subsequently adding 100\u00a0\u03bcl chloroform. Following phase separation  the aqueous phase was transferred into a fresh tube  then 0.16 volume NaAc 2\u00a0M  pH\u00a04.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20\u00a0\u03bcl water GIBCO and stored at \u201380\u00b0C until use. D.\u00a0rerio: 5\u00a0\u00b5g of total RNA was used for preparation of libraries using Illumina\u2019s mRNA Seq sample prep kit Illumina  San Diego  CA  USA following the manufacturer\u2019s instruction. M.\u00a0musculus: 2.5\u00a0\u00b5g of total RNA was used with Illumina\u2019s TruSeq RNA sample prep kit.", "GEO Accession:GSM1141117", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", null, "SRP022612", null, null, "Nr14_3.5y_l2_export.fq.gz", "fastq", 2300890044.0, 30274869.0, "GSM1141117 r1", "0:76", "A:631736236;C:525065199;G:510761115;T:633208038;N:119456", 76, null, null, null, 631736236, 525065199, 510761115, 633208038, 119456, "SRX277694", "SRS420757", "SRA076297", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.90718, null, 0.11607, null, 0.71997, null, 0.49141, null, 76, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "Germany", "2013-05-14", "Adult", "Adult", "Skin", "Surface Structure"], [36743, "SRR850606", "SRX277693", "SRS420790", "SRP022612", "PRJNA203029", "RNA seq of Danio rerio and Mus musculus skin for three different age groups", "GSE46916", "Other", "Background: Comparison of temporal gene expression profiles. The RNA seq data comprises 3 age groups: 2  15 month and 30 month for mouse skin; 5  24 month and 42 month for zebrafish skin. Illumina 50bp single stranded single read RNA sequencing Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 15 samples for mouse: 5 biological replicates for 2 month  6 biological replicates for 15 month and 4 biological replicates for 30 month; 20 samples for zebrafish: 9 biological replicates for 5 month  6 biological replicates for 24 month and 5 biological replicates for 42 month", null, "pubmed:26620638", null, "Nr13 danrer skin 42months rep3", "GSM1141116", null, "source name:total RNA extracted from skin|strain:TuAB|age:42 month|tissue:skin", "Nr13 danrer skin 42months rep3", "Illumina Casava software used for extraction of FASTQ files FASTQ files were mapped using Bowtie vs. the respective genomic sequence and a splice site data set created using UCSC's RefSeq annotation for each species Counting of uniquely mapped reads and assignment to RefSeq transcripts/genes using R Statistical Language and Bioconductor Calculation of RPKM values for each transcript and gene from the corresponding RefSeq annotation Genome build: D.\u00a0rerio: danRer7; M. musculus: mm9 Supplementary files format and content: Excel file include raw counts and RPKM values for each sample", "total RNA extracted from skin", null, "D.\u00a0rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen  Hilden  Germany at 80 \u00b0C. Total RNA was isolated with TRIzol Life Technologies  Darmstadt  Germany according to the instructions of the manufacturer. M.\u00a0musculus: The isolated skin was homogenized in 500\u00a0\u03bcl QIAzol Qiagen by subsequently adding 100\u00a0\u03bcl chloroform. Following phase separation  the aqueous phase was transferred into a fresh tube  then 0.16 volume NaAc 2\u00a0M  pH\u00a04.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20\u00a0\u03bcl water GIBCO and stored at \u201380\u00b0C until use. D.\u00a0rerio: 5\u00a0\u00b5g of total RNA was used for preparation of libraries using Illumina\u2019s mRNA Seq sample prep kit Illumina  San Diego  CA  USA following the manufacturer\u2019s instruction. M.\u00a0musculus: 2.5\u00a0\u00b5g of total RNA was used with Illumina\u2019s TruSeq RNA sample prep kit.", null, "strain:TuAB|age:42 month|tissue:skin", "GSM1141116", "GSM1141116: Nr13 danrer skin 42months rep3; Danio rerio; RNA Seq", "GSM1141116 1", null, "1", "D.\u00a0rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen  Hilden  Germany at 80 \u00b0C. Total RNA was isolated with TRIzol Life Technologies  Darmstadt  Germany according to the instructions of the manufacturer. M.\u00a0musculus: The isolated skin was homogenized in 500\u00a0\u03bcl QIAzol Qiagen by subsequently adding 100\u00a0\u03bcl chloroform. Following phase separation  the aqueous phase was transferred into a fresh tube  then 0.16 volume NaAc 2\u00a0M  pH\u00a04.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20\u00a0\u03bcl water GIBCO and stored at \u201380\u00b0C until use. D.\u00a0rerio: 5\u00a0\u00b5g of total RNA was used for preparation of libraries using Illumina\u2019s mRNA Seq sample prep kit Illumina  San Diego  CA  USA following the manufacturer\u2019s instruction. M.\u00a0musculus: 2.5\u00a0\u00b5g of total RNA was used with Illumina\u2019s TruSeq RNA sample prep kit.", "GEO Accession:GSM1141116", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", null, "SRP022612", null, null, "Nr13_3.5y_l1_export.fastq.gz", "fastq", 3508110372.0, 46159347.0, "GSM1141116 r1", "0:76", "A:959986155;C:782258637;G:803256847;T:962450623;N:158110", 76, null, null, null, 959986155, 782258637, 803256847, 962450623, 158110, "SRX277693", "SRS420790", "SRA076297", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.85747, null, 0.12068, null, 0.73819, null, 0.4917, null, 76, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "Germany", "2013-05-14", "Adult", "Adult", "Skin", "Surface Structure"], [36744, "SRR850605", "SRX277692", "SRS420789", "SRP022612", "PRJNA203029", "RNA seq of Danio rerio and Mus musculus skin for three different age groups", "GSE46916", "Other", "Background: Comparison of temporal gene expression profiles. The RNA seq data comprises 3 age groups: 2  15 month and 30 month for mouse skin; 5  24 month and 42 month for zebrafish skin. Illumina 50bp single stranded single read RNA sequencing Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 15 samples for mouse: 5 biological replicates for 2 month  6 biological replicates for 15 month and 4 biological replicates for 30 month; 20 samples for zebrafish: 9 biological replicates for 5 month  6 biological replicates for 24 month and 5 biological replicates for 42 month", null, "pubmed:26620638", null, "Nr12 danrer skin 42months rep2", "GSM1141115", null, "source name:total RNA extracted from skin|strain:TuAB|age:42 month|tissue:skin", "Nr12 danrer skin 42months rep2", "Illumina Casava software used for extraction of FASTQ files FASTQ files were mapped using Bowtie vs. the respective genomic sequence and a splice site data set created using UCSC's RefSeq annotation for each species Counting of uniquely mapped reads and assignment to RefSeq transcripts/genes using R Statistical Language and Bioconductor Calculation of RPKM values for each transcript and gene from the corresponding RefSeq annotation Genome build: D.\u00a0rerio: danRer7; M. musculus: mm9 Supplementary files format and content: Excel file include raw counts and RPKM values for each sample", "total RNA extracted from skin", null, "D.\u00a0rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen  Hilden  Germany at 80 \u00b0C. Total RNA was isolated with TRIzol Life Technologies  Darmstadt  Germany according to the instructions of the manufacturer. M.\u00a0musculus: The isolated skin was homogenized in 500\u00a0\u03bcl QIAzol Qiagen by subsequently adding 100\u00a0\u03bcl chloroform. Following phase separation  the aqueous phase was transferred into a fresh tube  then 0.16 volume NaAc 2\u00a0M  pH\u00a04.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20\u00a0\u03bcl water GIBCO and stored at \u201380\u00b0C until use. D.\u00a0rerio: 5\u00a0\u00b5g of total RNA was used for preparation of libraries using Illumina\u2019s mRNA Seq sample prep kit Illumina  San Diego  CA  USA following the manufacturer\u2019s instruction. M.\u00a0musculus: 2.5\u00a0\u00b5g of total RNA was used with Illumina\u2019s TruSeq RNA sample prep kit.", null, "strain:TuAB|age:42 month|tissue:skin", "GSM1141115", "GSM1141115: Nr12 danrer skin 42months rep2; Danio rerio; RNA Seq", "GSM1141115 1", null, "1", "D.\u00a0rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen  Hilden  Germany at 80 \u00b0C. Total RNA was isolated with TRIzol Life Technologies  Darmstadt  Germany according to the instructions of the manufacturer. M.\u00a0musculus: The isolated skin was homogenized in 500\u00a0\u03bcl QIAzol Qiagen by subsequently adding 100\u00a0\u03bcl chloroform. Following phase separation  the aqueous phase was transferred into a fresh tube  then 0.16 volume NaAc 2\u00a0M  pH\u00a04.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20\u00a0\u03bcl water GIBCO and stored at \u201380\u00b0C until use. D.\u00a0rerio: 5\u00a0\u00b5g of total RNA was used for preparation of libraries using Illumina\u2019s mRNA Seq sample prep kit Illumina  San Diego  CA  USA following the manufacturer\u2019s instruction. M.\u00a0musculus: 2.5\u00a0\u00b5g of total RNA was used with Illumina\u2019s TruSeq RNA sample prep kit.", "GEO Accession:GSM1141115", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", null, "SRP022612", null, null, "Nr12_3.5y_l3_export.fq.gz", "fastq", 3961243804.0, 52121629.0, "GSM1141115 r1", "0:76", "A:1092811778;C:874440215;G:892629531;T:1099367104;N:1995176", 76, null, null, null, 1092811778, 874440215, 892629531, 1099367104, 1995176, "SRX277692", "SRS420789", "SRA076297", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.88854, null, 0.12633, null, 0.73746, null, 0.53849, null, 76, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "Germany", "2013-05-14", "Adult", "Adult", "Skin", "Surface Structure"], [36745, "SRR850604", "SRX277691", "SRS420788", "SRP022612", "PRJNA203029", "RNA seq of Danio rerio and Mus musculus skin for three different age groups", "GSE46916", "Other", "Background: Comparison of temporal gene expression profiles. The RNA seq data comprises 3 age groups: 2  15 month and 30 month for mouse skin; 5  24 month and 42 month for zebrafish skin. Illumina 50bp single stranded single read RNA sequencing Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 15 samples for mouse: 5 biological replicates for 2 month  6 biological replicates for 15 month and 4 biological replicates for 30 month; 20 samples for zebrafish: 9 biological replicates for 5 month  6 biological replicates for 24 month and 5 biological replicates for 42 month", null, "pubmed:26620638", null, "Nr11 danrer skin 42months rep1", "GSM1141114", null, "source name:total RNA extracted from skin|strain:TuAB|age:42 month|tissue:skin", "Nr11 danrer skin 42months rep1", "Illumina Casava software used for extraction of FASTQ files FASTQ files were mapped using Bowtie vs. the respective genomic sequence and a splice site data set created using UCSC's RefSeq annotation for each species Counting of uniquely mapped reads and assignment to RefSeq transcripts/genes using R Statistical Language and Bioconductor Calculation of RPKM values for each transcript and gene from the corresponding RefSeq annotation Genome build: D.\u00a0rerio: danRer7; M. musculus: mm9 Supplementary files format and content: Excel file include raw counts and RPKM values for each sample", "total RNA extracted from skin", null, "D.\u00a0rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen  Hilden  Germany at 80 \u00b0C. Total RNA was isolated with TRIzol Life Technologies  Darmstadt  Germany according to the instructions of the manufacturer. M.\u00a0musculus: The isolated skin was homogenized in 500\u00a0\u03bcl QIAzol Qiagen by subsequently adding 100\u00a0\u03bcl chloroform. Following phase separation  the aqueous phase was transferred into a fresh tube  then 0.16 volume NaAc 2\u00a0M  pH\u00a04.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20\u00a0\u03bcl water GIBCO and stored at \u201380\u00b0C until use. D.\u00a0rerio: 5\u00a0\u00b5g of total RNA was used for preparation of libraries using Illumina\u2019s mRNA Seq sample prep kit Illumina  San Diego  CA  USA following the manufacturer\u2019s instruction. M.\u00a0musculus: 2.5\u00a0\u00b5g of total RNA was used with Illumina\u2019s TruSeq RNA sample prep kit.", null, "strain:TuAB|age:42 month|tissue:skin", "GSM1141114", "GSM1141114: Nr11 danrer skin 42months rep1; Danio rerio; RNA Seq", "GSM1141114 1", null, "1", "D.\u00a0rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen  Hilden  Germany at 80 \u00b0C. Total RNA was isolated with TRIzol Life Technologies  Darmstadt  Germany according to the instructions of the manufacturer. M.\u00a0musculus: The isolated skin was homogenized in 500\u00a0\u03bcl QIAzol Qiagen by subsequently adding 100\u00a0\u03bcl chloroform. Following phase separation  the aqueous phase was transferred into a fresh tube  then 0.16 volume NaAc 2\u00a0M  pH\u00a04.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20\u00a0\u03bcl water GIBCO and stored at \u201380\u00b0C until use. D.\u00a0rerio: 5\u00a0\u00b5g of total RNA was used for preparation of libraries using Illumina\u2019s mRNA Seq sample prep kit Illumina  San Diego  CA  USA following the manufacturer\u2019s instruction. M.\u00a0musculus: 2.5\u00a0\u00b5g of total RNA was used with Illumina\u2019s TruSeq RNA sample prep kit.", "GEO Accession:GSM1141114", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", null, "SRP022612", null, null, "Nr11_3.5y_l2_export.fq.gz", "fastq", 3327777040.0, 43786540.0, "GSM1141114 r1", "0:76", "A:920364748;C:745739060;G:758842746;T:901558784;N:1271702", 76, null, null, null, 920364748, 745739060, 758842746, 901558784, 1271702, "SRX277691", "SRS420788", "SRA076297", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.86781, null, 0.11618, null, 0.72888, null, 0.50217, null, 76, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "Germany", "2013-05-14", "Adult", "Adult", "Skin", "Surface Structure"], [36746, "SRR850603", "SRX277690", "SRS420756", "SRP022612", "PRJNA203029", "RNA seq of Danio rerio and Mus musculus skin for three different age groups", "GSE46916", "Other", "Background: Comparison of temporal gene expression profiles. The RNA seq data comprises 3 age groups: 2  15 month and 30 month for mouse skin; 5  24 month and 42 month for zebrafish skin. Illumina 50bp single stranded single read RNA sequencing Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 15 samples for mouse: 5 biological replicates for 2 month  6 biological replicates for 15 month and 4 biological replicates for 30 month; 20 samples for zebrafish: 9 biological replicates for 5 month  6 biological replicates for 24 month and 5 biological replicates for 42 month", null, "pubmed:26620638", null, "Nr76 danrer skin 24months rep6", "GSM1141113", null, "source name:total RNA extracted from skin|strain:TuAB|age:24 month|tissue:skin", "Nr76 danrer skin 24months rep6", "Illumina Casava software used for extraction of FASTQ files FASTQ files were mapped using Bowtie vs. the respective genomic sequence and a splice site data set created using UCSC's RefSeq annotation for each species Counting of uniquely mapped reads and assignment to RefSeq transcripts/genes using R Statistical Language and Bioconductor Calculation of RPKM values for each transcript and gene from the corresponding RefSeq annotation Genome build: D.\u00a0rerio: danRer7; M. musculus: mm9 Supplementary files format and content: Excel file include raw counts and RPKM values for each sample", "total RNA extracted from skin", null, "D.\u00a0rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen  Hilden  Germany at 80 \u00b0C. Total RNA was isolated with TRIzol Life Technologies  Darmstadt  Germany according to the instructions of the manufacturer. M.\u00a0musculus: The isolated skin was homogenized in 500\u00a0\u03bcl QIAzol Qiagen by subsequently adding 100\u00a0\u03bcl chloroform. Following phase separation  the aqueous phase was transferred into a fresh tube  then 0.16 volume NaAc 2\u00a0M  pH\u00a04.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20\u00a0\u03bcl water GIBCO and stored at \u201380\u00b0C until use. D.\u00a0rerio: 5\u00a0\u00b5g of total RNA was used for preparation of libraries using Illumina\u2019s mRNA Seq sample prep kit Illumina  San Diego  CA  USA following the manufacturer\u2019s instruction. M.\u00a0musculus: 2.5\u00a0\u00b5g of total RNA was used with Illumina\u2019s TruSeq RNA sample prep kit.", null, "strain:TuAB|age:24 month|tissue:skin", "GSM1141113", "GSM1141113: Nr76 danrer skin 24months rep6; Danio rerio; RNA Seq", "GSM1141113 1", null, "1", "D.\u00a0rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen  Hilden  Germany at 80 \u00b0C. Total RNA was isolated with TRIzol Life Technologies  Darmstadt  Germany according to the instructions of the manufacturer. M.\u00a0musculus: The isolated skin was homogenized in 500\u00a0\u03bcl QIAzol Qiagen by subsequently adding 100\u00a0\u03bcl chloroform. Following phase separation  the aqueous phase was transferred into a fresh tube  then 0.16 volume NaAc 2\u00a0M  pH\u00a04.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20\u00a0\u03bcl water GIBCO and stored at \u201380\u00b0C until use. D.\u00a0rerio: 5\u00a0\u00b5g of total RNA was used for preparation of libraries using Illumina\u2019s mRNA Seq sample prep kit Illumina  San Diego  CA  USA following the manufacturer\u2019s instruction. M.\u00a0musculus: 2.5\u00a0\u00b5g of total RNA was used with Illumina\u2019s TruSeq RNA sample prep kit.", "GEO Accession:GSM1141113", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", null, "SRP022612", null, null, "Nr76_2y.fastq.gz", "fastq", 2234765940.0, 29404815.0, "GSM1141113 r1", "0:76", "A:582794172;C:524083367;G:547601836;T:579473821;N:812744", 76, null, null, null, 582794172, 524083367, 547601836, 579473821, 812744, "SRX277690", "SRS420756", "SRA076297", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.89808, null, 0.07989, null, 0.73511, null, 0.47456, null, 76, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "Germany", "2013-05-14", "Adult", "Adult", "Skin", "Surface Structure"], [36747, "SRR850602", "SRX277689", "SRS420755", "SRP022612", "PRJNA203029", "RNA seq of Danio rerio and Mus musculus skin for three different age groups", "GSE46916", "Other", "Background: Comparison of temporal gene expression profiles. The RNA seq data comprises 3 age groups: 2  15 month and 30 month for mouse skin; 5  24 month and 42 month for zebrafish skin. Illumina 50bp single stranded single read RNA sequencing Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 15 samples for mouse: 5 biological replicates for 2 month  6 biological replicates for 15 month and 4 biological replicates for 30 month; 20 samples for zebrafish: 9 biological replicates for 5 month  6 biological replicates for 24 month and 5 biological replicates for 42 month", null, "pubmed:26620638", null, "Nr75 danrer skin 24months rep5", "GSM1141112", null, "source name:total RNA extracted from skin|strain:TuAB|age:24 month|tissue:skin", "Nr75 danrer skin 24months rep5", "Illumina Casava software used for extraction of FASTQ files FASTQ files were mapped using Bowtie vs. the respective genomic sequence and a splice site data set created using UCSC's RefSeq annotation for each species Counting of uniquely mapped reads and assignment to RefSeq transcripts/genes using R Statistical Language and Bioconductor Calculation of RPKM values for each transcript and gene from the corresponding RefSeq annotation Genome build: D.\u00a0rerio: danRer7; M. musculus: mm9 Supplementary files format and content: Excel file include raw counts and RPKM values for each sample", "total RNA extracted from skin", null, "D.\u00a0rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen  Hilden  Germany at 80 \u00b0C. Total RNA was isolated with TRIzol Life Technologies  Darmstadt  Germany according to the instructions of the manufacturer. M.\u00a0musculus: The isolated skin was homogenized in 500\u00a0\u03bcl QIAzol Qiagen by subsequently adding 100\u00a0\u03bcl chloroform. Following phase separation  the aqueous phase was transferred into a fresh tube  then 0.16 volume NaAc 2\u00a0M  pH\u00a04.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20\u00a0\u03bcl water GIBCO and stored at \u201380\u00b0C until use. D.\u00a0rerio: 5\u00a0\u00b5g of total RNA was used for preparation of libraries using Illumina\u2019s mRNA Seq sample prep kit Illumina  San Diego  CA  USA following the manufacturer\u2019s instruction. M.\u00a0musculus: 2.5\u00a0\u00b5g of total RNA was used with Illumina\u2019s TruSeq RNA sample prep kit.", null, "strain:TuAB|age:24 month|tissue:skin", "GSM1141112", "GSM1141112: Nr75 danrer skin 24months rep5; Danio rerio; RNA Seq", "GSM1141112 1", null, "1", "D.\u00a0rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen  Hilden  Germany at 80 \u00b0C. Total RNA was isolated with TRIzol Life Technologies  Darmstadt  Germany according to the instructions of the manufacturer. M.\u00a0musculus: The isolated skin was homogenized in 500\u00a0\u03bcl QIAzol Qiagen by subsequently adding 100\u00a0\u03bcl chloroform. Following phase separation  the aqueous phase was transferred into a fresh tube  then 0.16 volume NaAc 2\u00a0M  pH\u00a04.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20\u00a0\u03bcl water GIBCO and stored at \u201380\u00b0C until use. D.\u00a0rerio: 5\u00a0\u00b5g of total RNA was used for preparation of libraries using Illumina\u2019s mRNA Seq sample prep kit Illumina  San Diego  CA  USA following the manufacturer\u2019s instruction. M.\u00a0musculus: 2.5\u00a0\u00b5g of total RNA was used with Illumina\u2019s TruSeq RNA sample prep kit.", "GEO Accession:GSM1141112", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", null, "SRP022612", null, null, "Nr75_2y.fastq.gz", "fastq", 1000606196.0, 13165871.0, "GSM1141112 r1", "0:76", "A:270569436;C:233353660;G:238144829;T:258045669;N:492602", 76, null, null, null, 270569436, 233353660, 238144829, 258045669, 492602, "SRX277689", "SRS420755", "SRA076297", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.8949, null, 0.07966, null, 0.7293, null, 0.47729, null, 76, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "Germany", "2013-05-14", "Adult", "Adult", "Skin", "Surface Structure"], [36748, "SRR850601", "SRX277688", "SRS420754", "SRP022612", "PRJNA203029", "RNA seq of Danio rerio and Mus musculus skin for three different age groups", "GSE46916", "Other", "Background: Comparison of temporal gene expression profiles. The RNA seq data comprises 3 age groups: 2  15 month and 30 month for mouse skin; 5  24 month and 42 month for zebrafish skin. Illumina 50bp single stranded single read RNA sequencing Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 15 samples for mouse: 5 biological replicates for 2 month  6 biological replicates for 15 month and 4 biological replicates for 30 month; 20 samples for zebrafish: 9 biological replicates for 5 month  6 biological replicates for 24 month and 5 biological replicates for 42 month", null, "pubmed:26620638", null, "Nr73 danrer skin 24months rep4", "GSM1141111", null, "source name:total RNA extracted from skin|strain:TuAB|age:24 month|tissue:skin", "Nr73 danrer skin 24months rep4", "Illumina Casava software used for extraction of FASTQ files FASTQ files were mapped using Bowtie vs. the respective genomic sequence and a splice site data set created using UCSC's RefSeq annotation for each species Counting of uniquely mapped reads and assignment to RefSeq transcripts/genes using R Statistical Language and Bioconductor Calculation of RPKM values for each transcript and gene from the corresponding RefSeq annotation Genome build: D.\u00a0rerio: danRer7; M. musculus: mm9 Supplementary files format and content: Excel file include raw counts and RPKM values for each sample", "total RNA extracted from skin", null, "D.\u00a0rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen  Hilden  Germany at 80 \u00b0C. Total RNA was isolated with TRIzol Life Technologies  Darmstadt  Germany according to the instructions of the manufacturer. M.\u00a0musculus: The isolated skin was homogenized in 500\u00a0\u03bcl QIAzol Qiagen by subsequently adding 100\u00a0\u03bcl chloroform. Following phase separation  the aqueous phase was transferred into a fresh tube  then 0.16 volume NaAc 2\u00a0M  pH\u00a04.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20\u00a0\u03bcl water GIBCO and stored at \u201380\u00b0C until use. D.\u00a0rerio: 5\u00a0\u00b5g of total RNA was used for preparation of libraries using Illumina\u2019s mRNA Seq sample prep kit Illumina  San Diego  CA  USA following the manufacturer\u2019s instruction. M.\u00a0musculus: 2.5\u00a0\u00b5g of total RNA was used with Illumina\u2019s TruSeq RNA sample prep kit.", null, "strain:TuAB|age:24 month|tissue:skin", "GSM1141111", "GSM1141111: Nr73 danrer skin 24months rep4; Danio rerio; RNA Seq", "GSM1141111 1", null, "1", "D.\u00a0rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen  Hilden  Germany at 80 \u00b0C. Total RNA was isolated with TRIzol Life Technologies  Darmstadt  Germany according to the instructions of the manufacturer. M.\u00a0musculus: The isolated skin was homogenized in 500\u00a0\u03bcl QIAzol Qiagen by subsequently adding 100\u00a0\u03bcl chloroform. Following phase separation  the aqueous phase was transferred into a fresh tube  then 0.16 volume NaAc 2\u00a0M  pH\u00a04.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20\u00a0\u03bcl water GIBCO and stored at \u201380\u00b0C until use. D.\u00a0rerio: 5\u00a0\u00b5g of total RNA was used for preparation of libraries using Illumina\u2019s mRNA Seq sample prep kit Illumina  San Diego  CA  USA following the manufacturer\u2019s instruction. M.\u00a0musculus: 2.5\u00a0\u00b5g of total RNA was used with Illumina\u2019s TruSeq RNA sample prep kit.", "GEO Accession:GSM1141111", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", null, "SRP022612", null, null, "Nr73_2y.fastq.gz", "fastq", 2283103688.0, 30040838.0, "GSM1141111 r1", "0:76", "A:601138588;C:527906584;G:549863593;T:603391353;N:803570", 76, null, null, null, 601138588, 527906584, 549863593, 603391353, 803570, "SRX277688", "SRS420754", "SRA076297", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.90138, null, 0.08154, null, 0.72598, null, 0.49455, null, 76, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "Germany", "2013-05-14", "Adult", "Adult", "Skin", "Surface Structure"], [36749, "SRR850600", "SRX277687", "SRS420787", "SRP022612", "PRJNA203029", "RNA seq of Danio rerio and Mus musculus skin for three different age groups", "GSE46916", "Other", "Background: Comparison of temporal gene expression profiles. The RNA seq data comprises 3 age groups: 2  15 month and 30 month for mouse skin; 5  24 month and 42 month for zebrafish skin. Illumina 50bp single stranded single read RNA sequencing Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 15 samples for mouse: 5 biological replicates for 2 month  6 biological replicates for 15 month and 4 biological replicates for 30 month; 20 samples for zebrafish: 9 biological replicates for 5 month  6 biological replicates for 24 month and 5 biological replicates for 42 month", null, "pubmed:26620638", null, "Nr72 danrer skin 24months rep3", "GSM1141110", null, "source name:total RNA extracted from skin|strain:TuAB|age:24 month|tissue:skin", "Nr72 danrer skin 24months rep3", "Illumina Casava software used for extraction of FASTQ files FASTQ files were mapped using Bowtie vs. the respective genomic sequence and a splice site data set created using UCSC's RefSeq annotation for each species Counting of uniquely mapped reads and assignment to RefSeq transcripts/genes using R Statistical Language and Bioconductor Calculation of RPKM values for each transcript and gene from the corresponding RefSeq annotation Genome build: D.\u00a0rerio: danRer7; M. musculus: mm9 Supplementary files format and content: Excel file include raw counts and RPKM values for each sample", "total RNA extracted from skin", null, "D.\u00a0rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen  Hilden  Germany at 80 \u00b0C. Total RNA was isolated with TRIzol Life Technologies  Darmstadt  Germany according to the instructions of the manufacturer. M.\u00a0musculus: The isolated skin was homogenized in 500\u00a0\u03bcl QIAzol Qiagen by subsequently adding 100\u00a0\u03bcl chloroform. Following phase separation  the aqueous phase was transferred into a fresh tube  then 0.16 volume NaAc 2\u00a0M  pH\u00a04.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20\u00a0\u03bcl water GIBCO and stored at \u201380\u00b0C until use. D.\u00a0rerio: 5\u00a0\u00b5g of total RNA was used for preparation of libraries using Illumina\u2019s mRNA Seq sample prep kit Illumina  San Diego  CA  USA following the manufacturer\u2019s instruction. M.\u00a0musculus: 2.5\u00a0\u00b5g of total RNA was used with Illumina\u2019s TruSeq RNA sample prep kit.", null, "strain:TuAB|age:24 month|tissue:skin", "GSM1141110", "GSM1141110: Nr72 danrer skin 24months rep3; Danio rerio; RNA Seq", "GSM1141110 1", null, "1", "D.\u00a0rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen  Hilden  Germany at 80 \u00b0C. Total RNA was isolated with TRIzol Life Technologies  Darmstadt  Germany according to the instructions of the manufacturer. M.\u00a0musculus: The isolated skin was homogenized in 500\u00a0\u03bcl QIAzol Qiagen by subsequently adding 100\u00a0\u03bcl chloroform. Following phase separation  the aqueous phase was transferred into a fresh tube  then 0.16 volume NaAc 2\u00a0M  pH\u00a04.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20\u00a0\u03bcl water GIBCO and stored at \u201380\u00b0C until use. D.\u00a0rerio: 5\u00a0\u00b5g of total RNA was used for preparation of libraries using Illumina\u2019s mRNA Seq sample prep kit Illumina  San Diego  CA  USA following the manufacturer\u2019s instruction. M.\u00a0musculus: 2.5\u00a0\u00b5g of total RNA was used with Illumina\u2019s TruSeq RNA sample prep kit.", "GEO Accession:GSM1141110", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", null, "SRP022612", null, null, "Nr72_2y.fastq.gz", "fastq", 1692545916.0, 22270341.0, "GSM1141110 r1", "0:76", "A:447927627;C:393400289;G:405212681;T:445305247;N:700072", 76, null, null, null, 447927627, 393400289, 405212681, 445305247, 700072, "SRX277687", "SRS420787", "SRA076297", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.88704, null, 0.08604, null, 0.72833, null, 0.47215, null, 76, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "Germany", "2013-05-14", "Adult", "Adult", "Skin", "Surface Structure"], [36750, "SRR850599", "SRX277686", "SRS420786", "SRP022612", "PRJNA203029", "RNA seq of Danio rerio and Mus musculus skin for three different age groups", "GSE46916", "Other", "Background: Comparison of temporal gene expression profiles. The RNA seq data comprises 3 age groups: 2  15 month and 30 month for mouse skin; 5  24 month and 42 month for zebrafish skin. Illumina 50bp single stranded single read RNA sequencing Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 15 samples for mouse: 5 biological replicates for 2 month  6 biological replicates for 15 month and 4 biological replicates for 30 month; 20 samples for zebrafish: 9 biological replicates for 5 month  6 biological replicates for 24 month and 5 biological replicates for 42 month", null, "pubmed:26620638", null, "Nr71 danrer skin 24months rep2", "GSM1141109", null, "source name:total RNA extracted from skin|strain:TuAB|age:24 month|tissue:skin", "Nr71 danrer skin 24months rep2", "Illumina Casava software used for extraction of FASTQ files FASTQ files were mapped using Bowtie vs. the respective genomic sequence and a splice site data set created using UCSC's RefSeq annotation for each species Counting of uniquely mapped reads and assignment to RefSeq transcripts/genes using R Statistical Language and Bioconductor Calculation of RPKM values for each transcript and gene from the corresponding RefSeq annotation Genome build: D.\u00a0rerio: danRer7; M. musculus: mm9 Supplementary files format and content: Excel file include raw counts and RPKM values for each sample", "total RNA extracted from skin", null, "D.\u00a0rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen  Hilden  Germany at 80 \u00b0C. Total RNA was isolated with TRIzol Life Technologies  Darmstadt  Germany according to the instructions of the manufacturer. M.\u00a0musculus: The isolated skin was homogenized in 500\u00a0\u03bcl QIAzol Qiagen by subsequently adding 100\u00a0\u03bcl chloroform. Following phase separation  the aqueous phase was transferred into a fresh tube  then 0.16 volume NaAc 2\u00a0M  pH\u00a04.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20\u00a0\u03bcl water GIBCO and stored at \u201380\u00b0C until use. D.\u00a0rerio: 5\u00a0\u00b5g of total RNA was used for preparation of libraries using Illumina\u2019s mRNA Seq sample prep kit Illumina  San Diego  CA  USA following the manufacturer\u2019s instruction. M.\u00a0musculus: 2.5\u00a0\u00b5g of total RNA was used with Illumina\u2019s TruSeq RNA sample prep kit.", null, "strain:TuAB|age:24 month|tissue:skin", "GSM1141109", "GSM1141109: Nr71 danrer skin 24months rep2; Danio rerio; RNA Seq", "GSM1141109 1", null, "1", "D.\u00a0rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen  Hilden  Germany at 80 \u00b0C. Total RNA was isolated with TRIzol Life Technologies  Darmstadt  Germany according to the instructions of the manufacturer. M.\u00a0musculus: The isolated skin was homogenized in 500\u00a0\u03bcl QIAzol Qiagen by subsequently adding 100\u00a0\u03bcl chloroform. Following phase separation  the aqueous phase was transferred into a fresh tube  then 0.16 volume NaAc 2\u00a0M  pH\u00a04.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20\u00a0\u03bcl water GIBCO and stored at \u201380\u00b0C until use. D.\u00a0rerio: 5\u00a0\u00b5g of total RNA was used for preparation of libraries using Illumina\u2019s mRNA Seq sample prep kit Illumina  San Diego  CA  USA following the manufacturer\u2019s instruction. M.\u00a0musculus: 2.5\u00a0\u00b5g of total RNA was used with Illumina\u2019s TruSeq RNA sample prep kit.", "GEO Accession:GSM1141109", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", null, "SRP022612", null, null, "Nr71_2y.fastq.gz", "fastq", 1897129404.0, 24962229.0, "GSM1141109 r1", "0:76", "A:500740954;C:442627409;G:457159802;T:495689680;N:911559", 76, null, null, null, 500740954, 442627409, 457159802, 495689680, 911559, "SRX277686", "SRS420786", "SRA076297", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.88731, null, 0.07537, null, 0.73628, null, 0.4846, null, 76, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "Germany", "2013-05-14", "Adult", "Adult", "Skin", "Surface Structure"], [36751, "SRR850598", "SRX277685", "SRS420785", "SRP022612", "PRJNA203029", "RNA seq of Danio rerio and Mus musculus skin for three different age groups", "GSE46916", "Other", "Background: Comparison of temporal gene expression profiles. The RNA seq data comprises 3 age groups: 2  15 month and 30 month for mouse skin; 5  24 month and 42 month for zebrafish skin. Illumina 50bp single stranded single read RNA sequencing Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 15 samples for mouse: 5 biological replicates for 2 month  6 biological replicates for 15 month and 4 biological replicates for 30 month; 20 samples for zebrafish: 9 biological replicates for 5 month  6 biological replicates for 24 month and 5 biological replicates for 42 month", null, "pubmed:26620638", null, "Nr70 danrer skin 24months rep1", "GSM1141108", null, "source name:total RNA extracted from skin|strain:TuAB|age:24 month|tissue:skin", "Nr70 danrer skin 24months rep1", "Illumina Casava software used for extraction of FASTQ files FASTQ files were mapped using Bowtie vs. the respective genomic sequence and a splice site data set created using UCSC's RefSeq annotation for each species Counting of uniquely mapped reads and assignment to RefSeq transcripts/genes using R Statistical Language and Bioconductor Calculation of RPKM values for each transcript and gene from the corresponding RefSeq annotation Genome build: D.\u00a0rerio: danRer7; M. musculus: mm9 Supplementary files format and content: Excel file include raw counts and RPKM values for each sample", "total RNA extracted from skin", null, "D.\u00a0rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen  Hilden  Germany at 80 \u00b0C. Total RNA was isolated with TRIzol Life Technologies  Darmstadt  Germany according to the instructions of the manufacturer. M.\u00a0musculus: The isolated skin was homogenized in 500\u00a0\u03bcl QIAzol Qiagen by subsequently adding 100\u00a0\u03bcl chloroform. Following phase separation  the aqueous phase was transferred into a fresh tube  then 0.16 volume NaAc 2\u00a0M  pH\u00a04.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20\u00a0\u03bcl water GIBCO and stored at \u201380\u00b0C until use. D.\u00a0rerio: 5\u00a0\u00b5g of total RNA was used for preparation of libraries using Illumina\u2019s mRNA Seq sample prep kit Illumina  San Diego  CA  USA following the manufacturer\u2019s instruction. M.\u00a0musculus: 2.5\u00a0\u00b5g of total RNA was used with Illumina\u2019s TruSeq RNA sample prep kit.", null, "strain:TuAB|age:24 month|tissue:skin", "GSM1141108", "GSM1141108: Nr70 danrer skin 24months rep1; Danio rerio; RNA Seq", "GSM1141108 1", null, "1", "D.\u00a0rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen  Hilden  Germany at 80 \u00b0C. Total RNA was isolated with TRIzol Life Technologies  Darmstadt  Germany according to the instructions of the manufacturer. M.\u00a0musculus: The isolated skin was homogenized in 500\u00a0\u03bcl QIAzol Qiagen by subsequently adding 100\u00a0\u03bcl chloroform. Following phase separation  the aqueous phase was transferred into a fresh tube  then 0.16 volume NaAc 2\u00a0M  pH\u00a04.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20\u00a0\u03bcl water GIBCO and stored at \u201380\u00b0C until use. D.\u00a0rerio: 5\u00a0\u00b5g of total RNA was used for preparation of libraries using Illumina\u2019s mRNA Seq sample prep kit Illumina  San Diego  CA  USA following the manufacturer\u2019s instruction. M.\u00a0musculus: 2.5\u00a0\u00b5g of total RNA was used with Illumina\u2019s TruSeq RNA sample prep kit.", "GEO Accession:GSM1141108", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", null, "SRP022612", null, null, "Nr70_2y.fastq.gz", "fastq", 2239190508.0, 29463033.0, "GSM1141108 r1", "0:76", "A:599665392;C:514113743;G:531871299;T:592730477;N:809597", 76, null, null, null, 599665392, 514113743, 531871299, 592730477, 809597, "SRX277685", "SRS420785", "SRA076297", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.89167, null, 0.09031, null, 0.73515, null, 0.49129, null, 76, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "Germany", "2013-05-14", "Adult", "Adult", "Skin", "Surface Structure"], [36752, "SRR850597", "SRX277684", "SRS420784", "SRP022612", "PRJNA203029", "RNA seq of Danio rerio and Mus musculus skin for three different age groups", "GSE46916", "Other", "Background: Comparison of temporal gene expression profiles. The RNA seq data comprises 3 age groups: 2  15 month and 30 month for mouse skin; 5  24 month and 42 month for zebrafish skin. Illumina 50bp single stranded single read RNA sequencing Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 15 samples for mouse: 5 biological replicates for 2 month  6 biological replicates for 15 month and 4 biological replicates for 30 month; 20 samples for zebrafish: 9 biological replicates for 5 month  6 biological replicates for 24 month and 5 biological replicates for 42 month", null, "pubmed:26620638", null, "Nr30 danrer skin 5months rep9", "GSM1141107", null, "source name:total RNA extracted from skin|strain:TuAB|age:5 month|tissue:skin", "Nr30 danrer skin 5months rep9", "Illumina Casava software used for extraction of FASTQ files FASTQ files were mapped using Bowtie vs. the respective genomic sequence and a splice site data set created using UCSC's RefSeq annotation for each species Counting of uniquely mapped reads and assignment to RefSeq transcripts/genes using R Statistical Language and Bioconductor Calculation of RPKM values for each transcript and gene from the corresponding RefSeq annotation Genome build: D.\u00a0rerio: danRer7; M. musculus: mm9 Supplementary files format and content: Excel file include raw counts and RPKM values for each sample", "total RNA extracted from skin", null, "D.\u00a0rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen  Hilden  Germany at 80 \u00b0C. Total RNA was isolated with TRIzol Life Technologies  Darmstadt  Germany according to the instructions of the manufacturer. M.\u00a0musculus: The isolated skin was homogenized in 500\u00a0\u03bcl QIAzol Qiagen by subsequently adding 100\u00a0\u03bcl chloroform. Following phase separation  the aqueous phase was transferred into a fresh tube  then 0.16 volume NaAc 2\u00a0M  pH\u00a04.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20\u00a0\u03bcl water GIBCO and stored at \u201380\u00b0C until use. D.\u00a0rerio: 5\u00a0\u00b5g of total RNA was used for preparation of libraries using Illumina\u2019s mRNA Seq sample prep kit Illumina  San Diego  CA  USA following the manufacturer\u2019s instruction. M.\u00a0musculus: 2.5\u00a0\u00b5g of total RNA was used with Illumina\u2019s TruSeq RNA sample prep kit.", null, "strain:TuAB|age:5 month|tissue:skin", "GSM1141107", "GSM1141107: Nr30 danrer skin 5months rep9; Danio rerio; RNA Seq", "GSM1141107 1", null, "1", "D.\u00a0rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen  Hilden  Germany at 80 \u00b0C. Total RNA was isolated with TRIzol Life Technologies  Darmstadt  Germany according to the instructions of the manufacturer. M.\u00a0musculus: The isolated skin was homogenized in 500\u00a0\u03bcl QIAzol Qiagen by subsequently adding 100\u00a0\u03bcl chloroform. Following phase separation  the aqueous phase was transferred into a fresh tube  then 0.16 volume NaAc 2\u00a0M  pH\u00a04.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20\u00a0\u03bcl water GIBCO and stored at \u201380\u00b0C until use. D.\u00a0rerio: 5\u00a0\u00b5g of total RNA was used for preparation of libraries using Illumina\u2019s mRNA Seq sample prep kit Illumina  San Diego  CA  USA following the manufacturer\u2019s instruction. M.\u00a0musculus: 2.5\u00a0\u00b5g of total RNA was used with Illumina\u2019s TruSeq RNA sample prep kit.", "GEO Accession:GSM1141107", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", null, "SRP022612", null, null, "Nr30_5m.fastq.gz", "fastq", 2502725752.0, 32930602.0, "GSM1141107 r1", "0:76", "A:684745428;C:570860380;G:565883575;T:679750149;N:1486220", 76, null, null, null, 684745428, 570860380, 565883575, 679750149, 1486220, "SRX277684", "SRS420784", "SRA076297", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.91789, null, 0.10423, null, 0.7263, null, 0.4909, null, 76, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "Germany", "2013-05-14", "Adult", "Adult", "Skin", "Surface Structure"], [36753, "SRR850596", "SRX277683", "SRS420783", "SRP022612", "PRJNA203029", "RNA seq of Danio rerio and Mus musculus skin for three different age groups", "GSE46916", "Other", "Background: Comparison of temporal gene expression profiles. The RNA seq data comprises 3 age groups: 2  15 month and 30 month for mouse skin; 5  24 month and 42 month for zebrafish skin. Illumina 50bp single stranded single read RNA sequencing Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 15 samples for mouse: 5 biological replicates for 2 month  6 biological replicates for 15 month and 4 biological replicates for 30 month; 20 samples for zebrafish: 9 biological replicates for 5 month  6 biological replicates for 24 month and 5 biological replicates for 42 month", null, "pubmed:26620638", null, "Nr29 danrer skin 5months rep8", "GSM1141106", null, "source name:total RNA extracted from skin|strain:TuAB|age:5 month|tissue:skin", "Nr29 danrer skin 5months rep8", "Illumina Casava software used for extraction of FASTQ files FASTQ files were mapped using Bowtie vs. the respective genomic sequence and a splice site data set created using UCSC's RefSeq annotation for each species Counting of uniquely mapped reads and assignment to RefSeq transcripts/genes using R Statistical Language and Bioconductor Calculation of RPKM values for each transcript and gene from the corresponding RefSeq annotation Genome build: D.\u00a0rerio: danRer7; M. musculus: mm9 Supplementary files format and content: Excel file include raw counts and RPKM values for each sample", "total RNA extracted from skin", null, "D.\u00a0rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen  Hilden  Germany at 80 \u00b0C. Total RNA was isolated with TRIzol Life Technologies  Darmstadt  Germany according to the instructions of the manufacturer. M.\u00a0musculus: The isolated skin was homogenized in 500\u00a0\u03bcl QIAzol Qiagen by subsequently adding 100\u00a0\u03bcl chloroform. Following phase separation  the aqueous phase was transferred into a fresh tube  then 0.16 volume NaAc 2\u00a0M  pH\u00a04.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20\u00a0\u03bcl water GIBCO and stored at \u201380\u00b0C until use. D.\u00a0rerio: 5\u00a0\u00b5g of total RNA was used for preparation of libraries using Illumina\u2019s mRNA Seq sample prep kit Illumina  San Diego  CA  USA following the manufacturer\u2019s instruction. M.\u00a0musculus: 2.5\u00a0\u00b5g of total RNA was used with Illumina\u2019s TruSeq RNA sample prep kit.", null, "strain:TuAB|age:5 month|tissue:skin", "GSM1141106", "GSM1141106: Nr29 danrer skin 5months rep8; Danio rerio; RNA Seq", "GSM1141106 1", null, "1", "D.\u00a0rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen  Hilden  Germany at 80 \u00b0C. Total RNA was isolated with TRIzol Life Technologies  Darmstadt  Germany according to the instructions of the manufacturer. M.\u00a0musculus: The isolated skin was homogenized in 500\u00a0\u03bcl QIAzol Qiagen by subsequently adding 100\u00a0\u03bcl chloroform. Following phase separation  the aqueous phase was transferred into a fresh tube  then 0.16 volume NaAc 2\u00a0M  pH\u00a04.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20\u00a0\u03bcl water GIBCO and stored at \u201380\u00b0C until use. D.\u00a0rerio: 5\u00a0\u00b5g of total RNA was used for preparation of libraries using Illumina\u2019s mRNA Seq sample prep kit Illumina  San Diego  CA  USA following the manufacturer\u2019s instruction. M.\u00a0musculus: 2.5\u00a0\u00b5g of total RNA was used with Illumina\u2019s TruSeq RNA sample prep kit.", "GEO Accession:GSM1141106", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", null, "SRP022612", null, null, "Nr29_5m.fastq.gz", "fastq", 2012479468.0, 26479993.0, "GSM1141106 r1", "0:76", "A:558800574;C:450898608;G:447907004;T:553773824;N:1099458", 76, null, null, null, 558800574, 450898608, 447907004, 553773824, 1099458, "SRX277683", "SRS420783", "SRA076297", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.9055, null, 0.1197, null, 0.7119, null, 0.48553, null, 76, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "Germany", "2013-05-14", "Adult", "Adult", "Skin", "Surface Structure"], [36754, "SRR850595", "SRX277682", "SRS420782", "SRP022612", "PRJNA203029", "RNA seq of Danio rerio and Mus musculus skin for three different age groups", "GSE46916", "Other", "Background: Comparison of temporal gene expression profiles. The RNA seq data comprises 3 age groups: 2  15 month and 30 month for mouse skin; 5  24 month and 42 month for zebrafish skin. Illumina 50bp single stranded single read RNA sequencing Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 15 samples for mouse: 5 biological replicates for 2 month  6 biological replicates for 15 month and 4 biological replicates for 30 month; 20 samples for zebrafish: 9 biological replicates for 5 month  6 biological replicates for 24 month and 5 biological replicates for 42 month", null, "pubmed:26620638", null, "Nr28 danrer skin 5months rep7", "GSM1141105", null, "source name:total RNA extracted from skin|strain:TuAB|age:5 month|tissue:skin", "Nr28 danrer skin 5months rep7", "Illumina Casava software used for extraction of FASTQ files FASTQ files were mapped using Bowtie vs. the respective genomic sequence and a splice site data set created using UCSC's RefSeq annotation for each species Counting of uniquely mapped reads and assignment to RefSeq transcripts/genes using R Statistical Language and Bioconductor Calculation of RPKM values for each transcript and gene from the corresponding RefSeq annotation Genome build: D.\u00a0rerio: danRer7; M. musculus: mm9 Supplementary files format and content: Excel file include raw counts and RPKM values for each sample", "total RNA extracted from skin", null, "D.\u00a0rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen  Hilden  Germany at 80 \u00b0C. Total RNA was isolated with TRIzol Life Technologies  Darmstadt  Germany according to the instructions of the manufacturer. M.\u00a0musculus: The isolated skin was homogenized in 500\u00a0\u03bcl QIAzol Qiagen by subsequently adding 100\u00a0\u03bcl chloroform. Following phase separation  the aqueous phase was transferred into a fresh tube  then 0.16 volume NaAc 2\u00a0M  pH\u00a04.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20\u00a0\u03bcl water GIBCO and stored at \u201380\u00b0C until use. D.\u00a0rerio: 5\u00a0\u00b5g of total RNA was used for preparation of libraries using Illumina\u2019s mRNA Seq sample prep kit Illumina  San Diego  CA  USA following the manufacturer\u2019s instruction. M.\u00a0musculus: 2.5\u00a0\u00b5g of total RNA was used with Illumina\u2019s TruSeq RNA sample prep kit.", null, "strain:TuAB|age:5 month|tissue:skin", "GSM1141105", "GSM1141105: Nr28 danrer skin 5months rep7; Danio rerio; RNA Seq", "GSM1141105 1", null, "1", "D.\u00a0rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen  Hilden  Germany at 80 \u00b0C. Total RNA was isolated with TRIzol Life Technologies  Darmstadt  Germany according to the instructions of the manufacturer. M.\u00a0musculus: The isolated skin was homogenized in 500\u00a0\u03bcl QIAzol Qiagen by subsequently adding 100\u00a0\u03bcl chloroform. Following phase separation  the aqueous phase was transferred into a fresh tube  then 0.16 volume NaAc 2\u00a0M  pH\u00a04.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20\u00a0\u03bcl water GIBCO and stored at \u201380\u00b0C until use. D.\u00a0rerio: 5\u00a0\u00b5g of total RNA was used for preparation of libraries using Illumina\u2019s mRNA Seq sample prep kit Illumina  San Diego  CA  USA following the manufacturer\u2019s instruction. M.\u00a0musculus: 2.5\u00a0\u00b5g of total RNA was used with Illumina\u2019s TruSeq RNA sample prep kit.", "GEO Accession:GSM1141105", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", null, "SRP022612", null, null, "Nr28_5m.fastq.gz", "fastq", 2075098224.0, 27303924.0, "GSM1141105 r1", "0:76", "A:555062827;C:487427075;G:487360186;T:544381395;N:866741", 76, null, null, null, 555062827, 487427075, 487360186, 544381395, 866741, "SRX277682", "SRS420782", "SRA076297", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.91784, null, 0.08866, null, 0.73208, null, 0.47793, null, 76, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "Germany", "2013-05-14", "Adult", "Adult", "Skin", "Surface Structure"], [36755, "SRR850594", "SRX277681", "SRS420781", "SRP022612", "PRJNA203029", "RNA seq of Danio rerio and Mus musculus skin for three different age groups", "GSE46916", "Other", "Background: Comparison of temporal gene expression profiles. The RNA seq data comprises 3 age groups: 2  15 month and 30 month for mouse skin; 5  24 month and 42 month for zebrafish skin. Illumina 50bp single stranded single read RNA sequencing Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 15 samples for mouse: 5 biological replicates for 2 month  6 biological replicates for 15 month and 4 biological replicates for 30 month; 20 samples for zebrafish: 9 biological replicates for 5 month  6 biological replicates for 24 month and 5 biological replicates for 42 month", null, "pubmed:26620638", null, "Nr27 danrer skin 5months rep6", "GSM1141104", null, "source name:total RNA extracted from skin|strain:TuAB|age:5 month|tissue:skin", "Nr27 danrer skin 5months rep6", "Illumina Casava software used for extraction of FASTQ files FASTQ files were mapped using Bowtie vs. the respective genomic sequence and a splice site data set created using UCSC's RefSeq annotation for each species Counting of uniquely mapped reads and assignment to RefSeq transcripts/genes using R Statistical Language and Bioconductor Calculation of RPKM values for each transcript and gene from the corresponding RefSeq annotation Genome build: D.\u00a0rerio: danRer7; M. musculus: mm9 Supplementary files format and content: Excel file include raw counts and RPKM values for each sample", "total RNA extracted from skin", null, "D.\u00a0rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen  Hilden  Germany at 80 \u00b0C. Total RNA was isolated with TRIzol Life Technologies  Darmstadt  Germany according to the instructions of the manufacturer. M.\u00a0musculus: The isolated skin was homogenized in 500\u00a0\u03bcl QIAzol Qiagen by subsequently adding 100\u00a0\u03bcl chloroform. Following phase separation  the aqueous phase was transferred into a fresh tube  then 0.16 volume NaAc 2\u00a0M  pH\u00a04.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20\u00a0\u03bcl water GIBCO and stored at \u201380\u00b0C until use. D.\u00a0rerio: 5\u00a0\u00b5g of total RNA was used for preparation of libraries using Illumina\u2019s mRNA Seq sample prep kit Illumina  San Diego  CA  USA following the manufacturer\u2019s instruction. M.\u00a0musculus: 2.5\u00a0\u00b5g of total RNA was used with Illumina\u2019s TruSeq RNA sample prep kit.", null, "strain:TuAB|age:5 month|tissue:skin", "GSM1141104", "GSM1141104: Nr27 danrer skin 5months rep6; Danio rerio; RNA Seq", "GSM1141104 1", null, "1", "D.\u00a0rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen  Hilden  Germany at 80 \u00b0C. Total RNA was isolated with TRIzol Life Technologies  Darmstadt  Germany according to the instructions of the manufacturer. M.\u00a0musculus: The isolated skin was homogenized in 500\u00a0\u03bcl QIAzol Qiagen by subsequently adding 100\u00a0\u03bcl chloroform. Following phase separation  the aqueous phase was transferred into a fresh tube  then 0.16 volume NaAc 2\u00a0M  pH\u00a04.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20\u00a0\u03bcl water GIBCO and stored at \u201380\u00b0C until use. D.\u00a0rerio: 5\u00a0\u00b5g of total RNA was used for preparation of libraries using Illumina\u2019s mRNA Seq sample prep kit Illumina  San Diego  CA  USA following the manufacturer\u2019s instruction. M.\u00a0musculus: 2.5\u00a0\u00b5g of total RNA was used with Illumina\u2019s TruSeq RNA sample prep kit.", "GEO Accession:GSM1141104", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", null, "SRP022612", null, null, "Nr27_5m.fastq.gz", "fastq", 2415354480.0, 31780980.0, "GSM1141104 r1", "0:76", "A:661012615;C:552471296;G:546304105;T:654315033;N:1251431", 76, null, null, null, 661012615, 552471296, 546304105, 654315033, 1251431, "SRX277681", "SRS420781", "SRA076297", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.91282, null, 0.104, null, 0.7236, null, 0.48186, null, 76, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "Germany", "2013-05-14", "Adult", "Adult", "Skin", "Surface Structure"], [36756, "SRR850593", "SRX277680", "SRS420780", "SRP022612", "PRJNA203029", "RNA seq of Danio rerio and Mus musculus skin for three different age groups", "GSE46916", "Other", "Background: Comparison of temporal gene expression profiles. The RNA seq data comprises 3 age groups: 2  15 month and 30 month for mouse skin; 5  24 month and 42 month for zebrafish skin. Illumina 50bp single stranded single read RNA sequencing Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 15 samples for mouse: 5 biological replicates for 2 month  6 biological replicates for 15 month and 4 biological replicates for 30 month; 20 samples for zebrafish: 9 biological replicates for 5 month  6 biological replicates for 24 month and 5 biological replicates for 42 month", null, "pubmed:26620638", null, "Nr26 danrer skin 5months rep5", "GSM1141103", null, "source name:total RNA extracted from skin|strain:TuAB|age:5 month|tissue:skin", "Nr26 danrer skin 5months rep5", "Illumina Casava software used for extraction of FASTQ files FASTQ files were mapped using Bowtie vs. the respective genomic sequence and a splice site data set created using UCSC's RefSeq annotation for each species Counting of uniquely mapped reads and assignment to RefSeq transcripts/genes using R Statistical Language and Bioconductor Calculation of RPKM values for each transcript and gene from the corresponding RefSeq annotation Genome build: D.\u00a0rerio: danRer7; M. musculus: mm9 Supplementary files format and content: Excel file include raw counts and RPKM values for each sample", "total RNA extracted from skin", null, "D.\u00a0rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen  Hilden  Germany at 80 \u00b0C. Total RNA was isolated with TRIzol Life Technologies  Darmstadt  Germany according to the instructions of the manufacturer. M.\u00a0musculus: The isolated skin was homogenized in 500\u00a0\u03bcl QIAzol Qiagen by subsequently adding 100\u00a0\u03bcl chloroform. Following phase separation  the aqueous phase was transferred into a fresh tube  then 0.16 volume NaAc 2\u00a0M  pH\u00a04.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20\u00a0\u03bcl water GIBCO and stored at \u201380\u00b0C until use. D.\u00a0rerio: 5\u00a0\u00b5g of total RNA was used for preparation of libraries using Illumina\u2019s mRNA Seq sample prep kit Illumina  San Diego  CA  USA following the manufacturer\u2019s instruction. M.\u00a0musculus: 2.5\u00a0\u00b5g of total RNA was used with Illumina\u2019s TruSeq RNA sample prep kit.", null, "strain:TuAB|age:5 month|tissue:skin", "GSM1141103", "GSM1141103: Nr26 danrer skin 5months rep5; Danio rerio; RNA Seq", "GSM1141103 1", null, "1", "D.\u00a0rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen  Hilden  Germany at 80 \u00b0C. Total RNA was isolated with TRIzol Life Technologies  Darmstadt  Germany according to the instructions of the manufacturer. M.\u00a0musculus: The isolated skin was homogenized in 500\u00a0\u03bcl QIAzol Qiagen by subsequently adding 100\u00a0\u03bcl chloroform. Following phase separation  the aqueous phase was transferred into a fresh tube  then 0.16 volume NaAc 2\u00a0M  pH\u00a04.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20\u00a0\u03bcl water GIBCO and stored at \u201380\u00b0C until use. D.\u00a0rerio: 5\u00a0\u00b5g of total RNA was used for preparation of libraries using Illumina\u2019s mRNA Seq sample prep kit Illumina  San Diego  CA  USA following the manufacturer\u2019s instruction. M.\u00a0musculus: 2.5\u00a0\u00b5g of total RNA was used with Illumina\u2019s TruSeq RNA sample prep kit.", "GEO Accession:GSM1141103", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", null, "SRP022612", null, null, "Nr26_5m_l8_export.fq.gz", "fastq", 1866135464.0, 24554414.0, "GSM1141103 r1", "0:76", "A:495417130;C:442746432;G:436942898;T:490685510;N:343494", 76, null, null, null, 495417130, 442746432, 436942898, 490685510, 343494, "SRX277680", "SRS420780", "SRA076297", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.92443, null, 0.08023, null, 0.7288, null, 0.48902, null, 76, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "Germany", "2013-05-14", "Adult", "Adult", "Skin", "Surface Structure"], [36757, "SRR850592", "SRX277679", "SRS420778", "SRP022612", "PRJNA203029", "RNA seq of Danio rerio and Mus musculus skin for three different age groups", "GSE46916", "Other", "Background: Comparison of temporal gene expression profiles. The RNA seq data comprises 3 age groups: 2  15 month and 30 month for mouse skin; 5  24 month and 42 month for zebrafish skin. Illumina 50bp single stranded single read RNA sequencing Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 15 samples for mouse: 5 biological replicates for 2 month  6 biological replicates for 15 month and 4 biological replicates for 30 month; 20 samples for zebrafish: 9 biological replicates for 5 month  6 biological replicates for 24 month and 5 biological replicates for 42 month", null, "pubmed:26620638", null, "Nr25 danrer skin 5months rep4", "GSM1141102", null, "source name:total RNA extracted from skin|strain:TuAB|age:5 month|tissue:skin", "Nr25 danrer skin 5months rep4", "Illumina Casava software used for extraction of FASTQ files FASTQ files were mapped using Bowtie vs. the respective genomic sequence and a splice site data set created using UCSC's RefSeq annotation for each species Counting of uniquely mapped reads and assignment to RefSeq transcripts/genes using R Statistical Language and Bioconductor Calculation of RPKM values for each transcript and gene from the corresponding RefSeq annotation Genome build: D.\u00a0rerio: danRer7; M. musculus: mm9 Supplementary files format and content: Excel file include raw counts and RPKM values for each sample", "total RNA extracted from skin", null, "D.\u00a0rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen  Hilden  Germany at 80 \u00b0C. Total RNA was isolated with TRIzol Life Technologies  Darmstadt  Germany according to the instructions of the manufacturer. M.\u00a0musculus: The isolated skin was homogenized in 500\u00a0\u03bcl QIAzol Qiagen by subsequently adding 100\u00a0\u03bcl chloroform. Following phase separation  the aqueous phase was transferred into a fresh tube  then 0.16 volume NaAc 2\u00a0M  pH\u00a04.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20\u00a0\u03bcl water GIBCO and stored at \u201380\u00b0C until use. D.\u00a0rerio: 5\u00a0\u00b5g of total RNA was used for preparation of libraries using Illumina\u2019s mRNA Seq sample prep kit Illumina  San Diego  CA  USA following the manufacturer\u2019s instruction. M.\u00a0musculus: 2.5\u00a0\u00b5g of total RNA was used with Illumina\u2019s TruSeq RNA sample prep kit.", null, "strain:TuAB|age:5 month|tissue:skin", "GSM1141102", "GSM1141102: Nr25 danrer skin 5months rep4; Danio rerio; RNA Seq", "GSM1141102 1", null, "1", "D.\u00a0rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen  Hilden  Germany at 80 \u00b0C. Total RNA was isolated with TRIzol Life Technologies  Darmstadt  Germany according to the instructions of the manufacturer. M.\u00a0musculus: The isolated skin was homogenized in 500\u00a0\u03bcl QIAzol Qiagen by subsequently adding 100\u00a0\u03bcl chloroform. Following phase separation  the aqueous phase was transferred into a fresh tube  then 0.16 volume NaAc 2\u00a0M  pH\u00a04.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20\u00a0\u03bcl water GIBCO and stored at \u201380\u00b0C until use. D.\u00a0rerio: 5\u00a0\u00b5g of total RNA was used for preparation of libraries using Illumina\u2019s mRNA Seq sample prep kit Illumina  San Diego  CA  USA following the manufacturer\u2019s instruction. M.\u00a0musculus: 2.5\u00a0\u00b5g of total RNA was used with Illumina\u2019s TruSeq RNA sample prep kit.", "GEO Accession:GSM1141102", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", null, "SRP022612", null, null, "Nr25_5m_l7_export.fq.gz", "fastq", 2146470508.0, 28243033.0, "GSM1141102 r1", "0:76", "A:583770580;C:491677255;G:491536604;T:579365742;N:120327", 76, null, null, null, 583770580, 491677255, 491536604, 579365742, 120327, "SRX277679", "SRS420778", "SRA076297", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.89568, null, 0.11303, null, 0.71778, null, 0.47882, null, 76, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "Germany", "2013-05-14", "Adult", "Adult", "Skin", "Surface Structure"], [36758, "SRR850591", "SRX277678", "SRS420779", "SRP022612", "PRJNA203029", "RNA seq of Danio rerio and Mus musculus skin for three different age groups", "GSE46916", "Other", "Background: Comparison of temporal gene expression profiles. The RNA seq data comprises 3 age groups: 2  15 month and 30 month for mouse skin; 5  24 month and 42 month for zebrafish skin. Illumina 50bp single stranded single read RNA sequencing Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 15 samples for mouse: 5 biological replicates for 2 month  6 biological replicates for 15 month and 4 biological replicates for 30 month; 20 samples for zebrafish: 9 biological replicates for 5 month  6 biological replicates for 24 month and 5 biological replicates for 42 month", null, "pubmed:26620638", null, "Nr23 danrer skin 5months rep3", "GSM1141101", null, "source name:total RNA extracted from skin|strain:TuAB|age:5 month|tissue:skin", "Nr23 danrer skin 5months rep3", "Illumina Casava software used for extraction of FASTQ files FASTQ files were mapped using Bowtie vs. the respective genomic sequence and a splice site data set created using UCSC's RefSeq annotation for each species Counting of uniquely mapped reads and assignment to RefSeq transcripts/genes using R Statistical Language and Bioconductor Calculation of RPKM values for each transcript and gene from the corresponding RefSeq annotation Genome build: D.\u00a0rerio: danRer7; M. musculus: mm9 Supplementary files format and content: Excel file include raw counts and RPKM values for each sample", "total RNA extracted from skin", null, "D.\u00a0rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen  Hilden  Germany at 80 \u00b0C. Total RNA was isolated with TRIzol Life Technologies  Darmstadt  Germany according to the instructions of the manufacturer. M.\u00a0musculus: The isolated skin was homogenized in 500\u00a0\u03bcl QIAzol Qiagen by subsequently adding 100\u00a0\u03bcl chloroform. Following phase separation  the aqueous phase was transferred into a fresh tube  then 0.16 volume NaAc 2\u00a0M  pH\u00a04.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20\u00a0\u03bcl water GIBCO and stored at \u201380\u00b0C until use. D.\u00a0rerio: 5\u00a0\u00b5g of total RNA was used for preparation of libraries using Illumina\u2019s mRNA Seq sample prep kit Illumina  San Diego  CA  USA following the manufacturer\u2019s instruction. M.\u00a0musculus: 2.5\u00a0\u00b5g of total RNA was used with Illumina\u2019s TruSeq RNA sample prep kit.", null, "strain:TuAB|age:5 month|tissue:skin", "GSM1141101", "GSM1141101: Nr23 danrer skin 5months rep3; Danio rerio; RNA Seq", "GSM1141101 1", null, "1", "D.\u00a0rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen  Hilden  Germany at 80 \u00b0C. Total RNA was isolated with TRIzol Life Technologies  Darmstadt  Germany according to the instructions of the manufacturer. M.\u00a0musculus: The isolated skin was homogenized in 500\u00a0\u03bcl QIAzol Qiagen by subsequently adding 100\u00a0\u03bcl chloroform. Following phase separation  the aqueous phase was transferred into a fresh tube  then 0.16 volume NaAc 2\u00a0M  pH\u00a04.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20\u00a0\u03bcl water GIBCO and stored at \u201380\u00b0C until use. D.\u00a0rerio: 5\u00a0\u00b5g of total RNA was used for preparation of libraries using Illumina\u2019s mRNA Seq sample prep kit Illumina  San Diego  CA  USA following the manufacturer\u2019s instruction. M.\u00a0musculus: 2.5\u00a0\u00b5g of total RNA was used with Illumina\u2019s TruSeq RNA sample prep kit.", "GEO Accession:GSM1141101", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", null, "SRP022612", null, null, "Nr23_5m_l6_export.fq.gz", "fastq", 2628691268.0, 34588043.0, "GSM1141101 r1", "0:76", "A:693944705;C:617538873;G:611502862;T:705582669;N:122159", 76, null, null, null, 693944705, 617538873, 611502862, 705582669, 122159, "SRX277678", "SRS420779", "SRA076297", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.92203, null, 0.09747, null, 0.71378, null, 0.47796, null, 76, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "Germany", "2013-05-14", "Adult", "Adult", "Skin", "Surface Structure"], [36759, "SRR850590", "SRX277677", "SRS420777", "SRP022612", "PRJNA203029", "RNA seq of Danio rerio and Mus musculus skin for three different age groups", "GSE46916", "Other", "Background: Comparison of temporal gene expression profiles. The RNA seq data comprises 3 age groups: 2  15 month and 30 month for mouse skin; 5  24 month and 42 month for zebrafish skin. Illumina 50bp single stranded single read RNA sequencing Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 15 samples for mouse: 5 biological replicates for 2 month  6 biological replicates for 15 month and 4 biological replicates for 30 month; 20 samples for zebrafish: 9 biological replicates for 5 month  6 biological replicates for 24 month and 5 biological replicates for 42 month", null, "pubmed:26620638", null, "Nr22 danrer skin 5months rep2", "GSM1141100", null, "source name:total RNA extracted from skin|strain:TuAB|age:5 month|tissue:skin", "Nr22 danrer skin 5months rep2", "Illumina Casava software used for extraction of FASTQ files FASTQ files were mapped using Bowtie vs. the respective genomic sequence and a splice site data set created using UCSC's RefSeq annotation for each species Counting of uniquely mapped reads and assignment to RefSeq transcripts/genes using R Statistical Language and Bioconductor Calculation of RPKM values for each transcript and gene from the corresponding RefSeq annotation Genome build: D.\u00a0rerio: danRer7; M. musculus: mm9 Supplementary files format and content: Excel file include raw counts and RPKM values for each sample", "total RNA extracted from skin", null, "D.\u00a0rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen  Hilden  Germany at 80 \u00b0C. Total RNA was isolated with TRIzol Life Technologies  Darmstadt  Germany according to the instructions of the manufacturer. M.\u00a0musculus: The isolated skin was homogenized in 500\u00a0\u03bcl QIAzol Qiagen by subsequently adding 100\u00a0\u03bcl chloroform. Following phase separation  the aqueous phase was transferred into a fresh tube  then 0.16 volume NaAc 2\u00a0M  pH\u00a04.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20\u00a0\u03bcl water GIBCO and stored at \u201380\u00b0C until use. D.\u00a0rerio: 5\u00a0\u00b5g of total RNA was used for preparation of libraries using Illumina\u2019s mRNA Seq sample prep kit Illumina  San Diego  CA  USA following the manufacturer\u2019s instruction. M.\u00a0musculus: 2.5\u00a0\u00b5g of total RNA was used with Illumina\u2019s TruSeq RNA sample prep kit.", null, "strain:TuAB|age:5 month|tissue:skin", "GSM1141100", "GSM1141100: Nr22 danrer skin 5months rep2; Danio rerio; RNA Seq", "GSM1141100 1", null, "1", "D.\u00a0rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen  Hilden  Germany at 80 \u00b0C. Total RNA was isolated with TRIzol Life Technologies  Darmstadt  Germany according to the instructions of the manufacturer. M.\u00a0musculus: The isolated skin was homogenized in 500\u00a0\u03bcl QIAzol Qiagen by subsequently adding 100\u00a0\u03bcl chloroform. Following phase separation  the aqueous phase was transferred into a fresh tube  then 0.16 volume NaAc 2\u00a0M  pH\u00a04.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20\u00a0\u03bcl water GIBCO and stored at \u201380\u00b0C until use. D.\u00a0rerio: 5\u00a0\u00b5g of total RNA was used for preparation of libraries using Illumina\u2019s mRNA Seq sample prep kit Illumina  San Diego  CA  USA following the manufacturer\u2019s instruction. M.\u00a0musculus: 2.5\u00a0\u00b5g of total RNA was used with Illumina\u2019s TruSeq RNA sample prep kit.", "GEO Accession:GSM1141100", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", null, "SRP022612", null, null, "Nr22_5m.fastq.gz", "fastq", 3561382724.0, 46860299.0, "GSM1141100 r1", "0:76", "A:956105654;C:826498432;G:826128735;T:952426883;N:223020", 76, null, null, null, 956105654, 826498432, 826128735, 952426883, 223020, "SRX277677", "SRS420777", "SRA076297", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.93192, null, 0.09055, null, 0.72876, null, 0.52416, null, 76, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "Germany", "2013-05-14", "Adult", "Adult", "Skin", "Surface Structure"], [36760, "SRR850589", "SRX277676", "SRS420776", "SRP022612", "PRJNA203029", "RNA seq of Danio rerio and Mus musculus skin for three different age groups", "GSE46916", "Other", "Background: Comparison of temporal gene expression profiles. The RNA seq data comprises 3 age groups: 2  15 month and 30 month for mouse skin; 5  24 month and 42 month for zebrafish skin. Illumina 50bp single stranded single read RNA sequencing Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 15 samples for mouse: 5 biological replicates for 2 month  6 biological replicates for 15 month and 4 biological replicates for 30 month; 20 samples for zebrafish: 9 biological replicates for 5 month  6 biological replicates for 24 month and 5 biological replicates for 42 month", null, "pubmed:26620638", null, "Nr21 danrer skin 5months rep1", "GSM1141099", null, "source name:total RNA extracted from skin|strain:TuAB|age:5 month|tissue:skin", "Nr21 danrer skin 5months rep1", "Illumina Casava software used for extraction of FASTQ files FASTQ files were mapped using Bowtie vs. the respective genomic sequence and a splice site data set created using UCSC's RefSeq annotation for each species Counting of uniquely mapped reads and assignment to RefSeq transcripts/genes using R Statistical Language and Bioconductor Calculation of RPKM values for each transcript and gene from the corresponding RefSeq annotation Genome build: D.\u00a0rerio: danRer7; M. musculus: mm9 Supplementary files format and content: Excel file include raw counts and RPKM values for each sample", "total RNA extracted from skin", null, "D.\u00a0rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen  Hilden  Germany at 80 \u00b0C. Total RNA was isolated with TRIzol Life Technologies  Darmstadt  Germany according to the instructions of the manufacturer. M.\u00a0musculus: The isolated skin was homogenized in 500\u00a0\u03bcl QIAzol Qiagen by subsequently adding 100\u00a0\u03bcl chloroform. Following phase separation  the aqueous phase was transferred into a fresh tube  then 0.16 volume NaAc 2\u00a0M  pH\u00a04.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20\u00a0\u03bcl water GIBCO and stored at \u201380\u00b0C until use. D.\u00a0rerio: 5\u00a0\u00b5g of total RNA was used for preparation of libraries using Illumina\u2019s mRNA Seq sample prep kit Illumina  San Diego  CA  USA following the manufacturer\u2019s instruction. M.\u00a0musculus: 2.5\u00a0\u00b5g of total RNA was used with Illumina\u2019s TruSeq RNA sample prep kit.", null, "strain:TuAB|age:5 month|tissue:skin", "GSM1141099", "GSM1141099: Nr21 danrer skin 5months rep1; Danio rerio; RNA Seq", "GSM1141099 1", null, "1", "D.\u00a0rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen  Hilden  Germany at 80 \u00b0C. Total RNA was isolated with TRIzol Life Technologies  Darmstadt  Germany according to the instructions of the manufacturer. M.\u00a0musculus: The isolated skin was homogenized in 500\u00a0\u03bcl QIAzol Qiagen by subsequently adding 100\u00a0\u03bcl chloroform. Following phase separation  the aqueous phase was transferred into a fresh tube  then 0.16 volume NaAc 2\u00a0M  pH\u00a04.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20\u00a0\u03bcl water GIBCO and stored at \u201380\u00b0C until use. D.\u00a0rerio: 5\u00a0\u00b5g of total RNA was used for preparation of libraries using Illumina\u2019s mRNA Seq sample prep kit Illumina  San Diego  CA  USA following the manufacturer\u2019s instruction. M.\u00a0musculus: 2.5\u00a0\u00b5g of total RNA was used with Illumina\u2019s TruSeq RNA sample prep kit.", "GEO Accession:GSM1141099", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", null, "SRP022612", null, null, "Nr21_5m_l4_export.fq.gz", "fastq", 2709932304.0, 35657004.0, "GSM1141099 r1", "0:76", "A:730073083;C:631072920;G:619401848;T:729203191;N:181262", 76, null, null, null, 730073083, 631072920, 619401848, 729203191, 181262, "SRX277676", "SRS420776", "SRA076297", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.92839, null, 0.10379, null, 0.71392, null, 0.4865, null, 76, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "Germany", "2013-05-14", "Adult", "Adult", "Skin", "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", 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