{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_source = \"TRANSCRIPTOMIC\", technology = \"bulk\" and tissue_curation_coarse = \"Muscular System\"", "rows": [[25351, "SRR25868024", "SRX21589429", "SRS18767002", "SRP457978", "PRJNA1011839", "fhl2b expression ameliorates muscular dystrophy [20 month EOM and trunk]", "GSE242134", "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 innate resistance of extraocular muscle to muscular dystrophies we knocked down desmin and sequenced extraocular muscle as well as trunk muscle from zebrafish at two time points. We then performed gene expression analysis between WT and desmin knock down tissues of the same type at the same time points.", "parent bioproject:PRJNA1011837", "pubmed:38431640", null, "20m des EOM group 3", "GSM7749535", null, "source name:20 mpf extraocular muscle|age:20 mpf|tissue:extraocular muscle|strain:AB|cell type:extraocular myofibers|genotype:desma / ;desmb / |geo loc name:missing|collection date:missing", "20m des EOM group 3", "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", "20 mpf extraocular muscle", null, "Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at 80C. 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Strikingly the extraocular muscles EOMs controlling eye movements are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin plectin and obscurin intermediate filament proteins causing different muscle dystrophies and contributes to disease protection of the EOMs. Moreover we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje significantly improving their survival rate. Therefore fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the innate resistance of extraocular muscle to muscular dystrophies we knocked down desmin and sequenced extraocular muscle as well as trunk muscle from zebrafish at two time points. We then performed gene expression analysis between WT and desmin knock down tissues of the same type at the same time points.", "parent bioproject:PRJNA1011837", "pubmed:38431640", null, "20m des EOM group 2", "GSM7749534", null, "source name:20 mpf extraocular muscle|age:20 mpf|tissue:extraocular muscle|strain:AB|cell type:extraocular myofibers|genotype:desma / ;desmb / |geo loc name:missing|collection date:missing", "20m des EOM group 2", "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", "20 mpf extraocular muscle", 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. 200ng 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", "age:20 mpf|tissue:extraocular muscle|strain:AB|cell type:extraocular myofibers|genotype:desma / ;desmb / ", "GSM7749534", "GSM7749534: 20m des EOM group 2; Danio rerio; RNA Seq", "GSM7749534 r1", "GSM7749534", "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. 200ng total RNA was used for library construction. 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Strikingly the extraocular muscles EOMs controlling eye movements are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin plectin and obscurin intermediate filament proteins causing different muscle dystrophies and contributes to disease protection of the EOMs. Moreover we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje significantly improving their survival rate. Therefore fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the innate resistance of extraocular muscle to muscular dystrophies we knocked down desmin and sequenced extraocular muscle as well as trunk muscle from zebrafish at two time points. We then performed gene expression analysis between WT and desmin knock down tissues of the same type at the same time points.", "parent bioproject:PRJNA1011837", "pubmed:38431640", null, "20m des EOM group 1", "GSM7749533", null, "source name:20 mpf extraocular muscle|age:20 mpf|tissue:extraocular muscle|strain:AB|cell type:extraocular myofibers|genotype:desma / ;desmb / |geo loc name:missing|collection date:missing", "20m des EOM group 1", "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", "20 mpf extraocular muscle", 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. 200ng 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", "age:20 mpf|tissue:extraocular muscle|strain:AB|cell type:extraocular myofibers|genotype:desma / ;desmb / ", "GSM7749533", "GSM7749533: 20m des EOM group 1; Danio rerio; RNA Seq", "GSM7749533 r1", "GSM7749533", "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. 200ng total RNA was used for library construction. 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Strikingly the extraocular muscles EOMs controlling eye movements are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin plectin and obscurin intermediate filament proteins causing different muscle dystrophies and contributes to disease protection of the EOMs. Moreover we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje significantly improving their survival rate. Therefore fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the innate resistance of extraocular muscle to muscular dystrophies we knocked down desmin and sequenced extraocular muscle as well as trunk muscle from zebrafish at two time points. We then performed gene expression analysis between WT and desmin knock down tissues of the same type at the same time points.", "parent bioproject:PRJNA1011837", "pubmed:38431640", null, "20m wt EOM group 3", "GSM7749532", null, "source name:20 mpf extraocular muscle|age:20 mpf|tissue:extraocular muscle|strain:AB|cell type:extraocular myofibers|genotype:WT|geo loc name:missing|collection date:missing", "20m wt EOM group 3", "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", "20 mpf extraocular muscle", 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. 200ng 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", "age:20 mpf|tissue:extraocular muscle|strain:AB|cell type:extraocular myofibers|genotype:WT", "GSM7749532", "GSM7749532: 20m wt EOM group 3; Danio rerio; RNA Seq", "GSM7749532 r1", "GSM7749532", "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. 200ng total RNA was used for library construction. 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Strikingly the extraocular muscles EOMs controlling eye movements are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin plectin and obscurin intermediate filament proteins causing different muscle dystrophies and contributes to disease protection of the EOMs. Moreover we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje significantly improving their survival rate. Therefore fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the innate resistance of extraocular muscle to muscular dystrophies we knocked down desmin and sequenced extraocular muscle as well as trunk muscle from zebrafish at two time points. We then performed gene expression analysis between WT and desmin knock down tissues of the same type at the same time points.", "parent bioproject:PRJNA1011837", "pubmed:38431640", null, "20m wt EOM group 2", "GSM7749531", null, "source name:20 mpf extraocular muscle|age:20 mpf|tissue:extraocular muscle|strain:AB|cell type:extraocular myofibers|genotype:WT|geo loc name:missing|collection date:missing", "20m wt EOM group 2", "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", "20 mpf extraocular muscle", 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. 200ng 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", "age:20 mpf|tissue:extraocular muscle|strain:AB|cell type:extraocular myofibers|genotype:WT", "GSM7749531", "GSM7749531: 20m wt EOM group 2; Danio rerio; RNA Seq", "GSM7749531 r1", "GSM7749531", "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. 200ng total RNA was used for library construction. 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Strikingly the extraocular muscles EOMs controlling eye movements are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin plectin and obscurin intermediate filament proteins causing different muscle dystrophies and contributes to disease protection of the EOMs. Moreover we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje significantly improving their survival rate. Therefore fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the innate resistance of extraocular muscle to muscular dystrophies we knocked down desmin and sequenced extraocular muscle as well as trunk muscle from zebrafish at two time points. We then performed gene expression analysis between WT and desmin knock down tissues of the same type at the same time points.", "parent bioproject:PRJNA1011837", "pubmed:38431640", null, "20m wt EOM group 1", "GSM7749530", null, "source name:20 mpf extraocular muscle|age:20 mpf|tissue:extraocular muscle|strain:AB|cell type:extraocular myofibers|genotype:WT|geo loc name:missing|collection date:missing", "20m wt EOM group 1", "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", "20 mpf extraocular muscle", 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. 200ng 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", "age:20 mpf|tissue:extraocular muscle|strain:AB|cell type:extraocular myofibers|genotype:WT", "GSM7749530", "GSM7749530: 20m wt EOM group 1; Danio rerio; RNA Seq", "GSM7749530 r1", "GSM7749530", "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. 200ng total RNA was used for library construction. 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Strikingly the extraocular muscles EOMs controlling eye movements are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin plectin and obscurin intermediate filament proteins causing different muscle dystrophies and contributes to disease protection of the EOMs. Moreover we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje significantly improving their survival rate. Therefore fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the innate resistance of extraocular muscle to muscular dystrophies we knocked down desmin and sequenced extraocular muscle as well as trunk muscle from zebrafish at two time points. We then performed gene expression analysis between WT and desmin knock down tissues of the same type at the same time points.", "parent bioproject:PRJNA1011837", "pubmed:38431640", null, "des EOM group 3", "GSM7749563", null, "source name:extraocular muscle|tissue:extraocular muscle|age:5 mpf|strain:AB|cell type:extraocular myofibers|genotype:desma / ;desmb / |geo loc name:missing|collection date:missing", "des EOM group 3", "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", "extraocular muscle", 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:extraocular muscle|age:5 mpf|strain:AB|cell type:extraocular myofibers|genotype:desma / ;desmb / ", "GSM7749563", "GSM7749563: des EOM group 3; Danio rerio; RNA Seq", "GSM7749563 r1", "GSM7749563", "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, "SRP457980", null, "loader:fastq load.py", "P17251_106_S10_L001_R1_001.fastq.gz P17251_106_S10_L001_R2_001.fastq.gz", "fastq fastq", 30795037848.0, 101970324.0, "GSM7749563 r1", "0:151 1:151", "A:8369479918;C:7035512003;G:7341959696;T:8047708763;N:377468", 151, 151, null, null, 8369479918, 7035512003, 7341959696, 8047708763, 377468, "SRX21589470", "SRS18767043", "SRA1703878", "Ume\u00e5 Univeristy", "Ume\u00e5 Univeristy", 2, 0.95744, 0.94806, 0.06123, 0.06213, 0.75911, 0.76382, 0.53005, 0.53206, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "Sweden", "2023-09-01", "Adult", "Adult", "Muscle", "Muscular System"], [25364, "SRR25868066", "SRX21589469", "SRS18767042", "SRP457980", "PRJNA1011841", "fhl2b expression ameliorates muscular dystrophy [5 month EOM and trunk]", "GSE242136", "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 innate resistance of extraocular muscle to muscular dystrophies we knocked down desmin and sequenced extraocular muscle as well as trunk muscle from zebrafish at two time points. We then performed gene expression analysis between WT and desmin knock down tissues of the same type at the same time points.", "parent bioproject:PRJNA1011837", "pubmed:38431640", null, "des EOM group 2", "GSM7749562", null, "source name:extraocular muscle|tissue:extraocular muscle|age:5 mpf|strain:AB|cell type:extraocular myofibers|genotype:desma / ;desmb / |geo loc name:missing|collection date:missing", "des EOM group 2", "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", "extraocular muscle", 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:extraocular muscle|age:5 mpf|strain:AB|cell type:extraocular myofibers|genotype:desma / ;desmb / ", "GSM7749562", "GSM7749562: des EOM group 2; Danio rerio; RNA Seq", "GSM7749562 r1", "GSM7749562", "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, "SRP457980", null, "loader:fastq load.py", "P17251_105_S9_L001_R1_001.fastq.gz P17251_105_S9_L001_R2_001.fastq.gz", "fastq fastq", 24388992708.0, 80758254.0, "GSM7749562 r1", "0:151 1:151", "A:6579219632;C:5651892239;G:6170251564;T:5987329579;N:299694", 151, 151, null, null, 6579219632, 5651892239, 6170251564, 5987329579, 299694, "SRX21589469", "SRS18767042", "SRA1703878", "Ume\u00e5 Univeristy", "Ume\u00e5 Univeristy", 2, 0.96142, 0.94783, 0.02509, 0.02601, 0.81036, 0.81913, 0.52284, 0.51505, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "Sweden", "2023-09-01", "Adult", "Adult", "Muscle", "Muscular System"], [25365, "SRR25868067", "SRX21589468", "SRS18767041", "SRP457980", "PRJNA1011841", "fhl2b expression ameliorates muscular dystrophy [5 month EOM and trunk]", "GSE242136", "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 innate resistance of extraocular muscle to muscular dystrophies we knocked down desmin and sequenced extraocular muscle as well as trunk muscle from zebrafish at two time points. We then performed gene expression analysis between WT and desmin knock down tissues of the same type at the same time points.", "parent bioproject:PRJNA1011837", "pubmed:38431640", null, "des EOM group 1", "GSM7749561", null, "source name:extraocular muscle|tissue:extraocular muscle|age:5 mpf|strain:AB|cell type:extraocular myofibers|genotype:desma / ;desmb / |geo loc name:missing|collection date:missing", "des EOM group 1", "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", "extraocular muscle", 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:extraocular muscle|age:5 mpf|strain:AB|cell type:extraocular myofibers|genotype:desma / ;desmb / ", "GSM7749561", "GSM7749561: des EOM group 1; Danio rerio; RNA Seq", "GSM7749561 r1", "GSM7749561", "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, "SRP457980", null, "loader:fastq load.py", "P17251_104_S8_L001_R1_001.fastq.gz P17251_104_S8_L001_R2_001.fastq.gz", "fastq fastq", 29806211630.0, 98696065.0, "GSM7749561 r1", "0:151 1:151", "A:8054341813;C:6852446548;G:7265656917;T:7633398634;N:367718", 151, 151, null, null, 8054341813, 6852446548, 7265656917, 7633398634, 367718, "SRX21589468", "SRS18767041", "SRA1703878", "Ume\u00e5 Univeristy", "Ume\u00e5 Univeristy", 2, 0.96453, 0.95482, 0.03012, 0.03029, 0.81387, 0.8172, 0.58568, 0.59213, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "Sweden", "2023-09-01", "Adult", "Adult", "Muscle", "Muscular System"], [25366, "SRR25868068", "SRX21589467", "SRS18767040", "SRP457980", "PRJNA1011841", "fhl2b expression ameliorates muscular dystrophy [5 month EOM and trunk]", "GSE242136", "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 innate resistance of extraocular muscle to muscular dystrophies we knocked down desmin and sequenced extraocular muscle as well as trunk muscle from zebrafish at two time points. We then performed gene expression analysis between WT and desmin knock down tissues of the same type at the same time points.", "parent bioproject:PRJNA1011837", "pubmed:38431640", null, "wt EOM group 3", "GSM7749560", null, "source name:extraocular muscle|tissue:extraocular muscle|age:5 mpf|strain:AB|cell type:extraocular myofibers|genotype:WT|geo loc name:missing|collection date:missing", "wt EOM group 3", "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", "extraocular muscle", 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:extraocular muscle|age:5 mpf|strain:AB|cell type:extraocular myofibers|genotype:WT", "GSM7749560", "GSM7749560: wt EOM group 3; Danio rerio; RNA Seq", "GSM7749560 r1", "GSM7749560", "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, "SRP457980", null, "loader:fastq load.py", "P17251_103_S7_L001_R1_001.fastq.gz P17251_103_S7_L001_R2_001.fastq.gz", "fastq fastq", 26137673878.0, 86548589.0, "GSM7749560 r1", "0:151 1:151", "A:7187162255;C:5876920613;G:6131493954;T:6941780771;N:316285", 151, 151, null, null, 7187162255, 5876920613, 6131493954, 6941780771, 316285, "SRX21589467", "SRS18767040", "SRA1703878", "Ume\u00e5 Univeristy", "Ume\u00e5 Univeristy", 2, 0.95152, 0.94053, 0.05757, 0.05838, 0.76039, 0.76617, 0.53014, 0.53234, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "Sweden", "2023-09-01", "Adult", "Adult", "Muscle", "Muscular System"], [25367, "SRR25868069", "SRX21589466", "SRS18767039", "SRP457980", "PRJNA1011841", "fhl2b expression ameliorates muscular dystrophy [5 month EOM and trunk]", "GSE242136", "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 innate resistance of extraocular muscle to muscular dystrophies we knocked down desmin and sequenced extraocular muscle as well as trunk muscle from zebrafish at two time points. We then performed gene expression analysis between WT and desmin knock down tissues of the same type at the same time points.", "parent bioproject:PRJNA1011837", "pubmed:38431640", null, "wt EOM group 2", "GSM7749559", null, "source name:extraocular muscle|tissue:extraocular muscle|age:5 mpf|strain:AB|cell type:extraocular myofibers|genotype:WT|geo loc name:missing|collection date:missing", "wt EOM group 2", "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", "extraocular muscle", 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:extraocular muscle|age:5 mpf|strain:AB|cell type:extraocular myofibers|genotype:WT", "GSM7749559", "GSM7749559: wt EOM group 2; Danio rerio; RNA Seq", "GSM7749559 r1", "GSM7749559", "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, "SRP457980", null, "loader:fastq load.py", "P17251_102_S6_L001_R1_001.fastq.gz P17251_102_S6_L001_R2_001.fastq.gz", "fastq fastq", 34491293764.0, 114209582.0, "GSM7749559 r1", "0:151 1:151", "A:8992817747;C:8219342517;G:8708492755;T:8570219055;N:421690", 151, 151, null, null, 8992817747, 8219342517, 8708492755, 8570219055, 421690, "SRX21589466", "SRS18767039", "SRA1703878", "Ume\u00e5 Univeristy", "Ume\u00e5 Univeristy", 2, 0.9625, 0.95296, 0.02853, 0.02942, 0.78871, 0.79198, 0.52313, 0.52622, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "Sweden", "2023-09-01", "Adult", "Adult", "Muscle", "Muscular System"], [25368, "SRR25868070", "SRX21589465", "SRS18767038", "SRP457980", "PRJNA1011841", "fhl2b expression ameliorates muscular dystrophy [5 month EOM and trunk]", "GSE242136", "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 innate resistance of extraocular muscle to muscular dystrophies we knocked down desmin and sequenced extraocular muscle as well as trunk muscle from zebrafish at two time points. We then performed gene expression analysis between WT and desmin knock down tissues of the same type at the same time points.", "parent bioproject:PRJNA1011837", "pubmed:38431640", null, "wt EOM group 1", "GSM7749558", null, "source name:extraocular muscle|tissue:extraocular muscle|age:5 mpf|strain:AB|cell type:extraocular myofibers|genotype:WT|geo loc name:missing|collection date:missing", "wt EOM group 1", "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", "extraocular muscle", 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:extraocular muscle|age:5 mpf|strain:AB|cell type:extraocular myofibers|genotype:WT", "GSM7749558", "GSM7749558: wt EOM group 1; Danio rerio; RNA Seq", "GSM7749558 r1", "GSM7749558", "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, "SRP457980", null, "loader:fastq load.py", "P17251_101_S5_L001_R1_001.fastq.gz P17251_101_S5_L001_R2_001.fastq.gz", "fastq fastq", 30105044858.0, 99685579.0, "GSM7749558 r1", "0:151 1:151", "A:7737199705;C:7317149958;G:7543227439;T:7507099789;N:367967", 151, 151, null, null, 7737199705, 7317149958, 7543227439, 7507099789, 367967, "SRX21589465", "SRS18767038", "SRA1703878", "Ume\u00e5 Univeristy", "Ume\u00e5 Univeristy", 2, 0.96635, 0.95927, 0.02631, 0.02749, 0.80659, 0.81203, 0.5009, 0.49931, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "Sweden", "2023-09-01", "Adult", "Adult", "Muscle", "Muscular System"], [26511, "SRR26050756", "SRX21767126", "SRS18873431", "SRP460207", "PRJNA1016321", "The proteasome subunit psmb1 is essential for craniofacial cartilage maturation and morphogenesis", "GSE243072", "Transcriptome Analysis", "Craniofacial dysmorphisms are among the most common birth defects. Proteasome mutations frequently result in craniofacial dysmorphisms including lower jaw malformations; however the underlying mechanisms are unknown. Here we use a zebrafish proteasome subunit beta 1 psmb1 mutant to define the cellular mechanisms underlying proteasome mutation induced craniofacial dysmorphisms. psmb1 mutants exhibit a flattened ceratohyal and smaller Meckel's and palatoquadrate cartilages. Ceratohyal flattening is a result of failed chondrocyte convergent extension accompanied by reduced numbers of chondrocytes in the lower jaw due to defects in chondrocyte differentiation. Morphogenesis of craniofacial muscles and tendons is similarly perturbed. psmb1 mutants lack the hyohyal muscles and craniofacial tendons are shortened and disorganized. We additionally identify a critical period for proteasome function in craniofacial development specifically during chondrocyte and muscle differentiation. psmb1 overexpression in sox10+ cells of mutant embryos rescued both cartilage and tendon phenotypes but induced only a partial rescue of the muscle phenotype indicating that psmb1 is required in both tissue autonomous and non autonomous fashions during craniofacial development. Overall our work demonstrates that psmb1 is required for craniofacial cartilage tendon and muscle differentiation and morphogenesis. Overall design: To investigate the role of psmb1 in craniofacial chondrocyte and muscle development we sorted sox10+ cells or mylz2+ cells from the heads of psmb1 mutant zebrafish vs. pooled wild type and heterozygous larvae at 72hpf. We then performed bulk RNA sequencing and differential gene expression analysis.", null, "pubmed:39171526", null, "psmb1 mutants 72hpf biological replicate 4 cranial mylz2+ cells", "GSM7778667", null, "source name:cranial mylz2+ cells muscle|tissue:cranial mylz2+ cells muscle|genotype:psmb1 / |geo loc name:missing|collection date:missing", "psmb1 mutants 72hpf biological replicate 4 cranial mylz2+ cells", "Reads were aligned to the GRCz11 reference assembly using STAR Dobin et al. 2013 and differential gene expression analysis was performed with DESeq2 Love et al. 2014. Assembly: GRCz11 Supplementary files format and content: text file with raw counts for each sample for sox10 samples Supplementary files format and content: text file with raw counts for each sample for mylz2 samples", "cranial mylz2+ cells muscle", null, "20 25 heads per sample were dissected from 72hpf larvae. Dissociation was carried out using 25ug/ml liberase Sigma Aldrich 05401119001 and samples were incubated on a 600rpm shaker at 37C for 30 minutes. To encourage dissociation samples were pipetted 20 25 times every 8 10 minutes. Samples were then passed through a 40 \u03bcm filter. Cells were sorted into Buffer RLT with 1% \u03b2 mercaptoethanol and RNA was isolated using the Qiagen RNeasy MicroKit Qiagen 74004. For RNA seq on sox10:kaede+ cells 7000 cells were sorted per sample. For RNA seq on mylz2+ cells 1500 cells were sorted per sample. The SMART Seq HT kit was used for full length cDNA synthesis and amplification Takara San Jose CA USA and the Illumina Nextera XT kit Illumina San Diego CA USA was used for sequencing library preparation.", "Embryos were raised in E3 at 28.5C until 72hpf.", "tissue:cranial mylz2+ cells muscle|genotype:psmb1 / ", "GSM7778667", "GSM7778667: psmb1 mutants 72hpf biological replicate 4 cranial mylz2+ cells; Danio rerio; RNA Seq", "GSM7778667 r1", "GSM7778667", "1", "20 25 heads per sample were dissected from 72hpf larvae. Dissociation was carried out using 25ug/ml liberase Sigma Aldrich 05401119001 and samples were incubated on a 600rpm shaker at 37C for 30 minutes. To encourage dissociation samples were pipetted 20 25 times every 8 10 minutes. Samples were then passed through a 40 \u03bcm filter. Cells were sorted into Buffer RLT with 1% \u03b2 mercaptoethanol and RNA was isolated using the Qiagen RNeasy MicroKit Qiagen 74004. For RNA seq on sox10:kaede+ cells 7000 cells were sorted per sample. For RNA seq on mylz2+ cells 1500 cells were sorted per sample. The SMART Seq HT kit was used for full length cDNA synthesis and amplification Takara San Jose CA USA and the Illumina Nextera XT kit Illumina San Diego CA USA was used for sequencing library preparation.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP460207", null, "loader:fastq load.py", "mylz2_M4_R2_001.fastq.gz mylz2_M4_R1_001.fastq.gz", "fastq fastq", 16253832000.0, 54179440.0, "GSM7778667 r1", "0:150 1:150", "A:4172321085;C:3956578712;G:3980023180;T:4144541347;N:367676", 150, 150, null, null, 4172321085, 3956578712, 3980023180, 4144541347, 367676, "SRX21767126", "SRS18873431", "SRA1711572", "BWH", "BWH", 2, 0.95935, 0.95662, 0.03769, 0.03765, 0.76556, 0.76741, 0.42151, 0.41972, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "cdna_unspecified", "nextera", "bulk", "bulk", "bulk", null, "United States", "2023-09-13", "Larval", "Larval", "Muscle", "Muscular System"], [26512, "SRR26050757", "SRX21767125", "SRS18873430", "SRP460207", "PRJNA1016321", "The proteasome subunit psmb1 is essential for craniofacial cartilage maturation and morphogenesis", "GSE243072", "Transcriptome Analysis", "Craniofacial dysmorphisms are among the most common birth defects. Proteasome mutations frequently result in craniofacial dysmorphisms including lower jaw malformations; however the underlying mechanisms are unknown. Here we use a zebrafish proteasome subunit beta 1 psmb1 mutant to define the cellular mechanisms underlying proteasome mutation induced craniofacial dysmorphisms. psmb1 mutants exhibit a flattened ceratohyal and smaller Meckel's and palatoquadrate cartilages. Ceratohyal flattening is a result of failed chondrocyte convergent extension accompanied by reduced numbers of chondrocytes in the lower jaw due to defects in chondrocyte differentiation. Morphogenesis of craniofacial muscles and tendons is similarly perturbed. psmb1 mutants lack the hyohyal muscles and craniofacial tendons are shortened and disorganized. We additionally identify a critical period for proteasome function in craniofacial development specifically during chondrocyte and muscle differentiation. psmb1 overexpression in sox10+ cells of mutant embryos rescued both cartilage and tendon phenotypes but induced only a partial rescue of the muscle phenotype indicating that psmb1 is required in both tissue autonomous and non autonomous fashions during craniofacial development. Overall our work demonstrates that psmb1 is required for craniofacial cartilage tendon and muscle differentiation and morphogenesis. Overall design: To investigate the role of psmb1 in craniofacial chondrocyte and muscle development we sorted sox10+ cells or mylz2+ cells from the heads of psmb1 mutant zebrafish vs. pooled wild type and heterozygous larvae at 72hpf. We then performed bulk RNA sequencing and differential gene expression analysis.", null, "pubmed:39171526", null, "psmb1 mutants 72hpf biological replicate 3 cranial mylz2+ cells", "GSM7778666", null, "source name:cranial mylz2+ cells muscle|tissue:cranial mylz2+ cells muscle|genotype:psmb1 / |geo loc name:missing|collection date:missing", "psmb1 mutants 72hpf biological replicate 3 cranial mylz2+ cells", "Reads were aligned to the GRCz11 reference assembly using STAR Dobin et al. 2013 and differential gene expression analysis was performed with DESeq2 Love et al. 2014. Assembly: GRCz11 Supplementary files format and content: text file with raw counts for each sample for sox10 samples Supplementary files format and content: text file with raw counts for each sample for mylz2 samples", "cranial mylz2+ cells muscle", null, "20 25 heads per sample were dissected from 72hpf larvae. Dissociation was carried out using 25ug/ml liberase Sigma Aldrich 05401119001 and samples were incubated on a 600rpm shaker at 37C for 30 minutes. To encourage dissociation samples were pipetted 20 25 times every 8 10 minutes. Samples were then passed through a 40 \u03bcm filter. Cells were sorted into Buffer RLT with 1% \u03b2 mercaptoethanol and RNA was isolated using the Qiagen RNeasy MicroKit Qiagen 74004. For RNA seq on sox10:kaede+ cells 7000 cells were sorted per sample. For RNA seq on mylz2+ cells 1500 cells were sorted per sample. The SMART Seq HT kit was used for full length cDNA synthesis and amplification Takara San Jose CA USA and the Illumina Nextera XT kit Illumina San Diego CA USA was used for sequencing library preparation.", "Embryos were raised in E3 at 28.5C until 72hpf.", "tissue:cranial mylz2+ cells muscle|genotype:psmb1 / ", "GSM7778666", "GSM7778666: psmb1 mutants 72hpf biological replicate 3 cranial mylz2+ cells; Danio rerio; RNA Seq", "GSM7778666 r1", "GSM7778666", "1", "20 25 heads per sample were dissected from 72hpf larvae. Dissociation was carried out using 25ug/ml liberase Sigma Aldrich 05401119001 and samples were incubated on a 600rpm shaker at 37C for 30 minutes. To encourage dissociation samples were pipetted 20 25 times every 8 10 minutes. Samples were then passed through a 40 \u03bcm filter. Cells were sorted into Buffer RLT with 1% \u03b2 mercaptoethanol and RNA was isolated using the Qiagen RNeasy MicroKit Qiagen 74004. For RNA seq on sox10:kaede+ cells 7000 cells were sorted per sample. For RNA seq on mylz2+ cells 1500 cells were sorted per sample. The SMART Seq HT kit was used for full length cDNA synthesis and amplification Takara San Jose CA USA and the Illumina Nextera XT kit Illumina San Diego CA USA was used for sequencing library preparation.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP460207", null, "loader:fastq load.py", "mylz2_M2_R1_001.fastq.gz mylz2_M2_R2_001.fastq.gz", "fastq fastq", 20441581200.0, 68138604.0, "GSM7778666 r1", "0:150 1:150", "A:5286416350;C:4932599128;G:4952935975;T:5269152687;N:477060", 150, 150, null, null, 5286416350, 4932599128, 4952935975, 5269152687, 477060, "SRX21767125", "SRS18873430", "SRA1711572", "BWH", "BWH", 2, 0.95599, 0.95338, 0.04497, 0.04514, 0.74811, 0.74974, 0.43348, 0.43839, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "cdna_unspecified", "nextera", "bulk", "bulk", "bulk", null, "United States", "2023-09-13", "Larval", "Larval", "Muscle", "Muscular System"], [26513, "SRR26050758", "SRX21767124", "SRS18873429", "SRP460207", "PRJNA1016321", "The proteasome subunit psmb1 is essential for craniofacial cartilage maturation and morphogenesis", "GSE243072", "Transcriptome Analysis", "Craniofacial dysmorphisms are among the most common birth defects. Proteasome mutations frequently result in craniofacial dysmorphisms including lower jaw malformations; however the underlying mechanisms are unknown. Here we use a zebrafish proteasome subunit beta 1 psmb1 mutant to define the cellular mechanisms underlying proteasome mutation induced craniofacial dysmorphisms. psmb1 mutants exhibit a flattened ceratohyal and smaller Meckel's and palatoquadrate cartilages. Ceratohyal flattening is a result of failed chondrocyte convergent extension accompanied by reduced numbers of chondrocytes in the lower jaw due to defects in chondrocyte differentiation. Morphogenesis of craniofacial muscles and tendons is similarly perturbed. psmb1 mutants lack the hyohyal muscles and craniofacial tendons are shortened and disorganized. We additionally identify a critical period for proteasome function in craniofacial development specifically during chondrocyte and muscle differentiation. psmb1 overexpression in sox10+ cells of mutant embryos rescued both cartilage and tendon phenotypes but induced only a partial rescue of the muscle phenotype indicating that psmb1 is required in both tissue autonomous and non autonomous fashions during craniofacial development. Overall our work demonstrates that psmb1 is required for craniofacial cartilage tendon and muscle differentiation and morphogenesis. Overall design: To investigate the role of psmb1 in craniofacial chondrocyte and muscle development we sorted sox10+ cells or mylz2+ cells from the heads of psmb1 mutant zebrafish vs. pooled wild type and heterozygous larvae at 72hpf. We then performed bulk RNA sequencing and differential gene expression analysis.", null, "pubmed:39171526", null, "psmb1 mutants 72hpf biological replicate 1 cranial mylz2+ cells", "GSM7778665", null, "source name:cranial mylz2+ cells muscle|tissue:cranial mylz2+ cells muscle|genotype:psmb1 / |geo loc name:missing|collection date:missing", "psmb1 mutants 72hpf biological replicate 1 cranial mylz2+ cells", "Reads were aligned to the GRCz11 reference assembly using STAR Dobin et al. 2013 and differential gene expression analysis was performed with DESeq2 Love et al. 2014. Assembly: GRCz11 Supplementary files format and content: text file with raw counts for each sample for sox10 samples Supplementary files format and content: text file with raw counts for each sample for mylz2 samples", "cranial mylz2+ cells muscle", null, "20 25 heads per sample were dissected from 72hpf larvae. Dissociation was carried out using 25ug/ml liberase Sigma Aldrich 05401119001 and samples were incubated on a 600rpm shaker at 37C for 30 minutes. To encourage dissociation samples were pipetted 20 25 times every 8 10 minutes. Samples were then passed through a 40 \u03bcm filter. Cells were sorted into Buffer RLT with 1% \u03b2 mercaptoethanol and RNA was isolated using the Qiagen RNeasy MicroKit Qiagen 74004. For RNA seq on sox10:kaede+ cells 7000 cells were sorted per sample. For RNA seq on mylz2+ cells 1500 cells were sorted per sample. The SMART Seq HT kit was used for full length cDNA synthesis and amplification Takara San Jose CA USA and the Illumina Nextera XT kit Illumina San Diego CA USA was used for sequencing library preparation.", "Embryos were raised in E3 at 28.5C until 72hpf.", "tissue:cranial mylz2+ cells muscle|genotype:psmb1 / ", "GSM7778665", "GSM7778665: psmb1 mutants 72hpf biological replicate 1 cranial mylz2+ cells; Danio rerio; RNA Seq", "GSM7778665 r1", "GSM7778665", "1", "20 25 heads per sample were dissected from 72hpf larvae. Dissociation was carried out using 25ug/ml liberase Sigma Aldrich 05401119001 and samples were incubated on a 600rpm shaker at 37C for 30 minutes. To encourage dissociation samples were pipetted 20 25 times every 8 10 minutes. Samples were then passed through a 40 \u03bcm filter. Cells were sorted into Buffer RLT with 1% \u03b2 mercaptoethanol and RNA was isolated using the Qiagen RNeasy MicroKit Qiagen 74004. For RNA seq on sox10:kaede+ cells 7000 cells were sorted per sample. For RNA seq on mylz2+ cells 1500 cells were sorted per sample. The SMART Seq HT kit was used for full length cDNA synthesis and amplification Takara San Jose CA USA and the Illumina Nextera XT kit Illumina San Diego CA USA was used for sequencing library preparation.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP460207", null, "loader:fastq load.py", "mylz2_M1_R2_001.fastq.gz mylz2_M1_R1_001.fastq.gz", "fastq fastq", 16429988100.0, 54766627.0, "GSM7778665 r1", "0:150 1:150", "A:4233929382;C:3979539796;G:4000710274;T:4215435332;N:373316", 150, 150, null, null, 4233929382, 3979539796, 4000710274, 4215435332, 373316, "SRX21767124", "SRS18873429", "SRA1711572", "BWH", "BWH", 2, 0.95781, 0.95546, 0.04249, 0.04266, 0.75359, 0.7556, 0.42698, 0.43387, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "cdna_unspecified", "nextera", "bulk", "bulk", "bulk", null, "United States", "2023-09-13", "Larval", "Larval", "Muscle", "Muscular System"], [26514, "SRR26050759", "SRX21767123", "SRS18873428", "SRP460207", "PRJNA1016321", "The proteasome subunit psmb1 is essential for craniofacial cartilage maturation and morphogenesis", "GSE243072", "Transcriptome Analysis", "Craniofacial dysmorphisms are among the most common birth defects. Proteasome mutations frequently result in craniofacial dysmorphisms including lower jaw malformations; however the underlying mechanisms are unknown. Here we use a zebrafish proteasome subunit beta 1 psmb1 mutant to define the cellular mechanisms underlying proteasome mutation induced craniofacial dysmorphisms. psmb1 mutants exhibit a flattened ceratohyal and smaller Meckel's and palatoquadrate cartilages. Ceratohyal flattening is a result of failed chondrocyte convergent extension accompanied by reduced numbers of chondrocytes in the lower jaw due to defects in chondrocyte differentiation. Morphogenesis of craniofacial muscles and tendons is similarly perturbed. psmb1 mutants lack the hyohyal muscles and craniofacial tendons are shortened and disorganized. We additionally identify a critical period for proteasome function in craniofacial development specifically during chondrocyte and muscle differentiation. psmb1 overexpression in sox10+ cells of mutant embryos rescued both cartilage and tendon phenotypes but induced only a partial rescue of the muscle phenotype indicating that psmb1 is required in both tissue autonomous and non autonomous fashions during craniofacial development. Overall our work demonstrates that psmb1 is required for craniofacial cartilage tendon and muscle differentiation and morphogenesis. Overall design: To investigate the role of psmb1 in craniofacial chondrocyte and muscle development we sorted sox10+ cells or mylz2+ cells from the heads of psmb1 mutant zebrafish vs. pooled wild type and heterozygous larvae at 72hpf. We then performed bulk RNA sequencing and differential gene expression analysis.", null, "pubmed:39171526", null, "psmb1 wild type/heterozygous 72hpf biological replicate 4 cranial mylz2+ cells", "GSM7778664", null, "source name:cranial mylz2+ cells muscle|tissue:cranial mylz2+ cells muscle|genotype:psmb1+/+;+/ |geo loc name:missing|collection date:missing", "psmb1 wild type/heterozygous 72hpf biological replicate 4 cranial mylz2+ cells", "Reads were aligned to the GRCz11 reference assembly using STAR Dobin et al. 2013 and differential gene expression analysis was performed with DESeq2 Love et al. 2014. Assembly: GRCz11 Supplementary files format and content: text file with raw counts for each sample for sox10 samples Supplementary files format and content: text file with raw counts for each sample for mylz2 samples", "cranial mylz2+ cells muscle", null, "20 25 heads per sample were dissected from 72hpf larvae. Dissociation was carried out using 25ug/ml liberase Sigma Aldrich 05401119001 and samples were incubated on a 600rpm shaker at 37C for 30 minutes. To encourage dissociation samples were pipetted 20 25 times every 8 10 minutes. Samples were then passed through a 40 \u03bcm filter. Cells were sorted into Buffer RLT with 1% \u03b2 mercaptoethanol and RNA was isolated using the Qiagen RNeasy MicroKit Qiagen 74004. For RNA seq on sox10:kaede+ cells 7000 cells were sorted per sample. For RNA seq on mylz2+ cells 1500 cells were sorted per sample. The SMART Seq HT kit was used for full length cDNA synthesis and amplification Takara San Jose CA USA and the Illumina Nextera XT kit Illumina San Diego CA USA was used for sequencing library preparation.", "Embryos were raised in E3 at 28.5C until 72hpf.", "tissue:cranial mylz2+ cells muscle|genotype:psmb1+/+;+/ ", "GSM7778664", "GSM7778664: psmb1 wild type/heterozygous 72hpf biological replicate 4 cranial mylz2+ cells; Danio rerio; RNA Seq", "GSM7778664 r1", "GSM7778664", "1", "20 25 heads per sample were dissected from 72hpf larvae. Dissociation was carried out using 25ug/ml liberase Sigma Aldrich 05401119001 and samples were incubated on a 600rpm shaker at 37C for 30 minutes. To encourage dissociation samples were pipetted 20 25 times every 8 10 minutes. Samples were then passed through a 40 \u03bcm filter. Cells were sorted into Buffer RLT with 1% \u03b2 mercaptoethanol and RNA was isolated using the Qiagen RNeasy MicroKit Qiagen 74004. For RNA seq on sox10:kaede+ cells 7000 cells were sorted per sample. For RNA seq on mylz2+ cells 1500 cells were sorted per sample. The SMART Seq HT kit was used for full length cDNA synthesis and amplification Takara San Jose CA USA and the Illumina Nextera XT kit Illumina San Diego CA USA was used for sequencing library preparation.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP460207", null, "loader:fastq load.py", "mylz2_WH4_R1_001.fastq.gz mylz2_WH4_R2_001.fastq.gz", "fastq fastq", 14554941600.0, 48516472.0, "GSM7778664 r1", "0:150 1:150", "A:3762464429;C:3514503319;G:3535806865;T:3741838861;N:328126", 150, 150, null, null, 3762464429, 3514503319, 3535806865, 3741838861, 328126, "SRX21767123", "SRS18873428", "SRA1711572", "BWH", "BWH", 2, 0.96121, 0.95881, 0.04249, 0.04242, 0.77745, 0.77999, 0.43011, 0.42743, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "cdna_unspecified", "nextera", "bulk", "bulk", "bulk", null, "United States", "2023-09-13", "Larval", "Larval", "Muscle", "Muscular System"], [26515, "SRR26050760", "SRX21767122", "SRS18873427", "SRP460207", "PRJNA1016321", "The proteasome subunit psmb1 is essential for craniofacial cartilage maturation and morphogenesis", "GSE243072", "Transcriptome Analysis", "Craniofacial dysmorphisms are among the most common birth defects. Proteasome mutations frequently result in craniofacial dysmorphisms including lower jaw malformations; however the underlying mechanisms are unknown. Here we use a zebrafish proteasome subunit beta 1 psmb1 mutant to define the cellular mechanisms underlying proteasome mutation induced craniofacial dysmorphisms. psmb1 mutants exhibit a flattened ceratohyal and smaller Meckel's and palatoquadrate cartilages. Ceratohyal flattening is a result of failed chondrocyte convergent extension accompanied by reduced numbers of chondrocytes in the lower jaw due to defects in chondrocyte differentiation. Morphogenesis of craniofacial muscles and tendons is similarly perturbed. psmb1 mutants lack the hyohyal muscles and craniofacial tendons are shortened and disorganized. We additionally identify a critical period for proteasome function in craniofacial development specifically during chondrocyte and muscle differentiation. psmb1 overexpression in sox10+ cells of mutant embryos rescued both cartilage and tendon phenotypes but induced only a partial rescue of the muscle phenotype indicating that psmb1 is required in both tissue autonomous and non autonomous fashions during craniofacial development. Overall our work demonstrates that psmb1 is required for craniofacial cartilage tendon and muscle differentiation and morphogenesis. Overall design: To investigate the role of psmb1 in craniofacial chondrocyte and muscle development we sorted sox10+ cells or mylz2+ cells from the heads of psmb1 mutant zebrafish vs. pooled wild type and heterozygous larvae at 72hpf. We then performed bulk RNA sequencing and differential gene expression analysis.", null, "pubmed:39171526", null, "psmb1 wild type/heterozygous 72hpf biological replicate 3 cranial mylz2+ cells", "GSM7778663", null, "source name:cranial mylz2+ cells muscle|tissue:cranial mylz2+ cells muscle|genotype:psmb1+/+;+/ |geo loc name:missing|collection date:missing", "psmb1 wild type/heterozygous 72hpf biological replicate 3 cranial mylz2+ cells", "Reads were aligned to the GRCz11 reference assembly using STAR Dobin et al. 2013 and differential gene expression analysis was performed with DESeq2 Love et al. 2014. Assembly: GRCz11 Supplementary files format and content: text file with raw counts for each sample for sox10 samples Supplementary files format and content: text file with raw counts for each sample for mylz2 samples", "cranial mylz2+ cells muscle", null, "20 25 heads per sample were dissected from 72hpf larvae. Dissociation was carried out using 25ug/ml liberase Sigma Aldrich 05401119001 and samples were incubated on a 600rpm shaker at 37C for 30 minutes. To encourage dissociation samples were pipetted 20 25 times every 8 10 minutes. Samples were then passed through a 40 \u03bcm filter. Cells were sorted into Buffer RLT with 1% \u03b2 mercaptoethanol and RNA was isolated using the Qiagen RNeasy MicroKit Qiagen 74004. For RNA seq on sox10:kaede+ cells 7000 cells were sorted per sample. For RNA seq on mylz2+ cells 1500 cells were sorted per sample. The SMART Seq HT kit was used for full length cDNA synthesis and amplification Takara San Jose CA USA and the Illumina Nextera XT kit Illumina San Diego CA USA was used for sequencing library preparation.", "Embryos were raised in E3 at 28.5C until 72hpf.", "tissue:cranial mylz2+ cells muscle|genotype:psmb1+/+;+/ ", "GSM7778663", "GSM7778663: psmb1 wild type/heterozygous 72hpf biological replicate 3 cranial mylz2+ cells; Danio rerio; RNA Seq", "GSM7778663 r1", "GSM7778663", "1", "20 25 heads per sample were dissected from 72hpf larvae. Dissociation was carried out using 25ug/ml liberase Sigma Aldrich 05401119001 and samples were incubated on a 600rpm shaker at 37C for 30 minutes. To encourage dissociation samples were pipetted 20 25 times every 8 10 minutes. Samples were then passed through a 40 \u03bcm filter. Cells were sorted into Buffer RLT with 1% \u03b2 mercaptoethanol and RNA was isolated using the Qiagen RNeasy MicroKit Qiagen 74004. For RNA seq on sox10:kaede+ cells 7000 cells were sorted per sample. For RNA seq on mylz2+ cells 1500 cells were sorted per sample. The SMART Seq HT kit was used for full length cDNA synthesis and amplification Takara San Jose CA USA and the Illumina Nextera XT kit Illumina San Diego CA USA was used for sequencing library preparation.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP460207", null, "loader:fastq load.py", "mylz2_WH3_R1_001.fastq.gz mylz2_WH3_R2_001.fastq.gz", "fastq fastq", 14286753900.0, 47622513.0, "GSM7778663 r1", "0:150 1:150", "A:3670719741;C:3471994517;G:3491814119;T:3651899112;N:326411", 150, 150, null, null, 3670719741, 3471994517, 3491814119, 3651899112, 326411, "SRX21767122", "SRS18873427", "SRA1711572", "BWH", "BWH", 2, 0.96159, 0.96038, 0.03967, 0.04054, 0.7749, 0.77644, 0.43006, 0.42107, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "cdna_unspecified", "nextera", "bulk", "bulk", "bulk", null, "United States", "2023-09-13", "Larval", "Larval", "Muscle", "Muscular System"], [26516, "SRR26050761", "SRX21767121", "SRS18873426", "SRP460207", "PRJNA1016321", "The proteasome subunit psmb1 is essential for craniofacial cartilage maturation and morphogenesis", "GSE243072", "Transcriptome Analysis", "Craniofacial dysmorphisms are among the most common birth defects. Proteasome mutations frequently result in craniofacial dysmorphisms including lower jaw malformations; however the underlying mechanisms are unknown. Here we use a zebrafish proteasome subunit beta 1 psmb1 mutant to define the cellular mechanisms underlying proteasome mutation induced craniofacial dysmorphisms. psmb1 mutants exhibit a flattened ceratohyal and smaller Meckel's and palatoquadrate cartilages. Ceratohyal flattening is a result of failed chondrocyte convergent extension accompanied by reduced numbers of chondrocytes in the lower jaw due to defects in chondrocyte differentiation. Morphogenesis of craniofacial muscles and tendons is similarly perturbed. psmb1 mutants lack the hyohyal muscles and craniofacial tendons are shortened and disorganized. We additionally identify a critical period for proteasome function in craniofacial development specifically during chondrocyte and muscle differentiation. psmb1 overexpression in sox10+ cells of mutant embryos rescued both cartilage and tendon phenotypes but induced only a partial rescue of the muscle phenotype indicating that psmb1 is required in both tissue autonomous and non autonomous fashions during craniofacial development. Overall our work demonstrates that psmb1 is required for craniofacial cartilage tendon and muscle differentiation and morphogenesis. Overall design: To investigate the role of psmb1 in craniofacial chondrocyte and muscle development we sorted sox10+ cells or mylz2+ cells from the heads of psmb1 mutant zebrafish vs. pooled wild type and heterozygous larvae at 72hpf. We then performed bulk RNA sequencing and differential gene expression analysis.", null, "pubmed:39171526", null, "psmb1 wild type/heterozygous 72hpf biological replicate 2 cranial mylz2+ cells", "GSM7778662", null, "source name:cranial mylz2+ cells muscle|tissue:cranial mylz2+ cells muscle|genotype:psmb1+/+;+/ |geo loc name:missing|collection date:missing", "psmb1 wild type/heterozygous 72hpf biological replicate 2 cranial mylz2+ cells", "Reads were aligned to the GRCz11 reference assembly using STAR Dobin et al. 2013 and differential gene expression analysis was performed with DESeq2 Love et al. 2014. Assembly: GRCz11 Supplementary files format and content: text file with raw counts for each sample for sox10 samples Supplementary files format and content: text file with raw counts for each sample for mylz2 samples", "cranial mylz2+ cells muscle", null, "20 25 heads per sample were dissected from 72hpf larvae. Dissociation was carried out using 25ug/ml liberase Sigma Aldrich 05401119001 and samples were incubated on a 600rpm shaker at 37C for 30 minutes. To encourage dissociation samples were pipetted 20 25 times every 8 10 minutes. Samples were then passed through a 40 \u03bcm filter. Cells were sorted into Buffer RLT with 1% \u03b2 mercaptoethanol and RNA was isolated using the Qiagen RNeasy MicroKit Qiagen 74004. For RNA seq on sox10:kaede+ cells 7000 cells were sorted per sample. For RNA seq on mylz2+ cells 1500 cells were sorted per sample. The SMART Seq HT kit was used for full length cDNA synthesis and amplification Takara San Jose CA USA and the Illumina Nextera XT kit Illumina San Diego CA USA was used for sequencing library preparation.", "Embryos were raised in E3 at 28.5C until 72hpf.", "tissue:cranial mylz2+ cells muscle|genotype:psmb1+/+;+/ ", "GSM7778662", "GSM7778662: psmb1 wild type/heterozygous 72hpf biological replicate 2 cranial mylz2+ cells; Danio rerio; RNA Seq", "GSM7778662 r1", "GSM7778662", "1", "20 25 heads per sample were dissected from 72hpf larvae. Dissociation was carried out using 25ug/ml liberase Sigma Aldrich 05401119001 and samples were incubated on a 600rpm shaker at 37C for 30 minutes. To encourage dissociation samples were pipetted 20 25 times every 8 10 minutes. Samples were then passed through a 40 \u03bcm filter. Cells were sorted into Buffer RLT with 1% \u03b2 mercaptoethanol and RNA was isolated using the Qiagen RNeasy MicroKit Qiagen 74004. For RNA seq on sox10:kaede+ cells 7000 cells were sorted per sample. For RNA seq on mylz2+ cells 1500 cells were sorted per sample. The SMART Seq HT kit was used for full length cDNA synthesis and amplification Takara San Jose CA USA and the Illumina Nextera XT kit Illumina San Diego CA USA was used for sequencing library preparation.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP460207", null, "loader:fastq load.py", "mylz2_WH2_R1_001.fastq.gz mylz2_WH2_R2_001.fastq.gz", "fastq fastq", 13505114700.0, 45017049.0, "GSM7778662 r1", "0:150 1:150", "A:3494078647;C:3258926987;G:3282303631;T:3469494662;N:310773", 150, 150, null, null, 3494078647, 3258926987, 3282303631, 3469494662, 310773, "SRX21767121", "SRS18873426", "SRA1711572", "BWH", "BWH", 2, 0.95944, 0.95769, 0.04602, 0.04619, 0.78557, 0.78748, 0.43504, 0.43352, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "cdna_unspecified", "nextera", "bulk", "bulk", "bulk", null, "United States", "2023-09-13", "Larval", "Larval", "Muscle", "Muscular System"], [26517, "SRR26050762", "SRX21767120", "SRS18873425", "SRP460207", "PRJNA1016321", "The proteasome subunit psmb1 is essential for craniofacial cartilage maturation and morphogenesis", "GSE243072", "Transcriptome Analysis", "Craniofacial dysmorphisms are among the most common birth defects. Proteasome mutations frequently result in craniofacial dysmorphisms including lower jaw malformations; however the underlying mechanisms are unknown. Here we use a zebrafish proteasome subunit beta 1 psmb1 mutant to define the cellular mechanisms underlying proteasome mutation induced craniofacial dysmorphisms. psmb1 mutants exhibit a flattened ceratohyal and smaller Meckel's and palatoquadrate cartilages. Ceratohyal flattening is a result of failed chondrocyte convergent extension accompanied by reduced numbers of chondrocytes in the lower jaw due to defects in chondrocyte differentiation. Morphogenesis of craniofacial muscles and tendons is similarly perturbed. psmb1 mutants lack the hyohyal muscles and craniofacial tendons are shortened and disorganized. We additionally identify a critical period for proteasome function in craniofacial development specifically during chondrocyte and muscle differentiation. psmb1 overexpression in sox10+ cells of mutant embryos rescued both cartilage and tendon phenotypes but induced only a partial rescue of the muscle phenotype indicating that psmb1 is required in both tissue autonomous and non autonomous fashions during craniofacial development. Overall our work demonstrates that psmb1 is required for craniofacial cartilage tendon and muscle differentiation and morphogenesis. Overall design: To investigate the role of psmb1 in craniofacial chondrocyte and muscle development we sorted sox10+ cells or mylz2+ cells from the heads of psmb1 mutant zebrafish vs. pooled wild type and heterozygous larvae at 72hpf. We then performed bulk RNA sequencing and differential gene expression analysis.", null, "pubmed:39171526", null, "psmb1 wild type/heterozygous 72hpf biological replicate 1 cranial mylz2+ cells", "GSM7778661", null, "source name:cranial mylz2+ cells muscle|tissue:cranial mylz2+ cells muscle|genotype:psmb1+/+;+/ |geo loc name:missing|collection date:missing", "psmb1 wild type/heterozygous 72hpf biological replicate 1 cranial mylz2+ cells", "Reads were aligned to the GRCz11 reference assembly using STAR Dobin et al. 2013 and differential gene expression analysis was performed with DESeq2 Love et al. 2014. Assembly: GRCz11 Supplementary files format and content: text file with raw counts for each sample for sox10 samples Supplementary files format and content: text file with raw counts for each sample for mylz2 samples", "cranial mylz2+ cells muscle", null, "20 25 heads per sample were dissected from 72hpf larvae. Dissociation was carried out using 25ug/ml liberase Sigma Aldrich 05401119001 and samples were incubated on a 600rpm shaker at 37C for 30 minutes. To encourage dissociation samples were pipetted 20 25 times every 8 10 minutes. Samples were then passed through a 40 \u03bcm filter. Cells were sorted into Buffer RLT with 1% \u03b2 mercaptoethanol and RNA was isolated using the Qiagen RNeasy MicroKit Qiagen 74004. For RNA seq on sox10:kaede+ cells 7000 cells were sorted per sample. For RNA seq on mylz2+ cells 1500 cells were sorted per sample. The SMART Seq HT kit was used for full length cDNA synthesis and amplification Takara San Jose CA USA and the Illumina Nextera XT kit Illumina San Diego CA USA was used for sequencing library preparation.", "Embryos were raised in E3 at 28.5C until 72hpf.", "tissue:cranial mylz2+ cells muscle|genotype:psmb1+/+;+/ ", "GSM7778661", "GSM7778661: psmb1 wild type/heterozygous 72hpf biological replicate 1 cranial mylz2+ cells; Danio rerio; RNA Seq", "GSM7778661 r1", "GSM7778661", "1", "20 25 heads per sample were dissected from 72hpf larvae. Dissociation was carried out using 25ug/ml liberase Sigma Aldrich 05401119001 and samples were incubated on a 600rpm shaker at 37C for 30 minutes. To encourage dissociation samples were pipetted 20 25 times every 8 10 minutes. Samples were then passed through a 40 \u03bcm filter. Cells were sorted into Buffer RLT with 1% \u03b2 mercaptoethanol and RNA was isolated using the Qiagen RNeasy MicroKit Qiagen 74004. For RNA seq on sox10:kaede+ cells 7000 cells were sorted per sample. For RNA seq on mylz2+ cells 1500 cells were sorted per sample. The SMART Seq HT kit was used for full length cDNA synthesis and amplification Takara San Jose CA USA and the Illumina Nextera XT kit Illumina San Diego CA USA was used for sequencing library preparation.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP460207", null, "loader:fastq load.py", "mylz2_WH1_R1_001.fastq.gz mylz2_WH1_R2_001.fastq.gz", "fastq fastq", 14988184200.0, 49960614.0, "GSM7778661 r1", "0:150 1:150", "A:3819900785;C:3673988527;G:3696333011;T:3797617860;N:344017", 150, 150, null, null, 3819900785, 3673988527, 3696333011, 3797617860, 344017, "SRX21767120", "SRS18873425", "SRA1711572", "BWH", "BWH", 2, 0.96471, 0.96183, 0.03703, 0.03679, 0.77167, 0.7749, 0.43436, 0.43348, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "cdna_unspecified", "nextera", "bulk", "bulk", "bulk", null, "United States", "2023-09-13", "Larval", "Larval", "Muscle", "Muscular System"], [47641, "SRR6798780", "SRX3757617", "SRS3013125", "SRP133827", "PRJNA436713", "Inhibition of embryonic HSP 90 function causes variation of cold tolerance in zebrafish", "GSE111359", "Transcriptome Analysis", "Accumulating evidence suggests that HSP90 plays roles in modulation of phenotype in vertebrate development which is closely involved in adaptation and evolution. In this study we showed that inhibition of embryonic HSP90 function either by a chemical inhibitor radicicol or low conductivity stress induced variation of cold tolerance in adult zebrafish. Overall design: Three zebrafish showing significantly increased survival times in cold from radicicol group and three zebrafish from control group were selected for RNA Seq. Muscle tissue was separated from above mentioned fishes and used as materials for RNA Seq.", null, "pubmed:33343615", null, "RLT rep3", "GSM3029086", null, "source name:muscle tissues|tissue:muscle|treatment:radicicol", "RLT rep3", "Illumina Casava1.8 software used for basecalling. The raw reads were trimmed and filtered using Seqtk https://github.com/lh3/seqtk. Low quality Q < 20 bases were trimmed from 3\u2019 ends of the reads and the trimmed reads were filtered with read length \u2265 25 bp. Clean RNA Seq reads for each sample were aligned by HISAT2 2.0.4 with default setting to the zebrafish genome assembly using the Ensembl annotation DanRer10 Danio rerio.GRCz10.84.gtf 1. The number of reads mapped to the genes was counted by StringTie and normalized by TMM trimmed mean of M values method2. We next calculated fragments per kilobase per million mapped reads FPKM of each gene to indicate gene expression level. Genome build: GRCz10 Supplementary files format and content: tab delimited text files include FPKM values for each gene", "muscle tissues", "Treatment with radicicol was initiated at 50% epiboly and continued to 48 hpf followed by the removal of the drug using three rinses the whole process was carried in the dark because the light sensitivity of radicicol. Control group were treated with identical doses of DMSO.", "Total RNA was extracted using TRIZOL Reagent 15596 018 Life technologies following the manufacturer\u2019s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 Agilent technologies Santa Clara CA US. Qualified total RNA was further purified by RNAClean XP Kit A63987 Beckman Coulterand RNase Free DNase Set 79254 QIAGEN. Libraries were constructed using VAHTS Total RNA Seq\uff08H/M/R Library PrepKit for Illumina NR603 02 Vazyme. Libraries were pooled and sequenced using the Illumina\u00a0HiSeq\u00a0X\u00a0Ten machine as 150 bp paired end sequencing reads.", "Breeding fish were maintained at 28\u00b0C in a circulating water system on a 14 h light/10 h dark cycle. Embryos were collected by natural spawning and staged.", "tissue:muscle|treatment:radicicol", "GSM3029086", "GSM3029086: RLT rep3; Danio rerio; RNA Seq", "GSM3029086", null, "1", "Total RNA was extracted using TRIZOL Reagent 15596 018 Life technologies following the manufacturer's instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 Agilent technologies Santa Clara CA US. Qualified total RNA was further purified by RNAClean XP Kit A63987 Beckman Coulterand RNase Free DNase Set 79254 QIAGEN. Libraries were constructed using VAHTS Total RNA Seq\uff08H/M/R Library PrepKit for Illumina NR603 02 Vazyme. Libraries were pooled and sequenced using the Illumina\u00a0HiSeq\u00a0X\u00a0Ten machine as 150 bp paired end sequencing reads.", "GEO Accession:GSM3029086", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP133827", null, null, "WT3_1.fq.gz WT3_2.fq.gz", "fastq fastq", 8153906700.0, 27179689.0, "GSM3029086 r1", "0:150 1:150", "A:1876474081;C:2211352217;G:2118339495;T:1947510591;N:230316", 150, 150, null, null, 1876474081, 2211352217, 2118339495, 1947510591, 230316, "SRX3757617", "SRS3013125", "SRA663830", "GEO", "School of basic medicine science, Zhejiang University", 2, 0.93476, 0.93504, 0.13893, 0.13499, 0.82913, 0.83487, 0.53361, 0.54372, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "China", "2018-03-02", "Multi-stage", "Embryo", "Muscle", "Muscular System"], [47642, "SRR6798779", "SRX3757616", "SRS3013124", "SRP133827", "PRJNA436713", "Inhibition of embryonic HSP 90 function causes variation of cold tolerance in zebrafish", "GSE111359", "Transcriptome Analysis", "Accumulating evidence suggests that HSP90 plays roles in modulation of phenotype in vertebrate development which is closely involved in adaptation and evolution. In this study we showed that inhibition of embryonic HSP90 function either by a chemical inhibitor radicicol or low conductivity stress induced variation of cold tolerance in adult zebrafish. Overall design: Three zebrafish showing significantly increased survival times in cold from radicicol group and three zebrafish from control group were selected for RNA Seq. Muscle tissue was separated from above mentioned fishes and used as materials for RNA Seq.", null, "pubmed:33343615", null, "RLT rep2", "GSM3029085", null, "source name:muscle tissues|tissue:muscle|treatment:radicicol", "RLT rep2", "Illumina Casava1.8 software used for basecalling. The raw reads were trimmed and filtered using Seqtk https://github.com/lh3/seqtk. Low quality Q < 20 bases were trimmed from 3\u2019 ends of the reads and the trimmed reads were filtered with read length \u2265 25 bp. Clean RNA Seq reads for each sample were aligned by HISAT2 2.0.4 with default setting to the zebrafish genome assembly using the Ensembl annotation DanRer10 Danio rerio.GRCz10.84.gtf 1. The number of reads mapped to the genes was counted by StringTie and normalized by TMM trimmed mean of M values method2. We next calculated fragments per kilobase per million mapped reads FPKM of each gene to indicate gene expression level. Genome build: GRCz10 Supplementary files format and content: tab delimited text files include FPKM values for each gene", "muscle tissues", "Treatment with radicicol was initiated at 50% epiboly and continued to 48 hpf followed by the removal of the drug using three rinses the whole process was carried in the dark because the light sensitivity of radicicol. Control group were treated with identical doses of DMSO.", "Total RNA was extracted using TRIZOL Reagent 15596 018 Life technologies following the manufacturer\u2019s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 Agilent technologies Santa Clara CA US. Qualified total RNA was further purified by RNAClean XP Kit A63987 Beckman Coulterand RNase Free DNase Set 79254 QIAGEN. Libraries were constructed using VAHTS Total RNA Seq\uff08H/M/R Library PrepKit for Illumina NR603 02 Vazyme. Libraries were pooled and sequenced using the Illumina\u00a0HiSeq\u00a0X\u00a0Ten machine as 150 bp paired end sequencing reads.", "Breeding fish were maintained at 28\u00b0C in a circulating water system on a 14 h light/10 h dark cycle. Embryos were collected by natural spawning and staged.", "tissue:muscle|treatment:radicicol", "GSM3029085", "GSM3029085: RLT rep2; Danio rerio; RNA Seq", "GSM3029085", null, "1", "Total RNA was extracted using TRIZOL Reagent 15596 018 Life technologies following the manufacturer's instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 Agilent technologies Santa Clara CA US. Qualified total RNA was further purified by RNAClean XP Kit A63987 Beckman Coulterand RNase Free DNase Set 79254 QIAGEN. Libraries were constructed using VAHTS Total RNA Seq\uff08H/M/R Library PrepKit for Illumina NR603 02 Vazyme. Libraries were pooled and sequenced using the Illumina\u00a0HiSeq\u00a0X\u00a0Ten machine as 150 bp paired end sequencing reads.", "GEO Accession:GSM3029085", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP133827", null, null, "WT2_1.fq.gz WT2_2.fq.gz", "fastq fastq", 7278822000.0, 24262740.0, "GSM3029085 r1", "0:150 1:150", "A:1623249687;C:2023479004;G:1940623122;T:1691262512;N:207675", 150, 150, null, null, 1623249687, 2023479004, 1940623122, 1691262512, 207675, "SRX3757616", "SRS3013124", "SRA663830", "GEO", "School of basic medicine science, Zhejiang University", 2, 0.94445, 0.94327, 0.112, 0.10647, 0.83591, 0.84226, 0.5112, 0.52155, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "China", "2018-03-02", "Multi-stage", "Embryo", "Muscle", "Muscular System"], [47643, "SRR6798778", "SRX3757615", "SRS3013123", "SRP133827", "PRJNA436713", "Inhibition of embryonic HSP 90 function causes variation of cold tolerance in zebrafish", "GSE111359", "Transcriptome Analysis", "Accumulating evidence suggests that HSP90 plays roles in modulation of phenotype in vertebrate development which is closely involved in adaptation and evolution. In this study we showed that inhibition of embryonic HSP90 function either by a chemical inhibitor radicicol or low conductivity stress induced variation of cold tolerance in adult zebrafish. Overall design: Three zebrafish showing significantly increased survival times in cold from radicicol group and three zebrafish from control group were selected for RNA Seq. Muscle tissue was separated from above mentioned fishes and used as materials for RNA Seq.", null, "pubmed:33343615", null, "RLT rep1", "GSM3029084", null, "source name:muscle tissues|tissue:muscle|treatment:radicicol", "RLT rep1", "Illumina Casava1.8 software used for basecalling. The raw reads were trimmed and filtered using Seqtk https://github.com/lh3/seqtk. Low quality Q < 20 bases were trimmed from 3\u2019 ends of the reads and the trimmed reads were filtered with read length \u2265 25 bp. Clean RNA Seq reads for each sample were aligned by HISAT2 2.0.4 with default setting to the zebrafish genome assembly using the Ensembl annotation DanRer10 Danio rerio.GRCz10.84.gtf 1. The number of reads mapped to the genes was counted by StringTie and normalized by TMM trimmed mean of M values method2. We next calculated fragments per kilobase per million mapped reads FPKM of each gene to indicate gene expression level. Genome build: GRCz10 Supplementary files format and content: tab delimited text files include FPKM values for each gene", "muscle tissues", "Treatment with radicicol was initiated at 50% epiboly and continued to 48 hpf followed by the removal of the drug using three rinses the whole process was carried in the dark because the light sensitivity of radicicol. Control group were treated with identical doses of DMSO.", "Total RNA was extracted using TRIZOL Reagent 15596 018 Life technologies following the manufacturer\u2019s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 Agilent technologies Santa Clara CA US. Qualified total RNA was further purified by RNAClean XP Kit A63987 Beckman Coulterand RNase Free DNase Set 79254 QIAGEN. Libraries were constructed using VAHTS Total RNA Seq\uff08H/M/R Library PrepKit for Illumina NR603 02 Vazyme. Libraries were pooled and sequenced using the Illumina\u00a0HiSeq\u00a0X\u00a0Ten machine as 150 bp paired end sequencing reads.", "Breeding fish were maintained at 28\u00b0C in a circulating water system on a 14 h light/10 h dark cycle. Embryos were collected by natural spawning and staged.", "tissue:muscle|treatment:radicicol", "GSM3029084", "GSM3029084: RLT rep1; Danio rerio; RNA Seq", "GSM3029084", null, "1", "Total RNA was extracted using TRIZOL Reagent 15596 018 Life technologies following the manufacturer's instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 Agilent technologies Santa Clara CA US. Qualified total RNA was further purified by RNAClean XP Kit A63987 Beckman Coulterand RNase Free DNase Set 79254 QIAGEN. Libraries were constructed using VAHTS Total RNA Seq\uff08H/M/R Library PrepKit for Illumina NR603 02 Vazyme. Libraries were pooled and sequenced using the Illumina\u00a0HiSeq\u00a0X\u00a0Ten machine as 150 bp paired end sequencing reads.", "GEO Accession:GSM3029084", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP133827", null, null, "WT1_1.fq.gz WT1_2.fq.gz", "fastq fastq", 8127579000.0, 27091930.0, "GSM3029084 r1", "0:150 1:150", "A:1936609330;C:2121138923;G:2083423270;T:1986178311;N:229166", 150, 150, null, null, 1936609330, 2121138923, 2083423270, 1986178311, 229166, "SRX3757615", "SRS3013123", "SRA663830", "GEO", "School of basic medicine science, Zhejiang University", 2, 0.66403, 0.66289, 0.14695, 0.14227, 0.82503, 0.82958, 0.54774, 0.55661, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "China", "2018-03-02", "Multi-stage", "Embryo", "Muscle", "Muscular System"], [47644, "SRR6798777", "SRX3757614", "SRS3013122", "SRP133827", "PRJNA436713", "Inhibition of embryonic HSP 90 function causes variation of cold tolerance in zebrafish", "GSE111359", "Transcriptome Analysis", "Accumulating evidence suggests that HSP90 plays roles in modulation of phenotype in vertebrate development which is closely involved in adaptation and evolution. In this study we showed that inhibition of embryonic HSP90 function either by a chemical inhibitor radicicol or low conductivity stress induced variation of cold tolerance in adult zebrafish. Overall design: Three zebrafish showing significantly increased survival times in cold from radicicol group and three zebrafish from control group were selected for RNA Seq. Muscle tissue was separated from above mentioned fishes and used as materials for RNA Seq.", null, "pubmed:33343615", null, "WT rep3", "GSM3029083", null, "source name:muscle tissues|tissue:muscle|treatment:DMSO", "WT rep3", "Illumina Casava1.8 software used for basecalling. The raw reads were trimmed and filtered using Seqtk https://github.com/lh3/seqtk. Low quality Q < 20 bases were trimmed from 3\u2019 ends of the reads and the trimmed reads were filtered with read length \u2265 25 bp. Clean RNA Seq reads for each sample were aligned by HISAT2 2.0.4 with default setting to the zebrafish genome assembly using the Ensembl annotation DanRer10 Danio rerio.GRCz10.84.gtf 1. The number of reads mapped to the genes was counted by StringTie and normalized by TMM trimmed mean of M values method2. We next calculated fragments per kilobase per million mapped reads FPKM of each gene to indicate gene expression level. Genome build: GRCz10 Supplementary files format and content: tab delimited text files include FPKM values for each gene", "muscle tissues", "Treatment with radicicol was initiated at 50% epiboly and continued to 48 hpf followed by the removal of the drug using three rinses the whole process was carried in the dark because the light sensitivity of radicicol. Control group were treated with identical doses of DMSO.", "Total RNA was extracted using TRIZOL Reagent 15596 018 Life technologies following the manufacturer\u2019s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 Agilent technologies Santa Clara CA US. Qualified total RNA was further purified by RNAClean XP Kit A63987 Beckman Coulterand RNase Free DNase Set 79254 QIAGEN. Libraries were constructed using VAHTS Total RNA Seq\uff08H/M/R Library PrepKit for Illumina NR603 02 Vazyme. Libraries were pooled and sequenced using the Illumina\u00a0HiSeq\u00a0X\u00a0Ten machine as 150 bp paired end sequencing reads.", "Breeding fish were maintained at 28\u00b0C in a circulating water system on a 14 h light/10 h dark cycle. Embryos were collected by natural spawning and staged.", "tissue:muscle|treatment:DMSO", "GSM3029083", "GSM3029083: WT rep3; Danio rerio; RNA Seq", "GSM3029083", null, "1", "Total RNA was extracted using TRIZOL Reagent 15596 018 Life technologies following the manufacturer's instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 Agilent technologies Santa Clara CA US. Qualified total RNA was further purified by RNAClean XP Kit A63987 Beckman Coulterand RNase Free DNase Set 79254 QIAGEN. Libraries were constructed using VAHTS Total RNA Seq\uff08H/M/R Library PrepKit for Illumina NR603 02 Vazyme. Libraries were pooled and sequenced using the Illumina\u00a0HiSeq\u00a0X\u00a0Ten machine as 150 bp paired end sequencing reads.", "GEO Accession:GSM3029083", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP133827", null, null, "RLT3_1.fq.gz RLT3_2.fq.gz", "fastq fastq", 7458295500.0, 24860985.0, "GSM3029083 r1", "0:150 1:150", "A:1875422371;C:1858400851;G:1819493497;T:1904874518;N:104263", 150, 150, null, null, 1875422371, 1858400851, 1819493497, 1904874518, 104263, "SRX3757614", "SRS3013122", "SRA663830", "GEO", "School of basic medicine science, Zhejiang University", 2, 0.88642, 0.88696, 0.1881, 0.18533, 0.79537, 0.80073, 0.50351, 0.48568, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "China", "2018-03-02", "Multi-stage", "Embryo", "Muscle", "Muscular System"], [47645, "SRR6798776", "SRX3757613", "SRS3013120", "SRP133827", "PRJNA436713", "Inhibition of embryonic HSP 90 function causes variation of cold tolerance in zebrafish", "GSE111359", "Transcriptome Analysis", "Accumulating evidence suggests that HSP90 plays roles in modulation of phenotype in vertebrate development which is closely involved in adaptation and evolution. In this study we showed that inhibition of embryonic HSP90 function either by a chemical inhibitor radicicol or low conductivity stress induced variation of cold tolerance in adult zebrafish. Overall design: Three zebrafish showing significantly increased survival times in cold from radicicol group and three zebrafish from control group were selected for RNA Seq. Muscle tissue was separated from above mentioned fishes and used as materials for RNA Seq.", null, "pubmed:33343615", null, "WT rep2", "GSM3029082", null, "source name:muscle tissues|tissue:muscle|treatment:DMSO", "WT rep2", "Illumina Casava1.8 software used for basecalling. The raw reads were trimmed and filtered using Seqtk https://github.com/lh3/seqtk. Low quality Q < 20 bases were trimmed from 3\u2019 ends of the reads and the trimmed reads were filtered with read length \u2265 25 bp. Clean RNA Seq reads for each sample were aligned by HISAT2 2.0.4 with default setting to the zebrafish genome assembly using the Ensembl annotation DanRer10 Danio rerio.GRCz10.84.gtf 1. The number of reads mapped to the genes was counted by StringTie and normalized by TMM trimmed mean of M values method2. We next calculated fragments per kilobase per million mapped reads FPKM of each gene to indicate gene expression level. Genome build: GRCz10 Supplementary files format and content: tab delimited text files include FPKM values for each gene", "muscle tissues", "Treatment with radicicol was initiated at 50% epiboly and continued to 48 hpf followed by the removal of the drug using three rinses the whole process was carried in the dark because the light sensitivity of radicicol. Control group were treated with identical doses of DMSO.", "Total RNA was extracted using TRIZOL Reagent 15596 018 Life technologies following the manufacturer\u2019s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 Agilent technologies Santa Clara CA US. Qualified total RNA was further purified by RNAClean XP Kit A63987 Beckman Coulterand RNase Free DNase Set 79254 QIAGEN. Libraries were constructed using VAHTS Total RNA Seq\uff08H/M/R Library PrepKit for Illumina NR603 02 Vazyme. Libraries were pooled and sequenced using the Illumina\u00a0HiSeq\u00a0X\u00a0Ten machine as 150 bp paired end sequencing reads.", "Breeding fish were maintained at 28\u00b0C in a circulating water system on a 14 h light/10 h dark cycle. Embryos were collected by natural spawning and staged.", "tissue:muscle|treatment:DMSO", "GSM3029082", "GSM3029082: WT rep2; Danio rerio; RNA Seq", "GSM3029082", null, "1", "Total RNA was extracted using TRIZOL Reagent 15596 018 Life technologies following the manufacturer's instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 Agilent technologies Santa Clara CA US. Qualified total RNA was further purified by RNAClean XP Kit A63987 Beckman Coulterand RNase Free DNase Set 79254 QIAGEN. Libraries were constructed using VAHTS Total RNA Seq\uff08H/M/R Library PrepKit for Illumina NR603 02 Vazyme. Libraries were pooled and sequenced using the Illumina\u00a0HiSeq\u00a0X\u00a0Ten machine as 150 bp paired end sequencing reads.", "GEO Accession:GSM3029082", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP133827", null, null, "RLT2_2.fq.gz RLT2_1.fq.gz", "fastq fastq", 9462767100.0, 31542557.0, "GSM3029082 r1", "0:150 1:150", "A:2301678607;C:2445064584;G:2361534540;T:2354357373;N:131996", 150, 150, null, null, 2301678607, 2445064584, 2361534540, 2354357373, 131996, "SRX3757613", "SRS3013120", "SRA663830", "GEO", "School of basic medicine science, Zhejiang University", 2, 0.91337, 0.91337, 0.17924, 0.17526, 0.78317, 0.79011, 0.50203, 0.51647, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "China", "2018-03-02", "Multi-stage", "Embryo", "Muscle", "Muscular System"], [47646, "SRR6798775", "SRX3757612", "SRS3013121", "SRP133827", "PRJNA436713", "Inhibition of embryonic HSP 90 function causes variation of cold tolerance in zebrafish", "GSE111359", "Transcriptome Analysis", "Accumulating evidence suggests that HSP90 plays roles in modulation of phenotype in vertebrate development which is closely involved in adaptation and evolution. In this study we showed that inhibition of embryonic HSP90 function either by a chemical inhibitor radicicol or low conductivity stress induced variation of cold tolerance in adult zebrafish. Overall design: Three zebrafish showing significantly increased survival times in cold from radicicol group and three zebrafish from control group were selected for RNA Seq. Muscle tissue was separated from above mentioned fishes and used as materials for RNA Seq.", null, "pubmed:33343615", null, "WT rep1", "GSM3029081", null, "source name:muscle tissues|tissue:muscle|treatment:DMSO", "WT rep1", "Illumina Casava1.8 software used for basecalling. The raw reads were trimmed and filtered using Seqtk https://github.com/lh3/seqtk. Low quality Q < 20 bases were trimmed from 3\u2019 ends of the reads and the trimmed reads were filtered with read length \u2265 25 bp. Clean RNA Seq reads for each sample were aligned by HISAT2 2.0.4 with default setting to the zebrafish genome assembly using the Ensembl annotation DanRer10 Danio rerio.GRCz10.84.gtf 1. The number of reads mapped to the genes was counted by StringTie and normalized by TMM trimmed mean of M values method2. We next calculated fragments per kilobase per million mapped reads FPKM of each gene to indicate gene expression level. Genome build: GRCz10 Supplementary files format and content: tab delimited text files include FPKM values for each gene", "muscle tissues", "Treatment with radicicol was initiated at 50% epiboly and continued to 48 hpf followed by the removal of the drug using three rinses the whole process was carried in the dark because the light sensitivity of radicicol. Control group were treated with identical doses of DMSO.", "Total RNA was extracted using TRIZOL Reagent 15596 018 Life technologies following the manufacturer\u2019s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 Agilent technologies Santa Clara CA US. Qualified total RNA was further purified by RNAClean XP Kit A63987 Beckman Coulterand RNase Free DNase Set 79254 QIAGEN. Libraries were constructed using VAHTS Total RNA Seq\uff08H/M/R Library PrepKit for Illumina NR603 02 Vazyme. Libraries were pooled and sequenced using the Illumina\u00a0HiSeq\u00a0X\u00a0Ten machine as 150 bp paired end sequencing reads.", "Breeding fish were maintained at 28\u00b0C in a circulating water system on a 14 h light/10 h dark cycle. Embryos were collected by natural spawning and staged.", "tissue:muscle|treatment:DMSO", "GSM3029081", "GSM3029081: WT rep1; Danio rerio; RNA Seq", "GSM3029081", null, "1", "Total RNA was extracted using TRIZOL Reagent 15596 018 Life technologies following the manufacturer's instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 Agilent technologies Santa Clara CA US. Qualified total RNA was further purified by RNAClean XP Kit A63987 Beckman Coulterand RNase Free DNase Set 79254 QIAGEN. Libraries were constructed using VAHTS Total RNA Seq\uff08H/M/R Library PrepKit for Illumina NR603 02 Vazyme. Libraries were pooled and sequenced using the Illumina\u00a0HiSeq\u00a0X\u00a0Ten machine as 150 bp paired end sequencing reads.", "GEO Accession:GSM3029081", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP133827", null, null, "RLT1_1.fq.gz RLT1_2.fq.gz", "fastq fastq", 7599797400.0, 25332658.0, "GSM3029081 r1", "0:150 1:150", "A:1883972109;C:1921348946;G:1869717767;T:1924652451;N:106127", 150, 150, null, null, 1883972109, 1921348946, 1869717767, 1924652451, 106127, "SRX3757612", "SRS3013121", "SRA663830", "GEO", "School of basic medicine science, Zhejiang University", 2, 0.88692, 0.88623, 0.18432, 0.18166, 0.79928, 0.80693, 0.50362, 0.5124, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "China", "2018-03-02", "Multi-stage", "Embryo", "Muscle", "Muscular System"], [64385, "SRR14679147", "SRX11017528", "SRS9089834", "SRP321802", "PRJNA733247", "Danio rerio breed:Danio Raw sequence reads", "PRJNA733247", "Whole Genome Sequencing", "zebrafish muscle tissue for scRNA seq and bulk RNA seq", null, null, null, "Model organism or animal sample from Danio rerio", "zebrafish", null, "breed:Danio|dev stage:60 day|sex:missing|tissue:muscle|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "bulk RNA seq", "runx2b+/+ 2 bulk RNA seq", "runx2b+/+ 2 bulk RNA seq", "tail muscle with intermuscular bone", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP321802", null, null, "WT_2_60dpf.R1.fq.gz WT_2_60dpf.R2.fq.gz", "fastq fastq", 7007750400.0, 23359168.0, "WT 2 60dpf.R1.fq.gz", "0:150 1:150", "A:1714498514;C:1702913716;G:1897215939;T:1693105532;N:16699", 150, 150, null, null, 1714498514, 1702913716, 1897215939, 1693105532, 16699, "SRX11017528", "SRS9089834", "SRA1238123", "Huazhong Agricultural university|Huazhong Agricultural university", "Huazhong Agricultural university", 2, 0.93184, 0.92606, 0.01222, 0.01169, 0.84762, 0.85033, 0.67174, 0.64259, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc_generic", "bulk", "bulk", null, "China", "2021-05-28", "Juvenile", "Juvenile", "Muscle", "Muscular System"], [64386, "SRR14679148", "SRX11017527", "SRS9089834", "SRP321802", "PRJNA733247", "Danio rerio breed:Danio Raw sequence reads", "PRJNA733247", "Whole Genome Sequencing", "zebrafish muscle tissue for scRNA seq and bulk RNA seq", null, null, null, "Model organism or animal sample from Danio rerio", "zebrafish", null, "breed:Danio|dev stage:60 day|sex:missing|tissue:muscle|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "bulk RNA seq", "runx2b+/+ 1 bulk RNA seq", "runx2b+/+ 1 bulk RNA seq", "tail muscle with intermuscular bone", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP321802", null, null, "WT_1_60dpf.R1.fq.gz WT_1_60dpf.R2.fq.gz", "fastq fastq", 6785203800.0, 22617346.0, "WT 1 60dpf.R1.fq.gz", "0:150 1:150", "A:1660992152;C:1637869425;G:1843210897;T:1643114944;N:16382", 150, 150, null, null, 1660992152, 1637869425, 1843210897, 1643114944, 16382, "SRX11017527", "SRS9089834", "SRA1238123", "Huazhong Agricultural university|Huazhong Agricultural university", "Huazhong Agricultural university", 2, 0.92764, 0.92197, 0.00968, 0.00947, 0.84323, 0.84577, 0.65455, 0.6592, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc_generic", "bulk", "bulk", null, "China", "2021-05-28", "Juvenile", "Juvenile", "Muscle", "Muscular System"], [64389, "SRR14679151", "SRX11017524", "SRS9089834", "SRP321802", "PRJNA733247", "Danio rerio breed:Danio Raw sequence reads", "PRJNA733247", "Whole Genome Sequencing", "zebrafish muscle tissue for scRNA seq and bulk RNA seq", null, null, null, "Model organism or animal sample from Danio rerio", "zebrafish", null, "breed:Danio|dev stage:60 day|sex:missing|tissue:muscle|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "bulk RNA seq", "runx2b / 3 bulk RNA seq", "runx2b / 3 bulk RNA seq", "tail muscle without xxx bone", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP321802", null, null, "MUT_3_60dpf.R1.fq.gz MUT_3_60dpf.R2.fq.gz", "fastq fastq", 7358370600.0, 24527902.0, "MUT 3 60dpf.R1.fq.gz", "0:150 1:150", "A:1781646726;C:1790446433;G:2025455441;T:1760804227;N:17773", 150, 150, null, null, 1781646726, 1790446433, 2025455441, 1760804227, 17773, "SRX11017524", "SRS9089834", "SRA1238123", "Huazhong Agricultural university|Huazhong Agricultural university", "Huazhong Agricultural university", 2, 0.92552, 0.9218, 0.01223, 0.01223, 0.86222, 0.86348, 0.68246, 0.64029, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc_generic", "bulk", "bulk", null, "China", "2021-05-28", "Juvenile", "Juvenile", "Muscle", "Muscular System"], [64390, "SRR14679152", "SRX11017523", "SRS9089834", "SRP321802", "PRJNA733247", "Danio rerio breed:Danio Raw sequence reads", "PRJNA733247", "Whole Genome Sequencing", "zebrafish muscle tissue for scRNA seq and bulk RNA seq", null, null, null, "Model organism or animal sample from Danio rerio", "zebrafish", null, "breed:Danio|dev stage:60 day|sex:missing|tissue:muscle|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "bulk RNA seq", "runx2b / 2 bulk RNA seq", "runx2b / 2 bulk RNA seq", "tail muscle without xxx bone", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP321802", null, null, "MUT_2_60dpf.R1.fq.gz MUT_2_60dpf.R2.fq.gz", "fastq fastq", 5983046100.0, 19943487.0, "MUT 2 60dpf.R1.fq.gz", "0:150 1:150", "A:1456794159;C:1460953692;G:1613536834;T:1451747111;N:14304", 150, 150, null, null, 1456794159, 1460953692, 1613536834, 1451747111, 14304, "SRX11017523", "SRS9089834", "SRA1238123", "Huazhong Agricultural university|Huazhong Agricultural university", "Huazhong Agricultural university", 2, 0.93491, 0.9294, 0.01148, 0.01117, 0.85474, 0.85667, 0.69448, 0.63383, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc_generic", "bulk", "bulk", null, "China", "2021-05-28", "Juvenile", "Juvenile", "Muscle", "Muscular System"], [64391, "SRR14679153", "SRX11017522", "SRS9089834", "SRP321802", "PRJNA733247", "Danio rerio breed:Danio Raw sequence reads", "PRJNA733247", "Whole Genome Sequencing", "zebrafish muscle tissue for scRNA seq and bulk RNA seq", null, null, null, "Model organism or animal sample from Danio rerio", "zebrafish", null, "breed:Danio|dev stage:60 day|sex:missing|tissue:muscle|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "bulk RNA seq", "runx2b / 1 bulk RNA seq", "runx2b / 1 bulk RNA seq", "tail muscle without xxx bone", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP321802", null, null, "MUT_1_60dpf.R1.fq.gz MUT_1_60dpf.R2.fq.gz", "fastq fastq", 6876053100.0, 22920177.0, "MUT 1 60dpf.R1.fq.gz", "0:150 1:150", "A:1683687632;C:1665466650;G:1862910858;T:1663971371;N:16589", 150, 150, null, null, 1683687632, 1665466650, 1862910858, 1663971371, 16589, "SRX11017522", "SRS9089834", "SRA1238123", "Huazhong Agricultural university|Huazhong Agricultural university", "Huazhong Agricultural university", 2, 0.93272, 0.92802, 0.01179, 0.01133, 0.84861, 0.84993, 0.62206, 0.67726, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc_generic", "bulk", "bulk", null, "China", "2021-05-28", "Juvenile", "Juvenile", "Muscle", "Muscular System"], [64392, "SRR14679154", "SRX11017521", "SRS9089834", "SRP321802", "PRJNA733247", "Danio rerio breed:Danio Raw sequence reads", "PRJNA733247", "Whole Genome Sequencing", "zebrafish muscle tissue for scRNA seq and bulk RNA seq", null, null, null, "Model organism or animal sample from Danio rerio", "zebrafish", null, "breed:Danio|dev stage:60 day|sex:missing|tissue:muscle|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "bulk RNA seq", "runx2b+/+ 3 bulk RNA seq", "runx2b+/+ 3 bulk RNA seq", "tail muscle with intermuscular bone", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP321802", null, null, "WT_3_60dpf.R1.fq.gz WT_3_60dpf.R2.fq.gz", "fastq fastq", 6834033900.0, 22780113.0, "WT 3 60dpf.R1.fq.gz", "0:150 1:150", "A:1665713519;C:1660512523;G:1864685424;T:1643106338;N:16096", 150, 150, null, null, 1665713519, 1660512523, 1864685424, 1643106338, 16096, "SRX11017521", "SRS9089834", "SRA1238123", "Huazhong Agricultural university|Huazhong Agricultural university", "Huazhong Agricultural university", 2, 0.92968, 0.92349, 0.01013, 0.01013, 0.85811, 0.85999, 0.62541, 0.6776, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc_generic", "bulk", "bulk", null, "China", "2021-05-28", "Juvenile", "Juvenile", "Muscle", "Muscular System"], [70803, "SRR20651070", "SRX16674147", "SRS14305696", "SRP388214", "PRJNA861969", "RNA seq in KLHL40 KO zebrafish muscle", "PRJNA861969", "Other", "Mutations in KLHL40 gene results in nemaline myopathy in affected patients. To identify the contribution of transcriptome on disease pathology bulk RNA sequencing was performed in Control and KLHL40 knockout zebrafish at the onset of disease pathology at 3 month of age.", null, null, null, "klhl40a KO4", "klhl40a Mutant 4", null, "strain:TU|isolate:Not Applicable|breed:Not Applicable|cultivar:Not Applicable|ecotype:Not Applicable|age:3 Months|dev stage:Adult|sex:not collected|tissue:Skeletal Muscle|disease:Nemaline Myopathy|disease stg:Disease onset|genotype:klhl40a|phenotype:Nemaline Myopathy|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "KO4", "klhl40a4", "klhl40a4", "A total amount of 1 g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext UltraTM RNA. First strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H . Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. post adenylation of 3 ends of DNA fragments NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150200 bp in length the library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then 3 l USER Enzyme NEB USA was used with size selected adaptorligated cDNA at 37 C for 15 min followed by 5 min at 95 C before PCR. Then PCR was performed with Phusion High Fidelity DNA polymerase Universal PCR primers and Index X Primer. At last PCR products were purified AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot HS Illumina according to the manufacturers instructions. post cluster generation the library preparations were sequenced on an Illumina platform and paired end reads were generated.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP388214", null, null, "KO4_1.fq.gz KO4_2.fq.gz", "fastq fastq", 6711352800.0, 22371176.0, "KO4 1.fq.gz", "0:150 1:150", "A:1777166363;C:1589553466;G:1610514347;T:1734012530;N:106094", 150, 150, null, null, 1777166363, 1589553466, 1610514347, 1734012530, 106094, "SRX16674147", "SRS14305696", null, null, "Brigham and Women's Hospital", 2, 0.96541, 0.96534, 0.04564, 0.04561, 0.80478, 0.80594, 0.49645, 0.49712, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2022-07-26", "Adult", "Adult", "Muscle", "Muscular System"], [70804, "SRR20651071", "SRX16674146", "SRS14305695", "SRP388214", "PRJNA861969", "RNA seq in KLHL40 KO zebrafish muscle", "PRJNA861969", "Other", "Mutations in KLHL40 gene results in nemaline myopathy in affected patients. To identify the contribution of transcriptome on disease pathology bulk RNA sequencing was performed in Control and KLHL40 knockout zebrafish at the onset of disease pathology at 3 month of age.", null, null, null, "klhl40a KO3", "klhl40a Mutant 3", null, "strain:TU|isolate:Not Applicable|breed:Not Applicable|cultivar:Not Applicable|ecotype:Not Applicable|age:3 Months|dev stage:Adult|sex:not collected|tissue:Skeletal Muscle|disease:Nemaline Myopathy|disease stg:Disease onset|genotype:klhl40a|phenotype:Nemaline Myopathy|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "KO3", "klhl40a3", "klhl40a3", "A total amount of 1 g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext UltraTM RNA. First strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H . Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. post adenylation of 3 ends of DNA fragments NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150200 bp in length the library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then 3 l USER Enzyme NEB USA was used with size selected adaptorligated cDNA at 37 C for 15 min followed by 5 min at 95 C before PCR. Then PCR was performed with Phusion High Fidelity DNA polymerase Universal PCR primers and Index X Primer. At last PCR products were purified AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot HS Illumina according to the manufacturers instructions. post cluster generation the library preparations were sequenced on an Illumina platform and paired end reads were generated.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP388214", null, null, "KO3_1.fq.gz KO3_2.fq.gz", "fastq fastq", 6837271200.0, 22790904.0, "KO3 1.fq.gz", "0:150 1:150", "A:1889665334;C:1538962427;G:1555674788;T:1852860913;N:107738", 150, 150, null, null, 1889665334, 1538962427, 1555674788, 1852860913, 107738, "SRX16674146", "SRS14305695", null, null, "Brigham and Women's Hospital", 2, 0.9394, 0.93825, 0.07858, 0.07822, 0.7413, 0.74186, 0.50534, 0.49292, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2022-07-26", "Adult", "Adult", "Muscle", "Muscular System"], [70805, "SRR20651072", "SRX16674145", "SRS14305694", "SRP388214", "PRJNA861969", "RNA seq in KLHL40 KO zebrafish muscle", "PRJNA861969", "Other", "Mutations in KLHL40 gene results in nemaline myopathy in affected patients. To identify the contribution of transcriptome on disease pathology bulk RNA sequencing was performed in Control and KLHL40 knockout zebrafish at the onset of disease pathology at 3 month of age.", null, null, null, "klhl40a KO2", "klhl40a Mutant 2", null, "strain:TU|isolate:Not Applicable|breed:Not Applicable|cultivar:Not Applicable|ecotype:Not Applicable|age:3 Months|dev stage:Adult|sex:not collected|tissue:Skeletal Muscle|disease:Nemaline Myopathy|disease stg:Disease onset|genotype:klhl40a|phenotype:Nemaline Myopathy|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "KO2", "klhl40a2", "klhl40a2", "A total amount of 1 g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext UltraTM RNA. First strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H . Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. post adenylation of 3 ends of DNA fragments NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150200 bp in length the library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then 3 l USER Enzyme NEB USA was used with size selected adaptorligated cDNA at 37 C for 15 min followed by 5 min at 95 C before PCR. Then PCR was performed with Phusion High Fidelity DNA polymerase Universal PCR primers and Index X Primer. At last PCR products were purified AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot HS Illumina according to the manufacturers instructions. post cluster generation the library preparations were sequenced on an Illumina platform and paired end reads were generated.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP388214", null, null, "KO2_1.fq.gz KO2_2.fq.gz", "fastq fastq", 6551044800.0, 21836816.0, "KO2 1.fq.gz", "0:150 1:150", "A:1793351007;C:1490899611;G:1511714794;T:1754976004;N:103384", 150, 150, null, null, 1793351007, 1490899611, 1511714794, 1754976004, 103384, "SRX16674145", "SRS14305694", null, null, "Brigham and Women's Hospital", 2, 0.95416, 0.953, 0.06534, 0.06511, 0.76678, 0.76668, 0.51901, 0.49628, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2022-07-26", "Adult", "Adult", "Muscle", "Muscular System"], [70806, "SRR20651073", "SRX16674144", "SRS14305693", "SRP388214", "PRJNA861969", "RNA seq in KLHL40 KO zebrafish muscle", "PRJNA861969", "Other", "Mutations in KLHL40 gene results in nemaline myopathy in affected patients. To identify the contribution of transcriptome on disease pathology bulk RNA sequencing was performed in Control and KLHL40 knockout zebrafish at the onset of disease pathology at 3 month of age.", null, null, null, "klh40a KO1", "klhl40a Mutant 1", null, "strain:TU|isolate:Not Applicable|breed:Not Applicable|cultivar:Not Applicable|ecotype:Not Applicable|age:3 Months|dev stage:Adult|sex:not collected|tissue:Skeletal Muscle|disease:Nemaline Myopathy|disease stg:Disease onset|genotype:klhl40a|phenotype:Nemaline Myopathy|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "KO1", "klhl40a1", "klhl40a1", "A total amount of 1 g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext UltraTM RNA. First strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H . Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. post adenylation of 3 ends of DNA fragments NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150200 bp in length the library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then 3 l USER Enzyme NEB USA was used with size selected adaptorligated cDNA at 37 C for 15 min followed by 5 min at 95 C before PCR. Then PCR was performed with Phusion High Fidelity DNA polymerase Universal PCR primers and Index X Primer. At last PCR products were purified AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot HS Illumina according to the manufacturers instructions. post cluster generation the library preparations were sequenced on an Illumina platform and paired end reads were generated.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP388214", null, null, "KO1_1.fq.gz KO1_2.fq.gz", "fastq fastq", 7080009000.0, 23600030.0, "KO1 1.fq.gz", "0:150 1:150", "A:1927450674;C:1619718617;G:1639235237;T:1893497462;N:107010", 150, 150, null, null, 1927450674, 1619718617, 1639235237, 1893497462, 107010, "SRX16674144", "SRS14305693", null, null, "Brigham and Women's Hospital", 2, 0.94175, 0.94193, 0.06579, 0.06628, 0.75045, 0.7503, 0.49508, 0.50075, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2022-07-26", "Adult", "Adult", "Muscle", "Muscular System"], [70807, "SRR20651074", "SRX16674143", "SRS14305692", "SRP388214", "PRJNA861969", "RNA seq in KLHL40 KO zebrafish muscle", "PRJNA861969", "Other", "Mutations in KLHL40 gene results in nemaline myopathy in affected patients. To identify the contribution of transcriptome on disease pathology bulk RNA sequencing was performed in Control and KLHL40 knockout zebrafish at the onset of disease pathology at 3 month of age.", null, null, null, "WT4", "Wild type Control4", null, "strain:TU|isolate:Not Applicable|breed:Not Applicable|cultivar:Not Applicable|ecotype:Not Applicable|age:3 Months|dev stage:Adult|sex:not collected|tissue:Skeletal Muscle|disease:Nemaline Myopathy|disease stg:Disease onset|genotype:WT|phenotype:Normal|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "WT4", "WT4", "WT4", "A total amount of 1 g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext UltraTM RNA. First strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H . Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. post adenylation of 3 ends of DNA fragments NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150200 bp in length the library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then 3 l USER Enzyme NEB USA was used with size selected adaptorligated cDNA at 37 C for 15 min followed by 5 min at 95 C before PCR. Then PCR was performed with Phusion High Fidelity DNA polymerase Universal PCR primers and Index X Primer. At last PCR products were purified AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot HS Illumina according to the manufacturers instructions. post cluster generation the library preparations were sequenced on an Illumina platform and paired end reads were generated.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP388214", null, null, "WT4_1.fq.gz WT4_2.fq.gz", "fastq fastq", 7079022600.0, 23596742.0, "WT4 1.fq.gz", "0:150 1:150", "A:1901387601;C:1651068590;G:1657216811;T:1869243020;N:106578", 150, 150, null, null, 1901387601, 1651068590, 1657216811, 1869243020, 106578, "SRX16674143", "SRS14305692", null, null, "Brigham and Women's Hospital", 2, 0.95455, 0.95486, 0.07809, 0.07798, 0.75491, 0.75442, 0.49622, 0.50833, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2022-07-26", "Adult", "Adult", "Muscle", "Muscular System"], [70808, "SRR20651075", "SRX16674142", "SRS14305691", "SRP388214", "PRJNA861969", "RNA seq in KLHL40 KO zebrafish muscle", "PRJNA861969", "Other", "Mutations in KLHL40 gene results in nemaline myopathy in affected patients. To identify the contribution of transcriptome on disease pathology bulk RNA sequencing was performed in Control and KLHL40 knockout zebrafish at the onset of disease pathology at 3 month of age.", null, null, null, "WT3", "Wild type Control3", null, "strain:TU|isolate:Not Applicable|breed:Not Applicable|cultivar:Not Applicable|ecotype:Not Applicable|age:3 Months|dev stage:Adult|sex:not collected|tissue:Skeletal Muscle|disease:Nemaline Myopathy|disease stg:Disease onset|genotype:WT|phenotype:Normal|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "WT3", "WT3", "WT3", "A total amount of 1 g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext UltraTM RNA. First strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H . Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. post adenylation of 3 ends of DNA fragments NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150200 bp in length the library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then 3 l USER Enzyme NEB USA was used with size selected adaptorligated cDNA at 37 C for 15 min followed by 5 min at 95 C before PCR. Then PCR was performed with Phusion High Fidelity DNA polymerase Universal PCR primers and Index X Primer. At last PCR products were purified AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot HS Illumina according to the manufacturers instructions. post cluster generation the library preparations were sequenced on an Illumina platform and paired end reads were generated.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP388214", null, null, "WT3_1.fq.gz WT3_2.fq.gz", "fastq fastq", 6750141600.0, 22500472.0, "WT3 1.fq.gz", "0:150 1:150", "A:1809694888;C:1570721302;G:1597114393;T:1772508410;N:102607", 150, 150, null, null, 1809694888, 1570721302, 1597114393, 1772508410, 102607, "SRX16674142", "SRS14305691", null, null, "Brigham and Women's Hospital", 2, 0.95657, 0.95647, 0.06172, 0.06163, 0.76252, 0.76366, 0.49411, 0.49204, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2022-07-26", "Adult", "Adult", "Muscle", "Muscular System"], [70809, "SRR20651076", "SRX16674141", "SRS14305690", "SRP388214", "PRJNA861969", "RNA seq in KLHL40 KO zebrafish muscle", "PRJNA861969", "Other", "Mutations in KLHL40 gene results in nemaline myopathy in affected patients. To identify the contribution of transcriptome on disease pathology bulk RNA sequencing was performed in Control and KLHL40 knockout zebrafish at the onset of disease pathology at 3 month of age.", null, null, null, "WT2", "Wild type Control2", null, "strain:TU|isolate:Not Applicable|breed:Not Applicable|cultivar:Not Applicable|ecotype:Not Applicable|age:3 Months|dev stage:Adult|sex:not collected|tissue:Skeletal Muscle|disease:Nemaline Myopathy|disease stg:Disease onset|genotype:WT|phenotype:Normal|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "WT2", "WT2", "WT2", "A total amount of 1 g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext UltraTM RNA. First strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H . Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. post adenylation of 3 ends of DNA fragments NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150200 bp in length the library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then 3 l USER Enzyme NEB USA was used with size selected adaptorligated cDNA at 37 C for 15 min followed by 5 min at 95 C before PCR. Then PCR was performed with Phusion High Fidelity DNA polymerase Universal PCR primers and Index X Primer. At last PCR products were purified AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot HS Illumina according to the manufacturers instructions. post cluster generation the library preparations were sequenced on an Illumina platform and paired end reads were generated.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP388214", null, null, "WT2_1.fq.gz WT2_2.fq.gz", "fastq fastq", 6786893400.0, 22622978.0, "WT2 1.fq.gz", "0:150 1:150", "A:1835782156;C:1564402670;G:1586345899;T:1800260025;N:102650", 150, 150, null, null, 1835782156, 1564402670, 1586345899, 1800260025, 102650, "SRX16674141", "SRS14305690", null, null, "Brigham and Women's Hospital", 2, 0.95057, 0.9495, 0.06714, 0.06726, 0.75266, 0.75333, 0.50647, 0.50457, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2022-07-26", "Adult", "Adult", "Muscle", "Muscular System"], [70810, "SRR20651077", "SRX16674140", "SRS14305689", "SRP388214", "PRJNA861969", "RNA seq in KLHL40 KO zebrafish muscle", "PRJNA861969", "Other", "Mutations in KLHL40 gene results in nemaline myopathy in affected patients. To identify the contribution of transcriptome on disease pathology bulk RNA sequencing was performed in Control and KLHL40 knockout zebrafish at the onset of disease pathology at 3 month of age.", null, null, null, "WT1", "Wild type Control1", null, "strain:AB|isolate:N/A|breed:N/A|cultivar:N/A|ecotype:N/A|age:3 Months|dev stage:Adult|sex:male|tissue:Skeletal Muscle|disease:Nemaline Myopathy|genotype:WT|phenotype:Normal|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "WT1", "WT1", "WT1", "A total amount of 1 g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext UltraTM RNA. First strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H . Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. post adenylation of 3 ends of DNA fragments NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150200 bp in length the library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then 3 l USER Enzyme NEB USA was used with size selected adaptorligated cDNA at 37 C for 15 min followed by 5 min at 95 C before PCR. Then PCR was performed with Phusion High Fidelity DNA polymerase Universal PCR primers and Index X Primer. At last PCR products were purified AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot HS Illumina according to the manufacturers instructions. post cluster generation the library preparations were sequenced on an Illumina platform and paired end reads were generated.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP388214", null, null, "WT1_1.fq.gz WT1_2.fq.gz", "fastq fastq", 6946359900.0, 23154533.0, "WT1 1.fq.gz", "0:150 1:150", "A:1891340276;C:1588097676;G:1606011156;T:1860805584;N:105208", 150, 150, null, null, 1891340276, 1588097676, 1606011156, 1860805584, 105208, "SRX16674140", "SRS14305689", null, null, "Brigham and Women's Hospital", 2, 0.94444, 0.94509, 0.07758, 0.07756, 0.72943, 0.72878, 0.50732, 0.50723, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2022-07-26", "Adult", "Adult", "Muscle", "Muscular System"], [71456, "SRR21631159", "SRX17631561", "SRS15166364", "SRP398129", "PRJNA882122", "Mutations in cdon and boc affect trunk neural crest cell migration and slow twitch muscle development in zebrafish", "GSE213728", "Transcriptome Analysis", "Bulk RNA seq of isolated slow twtich muscle and neural crest cells from 24 hpf zebrafish. Overall design: Bulk RNA seq data from FAC sorted slow twitch muscle and neural crest cells isolated from trunks of 24 hpf zebrafish embryos. Trunks of embryos were manually dissected and cells were disassociated using Accumax. Embryos were doubly transgenic for tgsox10:mRFP transgene that labels neural crest cells and tgPACprdm1a:eGFP transgene that labels slow twitch muscle and muscle pioneer cells. Neural crest cells and slow twitch muscle cells were isolated by FACS on a MoFlow XDP100 prepared for stranded Illumina sequencing and sequenced on a NovaSeq600 PE 150bp. Gene expression summaries were produced using featurecounts subread package and DESeq2.", null, null, null, "Slow twitch Muscle tgPACPrdm1a:eGFP Sample2", "GSM6592891", null, "source name:slow twitch muscle|tissue:slow twitch muscle|genotype:wildtype|treatment:n1|geo loc name:missing|collection date:missing", "Slow twitch Muscle tgPACPrdm1a:eGFP Sample2", "Read aligment with STAR counts generated by featurecounts subread. Expression from DESeq2 using normTransform function Supplementary files format and content: tab delim text file Supplementary files format and content: tab delim text file", "slow twitch muscle", "For cyclopamine treated samples embryos were treated with 100uM cyclopamine from 50% epiboloy to 24hpf", "standard Illumina Kit for stranded RNAseq", "Embryos reared at 28C until 24hpf.", "tissue:slow twitch muscle|genotype:wildtype|treatment:n1", "GSM6592891", "GSM6592891: Slow twitch Muscle tgPACPrdm1a:eGFP Sample2; Danio rerio; RNA Seq", "GSM6592891 r1", "GSM6592891", "1", "standard Illumina Kit for stranded RNAseq", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP398129", null, "loader:fastq load.py", "Sample3_GFP_24hpf_S3_L002_R1_001.fastq.gz Sample3_GFP_24hpf_S3_L002_R2_001.fastq.gz", "fastq fastq", 19887469194.0, 65852547.0, "GSM6592891 r1", "0:151 1:151", "A:4595886435;C:4222799298;G:6711875529;T:4353875479;N:3032453", 151, 151, null, null, 4595886435, 4222799298, 6711875529, 4353875479, 3032453, "SRX17631561", "SRS15166364", "SRA1501497", "Lencer Laboratory, Department of Biology, Lafayette College", "Lencer Laboratory, Department of Biology, Lafayette College", 2, 0.92086, 0.91566, 0.10394, 0.10303, 0.75808, 0.76002, 0.51563, 0.51331, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2022-09-19", "Pharyngula", "Embryo", "Muscle", "Muscular System"], [71458, "SRR21631161", "SRX17631559", "SRS15166362", "SRP398129", "PRJNA882122", "Mutations in cdon and boc affect trunk neural crest cell migration and slow twitch muscle development in zebrafish", "GSE213728", "Transcriptome Analysis", "Bulk RNA seq of isolated slow twtich muscle and neural crest cells from 24 hpf zebrafish. Overall design: Bulk RNA seq data from FAC sorted slow twitch muscle and neural crest cells isolated from trunks of 24 hpf zebrafish embryos. Trunks of embryos were manually dissected and cells were disassociated using Accumax. Embryos were doubly transgenic for tgsox10:mRFP transgene that labels neural crest cells and tgPACprdm1a:eGFP transgene that labels slow twitch muscle and muscle pioneer cells. Neural crest cells and slow twitch muscle cells were isolated by FACS on a MoFlow XDP100 prepared for stranded Illumina sequencing and sequenced on a NovaSeq600 PE 150bp. Gene expression summaries were produced using featurecounts subread package and DESeq2.", null, null, null, "Slow twitch Muscle tgPACPrdm1a:eGFP Sample1", "GSM6592889", null, "source name:slow twitch muscle|tissue:slow twitch muscle|genotype:wildtype|treatment:n1|geo loc name:missing|collection date:missing", "Slow twitch Muscle tgPACPrdm1a:eGFP Sample1", "Read aligment with STAR counts generated by featurecounts subread. Expression from DESeq2 using normTransform function Supplementary files format and content: tab delim text file Supplementary files format and content: tab delim text file", "slow twitch muscle", "For cyclopamine treated samples embryos were treated with 100uM cyclopamine from 50% epiboloy to 24hpf", "standard Illumina Kit for stranded RNAseq", "Embryos reared at 28C until 24hpf.", "tissue:slow twitch muscle|genotype:wildtype|treatment:n1", "GSM6592889", "GSM6592889: Slow twitch Muscle tgPACPrdm1a:eGFP Sample1; Danio rerio; RNA Seq", "GSM6592889 r1", "GSM6592889", "1", "standard Illumina Kit for stranded RNAseq", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP398129", null, "loader:fastq load.py", "Sample1_GFP_24hpf_S1_L002_R1_001.fastq.gz Sample1_GFP_24hpf_S1_L002_R2_001.fastq.gz", "fastq fastq", 19122998172.0, 63321186.0, "GSM6592889 r1", "0:151 1:151", "A:4422627777;C:4011278190;G:6496127381;T:4190045039;N:2919785", 151, 151, null, null, 4422627777, 4011278190, 6496127381, 4190045039, 2919785, "SRX17631559", "SRS15166362", "SRA1501497", "Lencer Laboratory, Department of Biology, Lafayette College", "Lencer Laboratory, Department of Biology, Lafayette College", 2, 0.91304, 0.90702, 0.10612, 0.10501, 0.77242, 0.77415, 0.52048, 0.51584, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2022-09-19", "Pharyngula", "Embryo", "Muscle", "Muscular System"]], "truncated": false, "filtered_table_rows_count": 41, "expanded_columns": [], "expandable_columns": [], "columns": ["rowid", "run.accession", "experiment.accession", "sample.accession", "study.accession", "bioproject", "study.title", "study.alias", "study.type", "study.abstract", "study.attributes", "study.PMIDs", "sample.description", "sample.title", "sample.alias", "sample.centername", "sample.attributes", "GEOsample.title", "GEOsample.dataprocessing", "GEOsample.source", "GEOsample.treatmentprotocol", "GEOsample.extractprotocol", "GEOsample.growthprotocol", "GEOsample.characteristics", "GEOsample.accession", "experiment.title", "experiment.alias", "experiment.library_name", "experiment.design_description", "experiment.library_construction_protocol", "experiment.attributes", "experiment.library_strategy", "experiment.library_source", "experiment.library_selection", "experiment.library_layout", "experiment.platform", "experiment.instrument_model", "experiment.spot_descriptor", "experiment.study_ref", "run.title", "run.attributes", "run.filename", "run.semantic_name", "run.total_bases", "run.total_spots", "run.alias", "run.read_lengths", "run.base_counts", "run.r1_length", "run.r2_length", "run.r3_length", "run.r4_length", "run.Acount", "run.Ccount", "run.Gcount", "run.Tcount", "run.Ncount", "run.experiment", "run.pool_member", "submission.accession", "submission.srasource", "submission.bioprojectsource", "seqdetective.n_mates", "seqdetective.mapping_rate.mate1", "seqdetective.mapping_rate.mate2", "seqdetective.nofeature_rate.mate1", "seqdetective.nofeature_rate.mate2", "seqdetective.sparsity.mate1", "seqdetective.sparsity.mate2", "seqdetective.pos_strand_rate.mate1", "seqdetective.pos_strand_rate.mate2", "seqdetective.readlen.mate1", "seqdetective.readlen.mate2", "seqdetective.judgement.mate1", "seqdetective.judgement.mate2", "seqdetective.judgement.reason", "platform_family", "instrument_generation", "read_bias", "selection_class", "prep_kit", "sc_or_bulk", "tech_class", "technology", "tech_variant", "submission.bioprojectsource.country", "earliest_date", "devstage_curation", "devstage_curation_coarse", "tissue_curation", "tissue_curation_coarse"], "primary_keys": [], "units": {}, "query": {"sql": "select rowid, [run.accession], [experiment.accession], [sample.accession], [study.accession], bioproject, [study.title], [study.alias], [study.type], [study.abstract], [study.attributes], [study.PMIDs], [sample.description], [sample.title], [sample.alias], [sample.centername], [sample.attributes], [GEOsample.title], [GEOsample.dataprocessing], [GEOsample.source], [GEOsample.treatmentprotocol], [GEOsample.extractprotocol], [GEOsample.growthprotocol], [GEOsample.characteristics], [GEOsample.accession], [experiment.title], [experiment.alias], [experiment.library_name], [experiment.design_description], [experiment.library_construction_protocol], [experiment.attributes], [experiment.library_strategy], [experiment.library_source], [experiment.library_selection], [experiment.library_layout], [experiment.platform], [experiment.instrument_model], [experiment.spot_descriptor], [experiment.study_ref], [run.title], [run.attributes], [run.filename], [run.semantic_name], [run.total_bases], [run.total_spots], [run.alias], [run.read_lengths], [run.base_counts], [run.r1_length], [run.r2_length], [run.r3_length], [run.r4_length], [run.Acount], [run.Ccount], [run.Gcount], [run.Tcount], [run.Ncount], [run.experiment], [run.pool_member], [submission.accession], [submission.srasource], [submission.bioprojectsource], [seqdetective.n_mates], [seqdetective.mapping_rate.mate1], [seqdetective.mapping_rate.mate2], [seqdetective.nofeature_rate.mate1], [seqdetective.nofeature_rate.mate2], [seqdetective.sparsity.mate1], [seqdetective.sparsity.mate2], [seqdetective.pos_strand_rate.mate1], [seqdetective.pos_strand_rate.mate2], [seqdetective.readlen.mate1], [seqdetective.readlen.mate2], [seqdetective.judgement.mate1], [seqdetective.judgement.mate2], [seqdetective.judgement.reason], platform_family, instrument_generation, read_bias, selection_class, prep_kit, sc_or_bulk, tech_class, technology, tech_variant, [submission.bioprojectsource.country], earliest_date, devstage_curation, devstage_curation_coarse, tissue_curation, tissue_curation_coarse from run_metadata where \"experiment.library_source\" = :p0 and \"technology\" = :p1 and \"tissue_curation_coarse\" = :p2 order by rowid limit 101", "params": {"p0": "TRANSCRIPTOMIC", "p1": "bulk", "p2": "Muscular System"}}, "facet_results": {"experiment.library_strategy": {"name": "experiment.library_strategy", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=bulk&tissue_curation_coarse=Muscular+System", "results": [{"value": "RNA-Seq", "label": "RNA-Seq", "count": 41, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=bulk&tissue_curation_coarse=Muscular+System&experiment.library_strategy=RNA-Seq", "selected": false}], "truncated": false}, "experiment.library_source": {"name": "experiment.library_source", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=bulk&tissue_curation_coarse=Muscular+System", "results": [{"value": "TRANSCRIPTOMIC", "label": "TRANSCRIPTOMIC", "count": 41, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?technology=bulk&tissue_curation_coarse=Muscular+System", "selected": true}], "truncated": false}, "experiment.library_selection": {"name": "experiment.library_selection", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=bulk&tissue_curation_coarse=Muscular+System", "results": [{"value": "cDNA", "label": "cDNA", "count": 33, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=bulk&tissue_curation_coarse=Muscular+System&experiment.library_selection=cDNA", "selected": false}, {"value": "PCR", "label": "PCR", "count": 8, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=bulk&tissue_curation_coarse=Muscular+System&experiment.library_selection=PCR", "selected": false}], "truncated": false}, "experiment.library_layout": {"name": "experiment.library_layout", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=bulk&tissue_curation_coarse=Muscular+System", "results": [{"value": "PAIRED", "label": "PAIRED", "count": 41, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=bulk&tissue_curation_coarse=Muscular+System&experiment.library_layout=PAIRED", "selected": false}], "truncated": false}, "experiment.platform": {"name": "experiment.platform", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=bulk&tissue_curation_coarse=Muscular+System", "results": [{"value": "ILLUMINA", "label": "ILLUMINA", "count": 41, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=bulk&tissue_curation_coarse=Muscular+System&experiment.platform=ILLUMINA", "selected": false}], "truncated": false}, "devstage_curation_coarse": {"name": "devstage_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=bulk&tissue_curation_coarse=Muscular+System", "results": [{"value": "Adult", "label": "Adult", "count": 20, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=bulk&tissue_curation_coarse=Muscular+System&devstage_curation_coarse=Adult", "selected": false}, {"value": "Embryo", "label": "Embryo", "count": 8, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=bulk&tissue_curation_coarse=Muscular+System&devstage_curation_coarse=Embryo", "selected": false}, {"value": "Larval", "label": "Larval", "count": 7, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=bulk&tissue_curation_coarse=Muscular+System&devstage_curation_coarse=Larval", "selected": false}, {"value": "Juvenile", "label": "Juvenile", "count": 6, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=bulk&tissue_curation_coarse=Muscular+System&devstage_curation_coarse=Juvenile", "selected": false}], "truncated": false}, "devstage_curation": {"name": "devstage_curation", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=bulk&tissue_curation_coarse=Muscular+System", "results": [{"value": "Adult", "label": "Adult", "count": 20, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=bulk&tissue_curation_coarse=Muscular+System&devstage_curation=Adult", "selected": false}, {"value": "Larval", "label": "Larval", "count": 7, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=bulk&tissue_curation_coarse=Muscular+System&devstage_curation=Larval", "selected": false}, {"value": "Juvenile", "label": "Juvenile", "count": 6, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=bulk&tissue_curation_coarse=Muscular+System&devstage_curation=Juvenile", "selected": false}, {"value": "Multi-stage", "label": "Multi-stage", "count": 6, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=bulk&tissue_curation_coarse=Muscular+System&devstage_curation=Multi-stage", "selected": false}, {"value": "Pharyngula", "label": "Pharyngula", "count": 2, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=bulk&tissue_curation_coarse=Muscular+System&devstage_curation=Pharyngula", "selected": false}], "truncated": false}, "tissue_curation_coarse": {"name": "tissue_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=bulk&tissue_curation_coarse=Muscular+System", "results": [{"value": "Muscular System", "label": "Muscular System", "count": 41, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=bulk", "selected": true}], "truncated": false}, "tissue_curation": {"name": "tissue_curation", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=bulk&tissue_curation_coarse=Muscular+System", "results": [{"value": "Muscle", "label": "Muscle", "count": 41, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=bulk&tissue_curation_coarse=Muscular+System&tissue_curation=Muscle", "selected": false}], "truncated": false}, "technology": {"name": "technology", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=bulk&tissue_curation_coarse=Muscular+System", "results": [{"value": "bulk", "label": "bulk", "count": 41, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&tissue_curation_coarse=Muscular+System", "selected": true}], "truncated": false}}, "suggested_facets": [], "next": null, "next_url": null, "private": false, "allow_execute_sql": true, "query_ms": 77.24507698731031}