{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_layout = \"SINGLE\", technology = \"bulk\" and tissue_curation = \"Trunk\"", "rows": [[39771, "SRR2136297", "SRX1125768", "SRS1017739", "SRP061855", "PRJNA291531", "Identification of qkia/c target genes", "GSE71573", "Transcriptome Analysis", "Quaking are RNA binding proteins  which are known to regulate the expression of different genes at the post transcriptional level. Genetic interference with quaking a qkia and quaking c qkic leads to major myofibril defects during zebrafish development  without xxx early muscle differentiation. In order to understand how qkia and qkic jointly regulate myofibril formation  we performed a comparative analysis of the transcriptome of qkia/qkic qkia mutant injected with qkic morpholino versus control embryos. We show that Quaking activity is required for accumulation of the muscle specific tropomyosin 3 transcript  tpm3.1. Whereas interference with tmp3.1 function disrupts myofibril formation  reintroducing tpm3.1 transcripts into embryos with reduced Quaking activity can restore structured myofibrils. Thus  we identify tropomyosin as an essential component in the process of myofibril formation and as a relay downstream of the regulator proteins Quaking. Overall design: Transcriptome of control versus qkia/qkic embryos at 24 26hpf. Biological triplicate were prepared for both condition 3x2 samples.", null, "pubmed:28867488", null, "Qkiac 3", "GSM1838798", null, "tissue:trunk|Stage:embryo 24 26hpf|genotype:qkia / |injection:qkic morpholino", "Qkiac 3", "Before mapping  poly N read tails were trimmed  reads \u226440 bases were removed  and reads with quality mean \u226430 were discarded. To obtain the counts on the exon features  reads were then aligned against the genome using Bowtie version 0.12.9 with arguments  n 2  l 34  e 70  k 2   best. To obtain the counts on the gene features  reads were then aligned against the genome using STAR version 2.4.0j and Ensembl annotation v78. Alignments from reads matching more than once on the reference genome were removed using Java version of samtools. To compute gene expression  Danio rerio Zv9 GFF3 genome annotation version 78 from Ensembl database was used. All overlapping regions between alignments and referenced exons were counted using HTSeq count 0.5.3. To obtain the counts on the exon features  we used the bowtie alignments  excluding the junction reads. HTSeq count was used with arguments: genomictype=exon  attributeid=Name  stranded=no  overlapmode=union  removeambiguouscases=false. To obtain the counts on the gene features  we used the STAR alignments  including the junction reads. HTSeq count was used with arguments: genomictype=exon  stranded=no  overlapmode=union  removeambiguouscases=false and attributeid=Alias where Alias was the corresponding parent gene ID. The sample counts were normalized using DESeq 1.8.3. Statistical treatments and differential analyses were also performed using DESeq 1.8.3 with arguments: disp.est.method=pooled  disp.est.sharing.mode=maximum  disp.est.fit.type=parametric Genome build: Danio rerio Zv9 Supplementary files format and content: tab delimited text files include normalized reads counts for each Sample using DESeq 1.8.3 with arguments: disp.est.method=pooled  disp.est.sharing.mode=maximum  disp.est.fit.type=parametric.", "trunk", "Zebrafish trunks at 24 26hpf were dissected removal of head and yolk  flash frozen on dry ice and stored at  80\u00b0C until RNA extraction.", "total RNA was extracted using the RNeasy Plus Universal Mini kit Qiagen and treated with Dnase. Messenger polyA+ RNAs were purified from 0.7 \u00b5g of total RNA using oligodT. Libraries were prepared using the strand non specific RNA Seq library preparation TruSeq RNA Sample Prep v2 kit Illumina. Libraries were multiplexed by 6 on 2 flowcell lanes. A 50 bp read sequencing was performed on a HiSeq 1500 device Illumina. A mean of 27459238  \u00b1 1611623 million passing Illumina quality filter reads was obtained for each of the 6 samples.", "Embryos resulting from crossing between qkia+/  fish were injected at a cell stage with qkic morpholino or control morpholino 0 6pmol. We let them develop until 24 26hpf  stage where we could morphologically identify control embryos sibling qkia+/+ or qkia+/  with control morpholino and double qkia/c loss of function embryos qkia /  with qkic morpholino.", "Stage:embryo 24 26hpf|genotype:qkia / |injection:qkic morpholino", "GSM1838798", "GSM1838798: Qkiac 3; Danio rerio; RNA Seq", "GSM1838798", null, "1", "total RNA was extracted using the RNeasy Plus Universal Mini kit Qiagen and treated with Dnase. Messenger polyA+ RNAs were purified from 0.7 \u00b5g of total RNA using oligodT. Libraries were prepared using the strand non specific RNA Seq library preparation TruSeq RNA Sample Prep v2 kit Illumina. Libraries were multiplexed by 6 on 2 flowcell lanes. A 50 bp read sequencing was performed on a HiSeq 1500 device Illumina. A mean of 27459238  \u00b1 1611623 million passing Illumina quality filter reads was obtained for each of the 6 samples.", "GEO Accession:GSM1838798", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 1500", null, "SRP061855", null, null, "Sample6_CTTGTA.fastq.bz2", "fastq", 2507001849.0, 49156899.0, "GSM1838798 r1", "0:51", "A:683306529;C:570965534;G:570449436;T:679826815;N:2453535", 51, null, null, null, 683306529, 570965534, 570449436, 679826815, 2453535, "SRX1125768", "SRS1017739", "SRA281148", "GEO", "Plateforme transcriptome, Biologie, Ecole Normale Sup\u00e9rieure", 1, 0.92678, null, 0.08779, null, 0.72892, null, 0.48795, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "France", "2015-07-30", "Pharyngula", "Embryo", "Trunk", "Surface Structure"], [39772, "SRR2136296", "SRX1125767", "SRS1017740", "SRP061855", "PRJNA291531", "Identification of qkia/c target genes", "GSE71573", "Transcriptome Analysis", "Quaking are RNA binding proteins  which are known to regulate the expression of different genes at the post transcriptional level. Genetic interference with quaking a qkia and quaking c qkic leads to major myofibril defects during zebrafish development  without xxx early muscle differentiation. In order to understand how qkia and qkic jointly regulate myofibril formation  we performed a comparative analysis of the transcriptome of qkia/qkic qkia mutant injected with qkic morpholino versus control embryos. We show that Quaking activity is required for accumulation of the muscle specific tropomyosin 3 transcript  tpm3.1. Whereas interference with tmp3.1 function disrupts myofibril formation  reintroducing tpm3.1 transcripts into embryos with reduced Quaking activity can restore structured myofibrils. Thus  we identify tropomyosin as an essential component in the process of myofibril formation and as a relay downstream of the regulator proteins Quaking. Overall design: Transcriptome of control versus qkia/qkic embryos at 24 26hpf. Biological triplicate were prepared for both condition 3x2 samples.", null, "pubmed:28867488", null, "Qkiac 2", "GSM1838797", null, "tissue:trunk|Stage:embryo 24 26hpf|genotype:qkia / |injection:qkic morpholino", "Qkiac 2", "Before mapping  poly N read tails were trimmed  reads \u226440 bases were removed  and reads with quality mean \u226430 were discarded. To obtain the counts on the exon features  reads were then aligned against the genome using Bowtie version 0.12.9 with arguments  n 2  l 34  e 70  k 2   best. To obtain the counts on the gene features  reads were then aligned against the genome using STAR version 2.4.0j and Ensembl annotation v78. Alignments from reads matching more than once on the reference genome were removed using Java version of samtools. To compute gene expression  Danio rerio Zv9 GFF3 genome annotation version 78 from Ensembl database was used. All overlapping regions between alignments and referenced exons were counted using HTSeq count 0.5.3. To obtain the counts on the exon features  we used the bowtie alignments  excluding the junction reads. HTSeq count was used with arguments: genomictype=exon  attributeid=Name  stranded=no  overlapmode=union  removeambiguouscases=false. To obtain the counts on the gene features  we used the STAR alignments  including the junction reads. HTSeq count was used with arguments: genomictype=exon  stranded=no  overlapmode=union  removeambiguouscases=false and attributeid=Alias where Alias was the corresponding parent gene ID. The sample counts were normalized using DESeq 1.8.3. Statistical treatments and differential analyses were also performed using DESeq 1.8.3 with arguments: disp.est.method=pooled  disp.est.sharing.mode=maximum  disp.est.fit.type=parametric Genome build: Danio rerio Zv9 Supplementary files format and content: tab delimited text files include normalized reads counts for each Sample using DESeq 1.8.3 with arguments: disp.est.method=pooled  disp.est.sharing.mode=maximum  disp.est.fit.type=parametric.", "trunk", "Zebrafish trunks at 24 26hpf were dissected removal of head and yolk  flash frozen on dry ice and stored at  80\u00b0C until RNA extraction.", "total RNA was extracted using the RNeasy Plus Universal Mini kit Qiagen and treated with Dnase. Messenger polyA+ RNAs were purified from 0.7 \u00b5g of total RNA using oligodT. Libraries were prepared using the strand non specific RNA Seq library preparation TruSeq RNA Sample Prep v2 kit Illumina. Libraries were multiplexed by 6 on 2 flowcell lanes. A 50 bp read sequencing was performed on a HiSeq 1500 device Illumina. A mean of 27459238  \u00b1 1611623 million passing Illumina quality filter reads was obtained for each of the 6 samples.", "Embryos resulting from crossing between qkia+/  fish were injected at a cell stage with qkic morpholino or control morpholino 0 6pmol. We let them develop until 24 26hpf  stage where we could morphologically identify control embryos sibling qkia+/+ or qkia+/  with control morpholino and double qkia/c loss of function embryos qkia /  with qkic morpholino.", "Stage:embryo 24 26hpf|genotype:qkia / |injection:qkic morpholino", "GSM1838797", "GSM1838797: Qkiac 2; Danio rerio; RNA Seq", "GSM1838797", null, "1", "total RNA was extracted using the RNeasy Plus Universal Mini kit Qiagen and treated with Dnase. Messenger polyA+ RNAs were purified from 0.7 \u00b5g of total RNA using oligodT. Libraries were prepared using the strand non specific RNA Seq library preparation TruSeq RNA Sample Prep v2 kit Illumina. Libraries were multiplexed by 6 on 2 flowcell lanes. A 50 bp read sequencing was performed on a HiSeq 1500 device Illumina. A mean of 27459238  \u00b1 1611623 million passing Illumina quality filter reads was obtained for each of the 6 samples.", "GEO Accession:GSM1838797", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 1500", null, "SRP061855", null, null, "Sample5_CAGATC.fastq.bz2", "fastq", 2850272086.0, 55887688.0, "GSM1838797 r1", "0:51.00", "A:775475703;C:648531668;G:652753738;T:770730439;N:2780538", 51, null, null, null, 775475703, 648531668, 652753738, 770730439, 2780538, "SRX1125767", "SRS1017740", "SRA281148", "GEO", "Plateforme transcriptome, Biologie, Ecole Normale Sup\u00e9rieure", 1, 0.92802, null, 0.08465, null, 0.72744, null, 0.48656, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "France", "2015-07-30", "Pharyngula", "Embryo", "Trunk", "Surface Structure"], [39773, "SRR2136295", "SRX1125766", "SRS1017741", "SRP061855", "PRJNA291531", "Identification of qkia/c target genes", "GSE71573", "Transcriptome Analysis", "Quaking are RNA binding proteins  which are known to regulate the expression of different genes at the post transcriptional level. Genetic interference with quaking a qkia and quaking c qkic leads to major myofibril defects during zebrafish development  without xxx early muscle differentiation. In order to understand how qkia and qkic jointly regulate myofibril formation  we performed a comparative analysis of the transcriptome of qkia/qkic qkia mutant injected with qkic morpholino versus control embryos. We show that Quaking activity is required for accumulation of the muscle specific tropomyosin 3 transcript  tpm3.1. Whereas interference with tmp3.1 function disrupts myofibril formation  reintroducing tpm3.1 transcripts into embryos with reduced Quaking activity can restore structured myofibrils. Thus  we identify tropomyosin as an essential component in the process of myofibril formation and as a relay downstream of the regulator proteins Quaking. Overall design: Transcriptome of control versus qkia/qkic embryos at 24 26hpf. Biological triplicate were prepared for both condition 3x2 samples.", null, "pubmed:28867488", null, "Qkiac 1", "GSM1838796", null, "tissue:trunk|Stage:embryo 24 26hpf|genotype:qkia / |injection:qkic morpholino", "Qkiac 1", "Before mapping  poly N read tails were trimmed  reads \u226440 bases were removed  and reads with quality mean \u226430 were discarded. To obtain the counts on the exon features  reads were then aligned against the genome using Bowtie version 0.12.9 with arguments  n 2  l 34  e 70  k 2   best. To obtain the counts on the gene features  reads were then aligned against the genome using STAR version 2.4.0j and Ensembl annotation v78. Alignments from reads matching more than once on the reference genome were removed using Java version of samtools. To compute gene expression  Danio rerio Zv9 GFF3 genome annotation version 78 from Ensembl database was used. All overlapping regions between alignments and referenced exons were counted using HTSeq count 0.5.3. To obtain the counts on the exon features  we used the bowtie alignments  excluding the junction reads. HTSeq count was used with arguments: genomictype=exon  attributeid=Name  stranded=no  overlapmode=union  removeambiguouscases=false. To obtain the counts on the gene features  we used the STAR alignments  including the junction reads. HTSeq count was used with arguments: genomictype=exon  stranded=no  overlapmode=union  removeambiguouscases=false and attributeid=Alias where Alias was the corresponding parent gene ID. The sample counts were normalized using DESeq 1.8.3. Statistical treatments and differential analyses were also performed using DESeq 1.8.3 with arguments: disp.est.method=pooled  disp.est.sharing.mode=maximum  disp.est.fit.type=parametric Genome build: Danio rerio Zv9 Supplementary files format and content: tab delimited text files include normalized reads counts for each Sample using DESeq 1.8.3 with arguments: disp.est.method=pooled  disp.est.sharing.mode=maximum  disp.est.fit.type=parametric.", "trunk", "Zebrafish trunks at 24 26hpf were dissected removal of head and yolk  flash frozen on dry ice and stored at  80\u00b0C until RNA extraction.", "total RNA was extracted using the RNeasy Plus Universal Mini kit Qiagen and treated with Dnase. Messenger polyA+ RNAs were purified from 0.7 \u00b5g of total RNA using oligodT. Libraries were prepared using the strand non specific RNA Seq library preparation TruSeq RNA Sample Prep v2 kit Illumina. Libraries were multiplexed by 6 on 2 flowcell lanes. A 50 bp read sequencing was performed on a HiSeq 1500 device Illumina. A mean of 27459238  \u00b1 1611623 million passing Illumina quality filter reads was obtained for each of the 6 samples.", "Embryos resulting from crossing between qkia+/  fish were injected at a cell stage with qkic morpholino or control morpholino 0 6pmol. We let them develop until 24 26hpf  stage where we could morphologically identify control embryos sibling qkia+/+ or qkia+/  with control morpholino and double qkia/c loss of function embryos qkia /  with qkic morpholino.", "Stage:embryo 24 26hpf|genotype:qkia / |injection:qkic morpholino", "GSM1838796", "GSM1838796: Qkiac 1; Danio rerio; RNA Seq", "GSM1838796", null, "1", "total RNA was extracted using the RNeasy Plus Universal Mini kit Qiagen and treated with Dnase. Messenger polyA+ RNAs were purified from 0.7 \u00b5g of total RNA using oligodT. Libraries were prepared using the strand non specific RNA Seq library preparation TruSeq RNA Sample Prep v2 kit Illumina. Libraries were multiplexed by 6 on 2 flowcell lanes. A 50 bp read sequencing was performed on a HiSeq 1500 device Illumina. A mean of 27459238  \u00b1 1611623 million passing Illumina quality filter reads was obtained for each of the 6 samples.", "GEO Accession:GSM1838796", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 1500", null, "SRP061855", null, null, "Sample4_GCCAAT.fastq.bz2", "fastq", 2881827420.0, 56506420.0, "GSM1838796 r1", "0:51", "A:782512581;C:658453854;G:659856487;T:778195522;N:2808976", 51, null, null, null, 782512581, 658453854, 659856487, 778195522, 2808976, "SRX1125766", "SRS1017741", "SRA281148", "GEO", "Plateforme transcriptome, Biologie, Ecole Normale Sup\u00e9rieure", 1, 0.92629, null, 0.08316, null, 0.7276, null, 0.47801, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "France", "2015-07-30", "Pharyngula", "Embryo", "Trunk", "Surface Structure"], [39774, "SRR2136294", "SRX1125765", "SRS1017742", "SRP061855", "PRJNA291531", "Identification of qkia/c target genes", "GSE71573", "Transcriptome Analysis", "Quaking are RNA binding proteins  which are known to regulate the expression of different genes at the post transcriptional level. Genetic interference with quaking a qkia and quaking c qkic leads to major myofibril defects during zebrafish development  without xxx early muscle differentiation. In order to understand how qkia and qkic jointly regulate myofibril formation  we performed a comparative analysis of the transcriptome of qkia/qkic qkia mutant injected with qkic morpholino versus control embryos. We show that Quaking activity is required for accumulation of the muscle specific tropomyosin 3 transcript  tpm3.1. Whereas interference with tmp3.1 function disrupts myofibril formation  reintroducing tpm3.1 transcripts into embryos with reduced Quaking activity can restore structured myofibrils. Thus  we identify tropomyosin as an essential component in the process of myofibril formation and as a relay downstream of the regulator proteins Quaking. Overall design: Transcriptome of control versus qkia/qkic embryos at 24 26hpf. Biological triplicate were prepared for both condition 3x2 samples.", null, "pubmed:28867488", null, "Control 3", "GSM1838795", null, "tissue:trunk|Stage:embryo 24 26hpf|genotype:qkia+/+ or qkia+/ |injection:control morpholino", "Control 3", "Before mapping  poly N read tails were trimmed  reads \u226440 bases were removed  and reads with quality mean \u226430 were discarded. To obtain the counts on the exon features  reads were then aligned against the genome using Bowtie version 0.12.9 with arguments  n 2  l 34  e 70  k 2   best. To obtain the counts on the gene features  reads were then aligned against the genome using STAR version 2.4.0j and Ensembl annotation v78. Alignments from reads matching more than once on the reference genome were removed using Java version of samtools. To compute gene expression  Danio rerio Zv9 GFF3 genome annotation version 78 from Ensembl database was used. All overlapping regions between alignments and referenced exons were counted using HTSeq count 0.5.3. To obtain the counts on the exon features  we used the bowtie alignments  excluding the junction reads. HTSeq count was used with arguments: genomictype=exon  attributeid=Name  stranded=no  overlapmode=union  removeambiguouscases=false. To obtain the counts on the gene features  we used the STAR alignments  including the junction reads. HTSeq count was used with arguments: genomictype=exon  stranded=no  overlapmode=union  removeambiguouscases=false and attributeid=Alias where Alias was the corresponding parent gene ID. The sample counts were normalized using DESeq 1.8.3. Statistical treatments and differential analyses were also performed using DESeq 1.8.3 with arguments: disp.est.method=pooled  disp.est.sharing.mode=maximum  disp.est.fit.type=parametric Genome build: Danio rerio Zv9 Supplementary files format and content: tab delimited text files include normalized reads counts for each Sample using DESeq 1.8.3 with arguments: disp.est.method=pooled  disp.est.sharing.mode=maximum  disp.est.fit.type=parametric.", "trunk", "Zebrafish trunks at 24 26hpf were dissected removal of head and yolk  flash frozen on dry ice and stored at  80\u00b0C until RNA extraction.", "total RNA was extracted using the RNeasy Plus Universal Mini kit Qiagen and treated with Dnase. Messenger polyA+ RNAs were purified from 0.7 \u00b5g of total RNA using oligodT. Libraries were prepared using the strand non specific RNA Seq library preparation TruSeq RNA Sample Prep v2 kit Illumina. Libraries were multiplexed by 6 on 2 flowcell lanes. A 50 bp read sequencing was performed on a HiSeq 1500 device Illumina. A mean of 27459238  \u00b1 1611623 million passing Illumina quality filter reads was obtained for each of the 6 samples.", "Embryos resulting from crossing between qkia+/  fish were injected at a cell stage with qkic morpholino or control morpholino 0 6pmol. We let them develop until 24 26hpf  stage where we could morphologically identify control embryos sibling qkia+/+ or qkia+/  with control morpholino and double qkia/c loss of function embryos qkia /  with qkic morpholino.", "Stage:embryo 24 26hpf|genotype:qkia+/+ or qkia+/ |injection:control morpholino", "GSM1838795", "GSM1838795: Control 3; Danio rerio; RNA Seq", "GSM1838795", null, "1", "total RNA was extracted using the RNeasy Plus Universal Mini kit Qiagen and treated with Dnase. Messenger polyA+ RNAs were purified from 0.7 \u00b5g of total RNA using oligodT. Libraries were prepared using the strand non specific RNA Seq library preparation TruSeq RNA Sample Prep v2 kit Illumina. Libraries were multiplexed by 6 on 2 flowcell lanes. A 50 bp read sequencing was performed on a HiSeq 1500 device Illumina. A mean of 27459238  \u00b1 1611623 million passing Illumina quality filter reads was obtained for each of the 6 samples.", "GEO Accession:GSM1838795", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 1500", null, "SRP061855", null, null, "Sample3_ACAGTG.fastq.bz2", "fastq", 2611892782.0, 51213584.0, "GSM1838795 r1", "0:51.00", "A:707525221;C:599202602;G:597562199;T:705047589;N:2555171", 51, null, null, null, 707525221, 599202602, 597562199, 705047589, 2555171, "SRX1125765", "SRS1017742", "SRA281148", "GEO", "Plateforme transcriptome, Biologie, Ecole Normale Sup\u00e9rieure", 1, 0.9282, null, 0.09007, null, 0.72147, null, 0.47387, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "France", "2015-07-30", "Pharyngula", "Embryo", "Trunk", "Surface Structure"], [39775, "SRR2136293", "SRX1125764", "SRS1017743", "SRP061855", "PRJNA291531", "Identification of qkia/c target genes", "GSE71573", "Transcriptome Analysis", "Quaking are RNA binding proteins  which are known to regulate the expression of different genes at the post transcriptional level. Genetic interference with quaking a qkia and quaking c qkic leads to major myofibril defects during zebrafish development  without xxx early muscle differentiation. In order to understand how qkia and qkic jointly regulate myofibril formation  we performed a comparative analysis of the transcriptome of qkia/qkic qkia mutant injected with qkic morpholino versus control embryos. We show that Quaking activity is required for accumulation of the muscle specific tropomyosin 3 transcript  tpm3.1. Whereas interference with tmp3.1 function disrupts myofibril formation  reintroducing tpm3.1 transcripts into embryos with reduced Quaking activity can restore structured myofibrils. Thus  we identify tropomyosin as an essential component in the process of myofibril formation and as a relay downstream of the regulator proteins Quaking. Overall design: Transcriptome of control versus qkia/qkic embryos at 24 26hpf. Biological triplicate were prepared for both condition 3x2 samples.", null, "pubmed:28867488", null, "Control 2", "GSM1838794", null, "tissue:trunk|Stage:embryo 24 26hpf|genotype:qkia+/+ or qkia+/ |injection:control morpholino", "Control 2", "Before mapping  poly N read tails were trimmed  reads \u226440 bases were removed  and reads with quality mean \u226430 were discarded. To obtain the counts on the exon features  reads were then aligned against the genome using Bowtie version 0.12.9 with arguments  n 2  l 34  e 70  k 2   best. To obtain the counts on the gene features  reads were then aligned against the genome using STAR version 2.4.0j and Ensembl annotation v78. Alignments from reads matching more than once on the reference genome were removed using Java version of samtools. To compute gene expression  Danio rerio Zv9 GFF3 genome annotation version 78 from Ensembl database was used. All overlapping regions between alignments and referenced exons were counted using HTSeq count 0.5.3. To obtain the counts on the exon features  we used the bowtie alignments  excluding the junction reads. HTSeq count was used with arguments: genomictype=exon  attributeid=Name  stranded=no  overlapmode=union  removeambiguouscases=false. To obtain the counts on the gene features  we used the STAR alignments  including the junction reads. HTSeq count was used with arguments: genomictype=exon  stranded=no  overlapmode=union  removeambiguouscases=false and attributeid=Alias where Alias was the corresponding parent gene ID. The sample counts were normalized using DESeq 1.8.3. Statistical treatments and differential analyses were also performed using DESeq 1.8.3 with arguments: disp.est.method=pooled  disp.est.sharing.mode=maximum  disp.est.fit.type=parametric Genome build: Danio rerio Zv9 Supplementary files format and content: tab delimited text files include normalized reads counts for each Sample using DESeq 1.8.3 with arguments: disp.est.method=pooled  disp.est.sharing.mode=maximum  disp.est.fit.type=parametric.", "trunk", "Zebrafish trunks at 24 26hpf were dissected removal of head and yolk  flash frozen on dry ice and stored at  80\u00b0C until RNA extraction.", "total RNA was extracted using the RNeasy Plus Universal Mini kit Qiagen and treated with Dnase. Messenger polyA+ RNAs were purified from 0.7 \u00b5g of total RNA using oligodT. Libraries were prepared using the strand non specific RNA Seq library preparation TruSeq RNA Sample Prep v2 kit Illumina. Libraries were multiplexed by 6 on 2 flowcell lanes. A 50 bp read sequencing was performed on a HiSeq 1500 device Illumina. A mean of 27459238  \u00b1 1611623 million passing Illumina quality filter reads was obtained for each of the 6 samples.", "Embryos resulting from crossing between qkia+/  fish were injected at a cell stage with qkic morpholino or control morpholino 0 6pmol. We let them develop until 24 26hpf  stage where we could morphologically identify control embryos sibling qkia+/+ or qkia+/  with control morpholino and double qkia/c loss of function embryos qkia /  with qkic morpholino.", "Stage:embryo 24 26hpf|genotype:qkia+/+ or qkia+/ |injection:control morpholino", "GSM1838794", "GSM1838794: Control 2; Danio rerio; RNA Seq", "GSM1838794", null, "1", "total RNA was extracted using the RNeasy Plus Universal Mini kit Qiagen and treated with Dnase. Messenger polyA+ RNAs were purified from 0.7 \u00b5g of total RNA using oligodT. Libraries were prepared using the strand non specific RNA Seq library preparation TruSeq RNA Sample Prep v2 kit Illumina. Libraries were multiplexed by 6 on 2 flowcell lanes. A 50 bp read sequencing was performed on a HiSeq 1500 device Illumina. A mean of 27459238  \u00b1 1611623 million passing Illumina quality filter reads was obtained for each of the 6 samples.", "GEO Accession:GSM1838794", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 1500", null, "SRP061855", null, null, "Sample2_TGACCA.fastq.bz2", "fastq", 2686989417.0, 52686067.0, "GSM1838794 r1", "0:51", "A:728607816;C:615847292;G:614033432;T:725881768;N:2619109", 51, null, null, null, 728607816, 615847292, 614033432, 725881768, 2619109, "SRX1125764", "SRS1017743", "SRA281148", "GEO", "Plateforme transcriptome, Biologie, Ecole Normale Sup\u00e9rieure", 1, 0.92483, null, 0.09787, null, 0.7203, null, 0.45884, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "France", "2015-07-30", "Pharyngula", "Embryo", "Trunk", "Surface Structure"], [39776, "SRR2136292", "SRX1125763", "SRS1017744", "SRP061855", "PRJNA291531", "Identification of qkia/c target genes", "GSE71573", "Transcriptome Analysis", "Quaking are RNA binding proteins  which are known to regulate the expression of different genes at the post transcriptional level. Genetic interference with quaking a qkia and quaking c qkic leads to major myofibril defects during zebrafish development  without xxx early muscle differentiation. In order to understand how qkia and qkic jointly regulate myofibril formation  we performed a comparative analysis of the transcriptome of qkia/qkic qkia mutant injected with qkic morpholino versus control embryos. We show that Quaking activity is required for accumulation of the muscle specific tropomyosin 3 transcript  tpm3.1. Whereas interference with tmp3.1 function disrupts myofibril formation  reintroducing tpm3.1 transcripts into embryos with reduced Quaking activity can restore structured myofibrils. Thus  we identify tropomyosin as an essential component in the process of myofibril formation and as a relay downstream of the regulator proteins Quaking. Overall design: Transcriptome of control versus qkia/qkic embryos at 24 26hpf. Biological triplicate were prepared for both condition 3x2 samples.", null, "pubmed:28867488", null, "Control 1", "GSM1838793", null, "tissue:trunk|Stage:embryo 24 26hpf|genotype:qkia+/+ or qkia+/ |injection:control morpholino", "Control 1", "Before mapping  poly N read tails were trimmed  reads \u226440 bases were removed  and reads with quality mean \u226430 were discarded. To obtain the counts on the exon features  reads were then aligned against the genome using Bowtie version 0.12.9 with arguments  n 2  l 34  e 70  k 2   best. To obtain the counts on the gene features  reads were then aligned against the genome using STAR version 2.4.0j and Ensembl annotation v78. Alignments from reads matching more than once on the reference genome were removed using Java version of samtools. To compute gene expression  Danio rerio Zv9 GFF3 genome annotation version 78 from Ensembl database was used. All overlapping regions between alignments and referenced exons were counted using HTSeq count 0.5.3. To obtain the counts on the exon features  we used the bowtie alignments  excluding the junction reads. HTSeq count was used with arguments: genomictype=exon  attributeid=Name  stranded=no  overlapmode=union  removeambiguouscases=false. To obtain the counts on the gene features  we used the STAR alignments  including the junction reads. HTSeq count was used with arguments: genomictype=exon  stranded=no  overlapmode=union  removeambiguouscases=false and attributeid=Alias where Alias was the corresponding parent gene ID. The sample counts were normalized using DESeq 1.8.3. Statistical treatments and differential analyses were also performed using DESeq 1.8.3 with arguments: disp.est.method=pooled  disp.est.sharing.mode=maximum  disp.est.fit.type=parametric Genome build: Danio rerio Zv9 Supplementary files format and content: tab delimited text files include normalized reads counts for each Sample using DESeq 1.8.3 with arguments: disp.est.method=pooled  disp.est.sharing.mode=maximum  disp.est.fit.type=parametric.", "trunk", "Zebrafish trunks at 24 26hpf were dissected removal of head and yolk  flash frozen on dry ice and stored at  80\u00b0C until RNA extraction.", "total RNA was extracted using the RNeasy Plus Universal Mini kit Qiagen and treated with Dnase. Messenger polyA+ RNAs were purified from 0.7 \u00b5g of total RNA using oligodT. Libraries were prepared using the strand non specific RNA Seq library preparation TruSeq RNA Sample Prep v2 kit Illumina. Libraries were multiplexed by 6 on 2 flowcell lanes. A 50 bp read sequencing was performed on a HiSeq 1500 device Illumina. A mean of 27459238  \u00b1 1611623 million passing Illumina quality filter reads was obtained for each of the 6 samples.", "Embryos resulting from crossing between qkia+/  fish were injected at a cell stage with qkic morpholino or control morpholino 0 6pmol. We let them develop until 24 26hpf  stage where we could morphologically identify control embryos sibling qkia+/+ or qkia+/  with control morpholino and double qkia/c loss of function embryos qkia /  with qkic morpholino.", "Stage:embryo 24 26hpf|genotype:qkia+/+ or qkia+/ |injection:control morpholino", "GSM1838793", "GSM1838793: Control 1; Danio rerio; RNA Seq", "GSM1838793", null, "1", "total RNA was extracted using the RNeasy Plus Universal Mini kit Qiagen and treated with Dnase. Messenger polyA+ RNAs were purified from 0.7 \u00b5g of total RNA using oligodT. Libraries were prepared using the strand non specific RNA Seq library preparation TruSeq RNA Sample Prep v2 kit Illumina. Libraries were multiplexed by 6 on 2 flowcell lanes. A 50 bp read sequencing was performed on a HiSeq 1500 device Illumina. A mean of 27459238  \u00b1 1611623 million passing Illumina quality filter reads was obtained for each of the 6 samples.", "GEO Accession:GSM1838793", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 1500", null, "SRP061855", null, null, "Sample1_CGATGT.fastq.bz2", "fastq", 2920348075.0, 57261727.0, "GSM1838793 r1", "0:51.00", "A:788971393;C:671861209;G:669575375;T:787095383;N:2844715", 51, null, null, null, 788971393, 671861209, 669575375, 787095383, 2844715, "SRX1125763", "SRS1017744", "SRA281148", "GEO", "Plateforme transcriptome, Biologie, Ecole Normale Sup\u00e9rieure", 1, 0.92794, null, 0.09884, null, 0.71711, null, 0.4721, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "France", "2015-07-30", "Pharyngula", "Embryo", "Trunk", "Surface Structure"], [48110, "SRR7049634", "SRX3981085", "SRS3205926", "SRP141415", "PRJNA451191", "RNA seq of zebrafish ptk7 mutants with severe spinal curvature and heterozygous straight siblings", "PRJNA451191", "Other", "To identify molecular mechanisms underlying scoliosis spine curvature  we performed next generation RNA sequencing on ptk7 mutant vs. ptk7/+ sibling fish  at an age correlating with severe scoliosis progression 1 cm length. Because the tissue of idiopathic scoliosis origin remains unknown  RNA Seq was performed on bulk RNA samples collected from the entire trunk and tail heads were removed at the level of the gill to eliminate signals associated with abnormal Ptk7 function in the brain.", null, null, null, null, "ptk7/+ 11", null, "isolate:fish #11|age:21 dpf|sex:NA|tissue:trunk|genotype:ptk7/+|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA sequencing of Danio rerio: scoliosis trunk", "ptk7 het 11", "ptk7 het 11", "Total RNA extraction was preformed using the Qiagen RNeasy kit following the manufacturer's instructions Qiagen. RNA sample quality was assessed using an Agilent Bioanalyzer. Library prep and subsequent sequencing was performed by The Centre for Applied Genomics at The Hospital for Sick Children SickKids using the NEBNext stranded RNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP141415", null, "loader:fastq load.py", "Ptk7_het_straight_11_R2.fastq.gz Ptk7_het_straight_11_R1.fastq", "fastq fastq", 10112242392.0, 40127946.0, "Ptk7 het straight 11 R2.fastq.gz", "0:126 1:126", "A:2526420409;C:2531445826;G:2613534392;T:2439160326;N:1681439", 126, 126, null, null, 2526420409, 2531445826, 2613534392, 2439160326, 1681439, "SRX3981085", "SRS3205926", "SRA693409", "The Hospital for Sick Children|Developmental and Stem Cell Biology", "The Hospital for Sick Children", 2, 0.83476, 0.83453, 0.10235, 0.10313, 0.73614, 0.73799, 0.46442, 0.52808, 126, 126, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "Canada", "2018-05-16", "Larval", "Larval", "Trunk", "Surface Structure"], [70891, "SRR20869073", "SRX16888179", "SRS14475663", "SRP390172", "PRJNA866536", "X linked myotubular myopathy is associated with epigenetic alterations and is ameliorated by HDAC inhibition", "GSE210642", "Other", "X linked myotubular myopathy XLMTM is a fatal neuromuscular disorder caused by loss of function mutations in MTM1 . At present  there are no directed therapies for XLMTM  and incomplete understanding of disease pathomechanisms. To address these knowledge gaps  we performed a drug screen in mtm1 mutant zebrafish andidentified four positive hits  including valproic acid  which functions as a potent suppressor of the mtm1 zebrafish phenotype via HDAC inhibition. We translated these findings to a mouse XLMTM model  and showed that valproic acid ameliorates the murine phenotype. Overall design: Zebrafish: At 1 dpf  embryos from single pair in crossings of mtm1+/zf711 adults were divided equally into three chemical treatment groups: DMSO  sodium valproate VPA  or trichostatin A. For tissue collection  the posterior section of larvae and fin fold tissues was dissected and snap frozen on dry ice at 4 dpf. A total of n=6 10 larvae per pool per condition with 5 biological replicates were used for RNA extraction.  Mice: Bulk RNA sequencing was performed on RNA extracts from tibialis anterior muscle from 35 dpf Mtm1KO and WT mice  either treated with PBS or valproic acid VPA starting at 21 days.", null, "pubmed:35844027", null, "Mtm1 KO  DMSO treatment  zebrafish  rep4", "GSM6434013", null, "source name:posterior half of larvae|tissue:posterior half of larvae|genotype:Mtm1 KO|treatment:DMSO treatment", "Mtm1 KO  DMSO treatment  zebrafish  rep4", "Sequencing reads were aligned to the mouseGRCm38 /zebrafish genomeGRCz9 using STAR. Read quality was assessed with FastQC  and adaptors were trimmed from reads using Cutadapt. STAR gene level counts ReadsPerGene.out.tab files were used for differential expression with DESeq2 package Assembly: Zebrafish: GRCz9 / Mus musculus: GRCm38 Supplementary files format and content: tab delimited text files include the raw count values for each Sample. Rows = genes; Columns = samples.", "posterior half of larvae", null, "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer\u2019s protocol Zebrafish: RNA libraries were generated using the QuantSeq 3\u2019 mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "tissue:posterior half of larvae|genotype:Mtm1 KO|treatment:DMSO treatment", "GSM6434013", "GSM6434013: Mtm1 KO  DMSO treatment  zebrafish  rep4; Danio rerio; RNA Seq", "GSM6434013 r1", "GSM6434013", "1", "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer's protocol Zebrafish: RNA libraries were generated using the QuantSeq three prime mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP390172", null, null, "WL1504_KY23_168_35_R1.fastq.gz", "fastq", 819472624.0, 12051068.0, "GSM6434013 r1", "0:68 1:0", "A:253867899;C:150713999;G:186967145;T:227898369;N:25212", 68, 0, null, null, 253867899, 150713999, 186967145, 227898369, 25212, "SRX16888179", "SRS14475663", "SRA1470408", "Hospital for Sick Children", "Hospital for Sick Children", 1, 0.84057, null, 0.09126, null, 0.81393, null, 0.5072, null, 68, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "lexogen", "bulk", "bulk", "bulk", null, "Canada", "2022-08-05", "Larval", "Larval", "Trunk", "Surface Structure"], [70892, "SRR20869074", "SRX16888178", "SRS14475662", "SRP390172", "PRJNA866536", "X linked myotubular myopathy is associated with epigenetic alterations and is ameliorated by HDAC inhibition", "GSE210642", "Other", "X linked myotubular myopathy XLMTM is a fatal neuromuscular disorder caused by loss of function mutations in MTM1 . At present  there are no directed therapies for XLMTM  and incomplete understanding of disease pathomechanisms. To address these knowledge gaps  we performed a drug screen in mtm1 mutant zebrafish andidentified four positive hits  including valproic acid  which functions as a potent suppressor of the mtm1 zebrafish phenotype via HDAC inhibition. We translated these findings to a mouse XLMTM model  and showed that valproic acid ameliorates the murine phenotype. Overall design: Zebrafish: At 1 dpf  embryos from single pair in crossings of mtm1+/zf711 adults were divided equally into three chemical treatment groups: DMSO  sodium valproate VPA  or trichostatin A. For tissue collection  the posterior section of larvae and fin fold tissues was dissected and snap frozen on dry ice at 4 dpf. A total of n=6 10 larvae per pool per condition with 5 biological replicates were used for RNA extraction.  Mice: Bulk RNA sequencing was performed on RNA extracts from tibialis anterior muscle from 35 dpf Mtm1KO and WT mice  either treated with PBS or valproic acid VPA starting at 21 days.", null, "pubmed:35844027", null, "Mtm1 KO  DMSO treatment  zebrafish  rep3", "GSM6434012", null, "source name:posterior half of larvae|tissue:posterior half of larvae|genotype:Mtm1 KO|treatment:DMSO treatment", "Mtm1 KO  DMSO treatment  zebrafish  rep3", "Sequencing reads were aligned to the mouseGRCm38 /zebrafish genomeGRCz9 using STAR. Read quality was assessed with FastQC  and adaptors were trimmed from reads using Cutadapt. STAR gene level counts ReadsPerGene.out.tab files were used for differential expression with DESeq2 package Assembly: Zebrafish: GRCz9 / Mus musculus: GRCm38 Supplementary files format and content: tab delimited text files include the raw count values for each Sample. Rows = genes; Columns = samples.", "posterior half of larvae", null, "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer\u2019s protocol Zebrafish: RNA libraries were generated using the QuantSeq 3\u2019 mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "tissue:posterior half of larvae|genotype:Mtm1 KO|treatment:DMSO treatment", "GSM6434012", "GSM6434012: Mtm1 KO  DMSO treatment  zebrafish  rep3; Danio rerio; RNA Seq", "GSM6434012 r1", "GSM6434012", "1", "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer's protocol Zebrafish: RNA libraries were generated using the QuantSeq three prime mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP390172", null, null, "WL1503_KY23_168_34_R1.fastq.gz", "fastq", 942579960.0, 13861470.0, "GSM6434012 r1", "0:68 1:0", "A:286773879;C:173045305;G:212203970;T:270527789;N:29017", 68, 0, null, null, 286773879, 173045305, 212203970, 270527789, 29017, "SRX16888178", "SRS14475662", "SRA1470408", "Hospital for Sick Children", "Hospital for Sick Children", 1, 0.85221, null, 0.07868, null, 0.802, null, 0.517, null, 68, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "lexogen", "bulk", "bulk", "bulk", null, "Canada", "2022-08-05", "Larval", "Larval", "Trunk", "Surface Structure"], [70893, "SRR20869075", "SRX16888177", "SRS14475661", "SRP390172", "PRJNA866536", "X linked myotubular myopathy is associated with epigenetic alterations and is ameliorated by HDAC inhibition", "GSE210642", "Other", "X linked myotubular myopathy XLMTM is a fatal neuromuscular disorder caused by loss of function mutations in MTM1 . At present  there are no directed therapies for XLMTM  and incomplete understanding of disease pathomechanisms. To address these knowledge gaps  we performed a drug screen in mtm1 mutant zebrafish andidentified four positive hits  including valproic acid  which functions as a potent suppressor of the mtm1 zebrafish phenotype via HDAC inhibition. We translated these findings to a mouse XLMTM model  and showed that valproic acid ameliorates the murine phenotype. Overall design: Zebrafish: At 1 dpf  embryos from single pair in crossings of mtm1+/zf711 adults were divided equally into three chemical treatment groups: DMSO  sodium valproate VPA  or trichostatin A. For tissue collection  the posterior section of larvae and fin fold tissues was dissected and snap frozen on dry ice at 4 dpf. A total of n=6 10 larvae per pool per condition with 5 biological replicates were used for RNA extraction.  Mice: Bulk RNA sequencing was performed on RNA extracts from tibialis anterior muscle from 35 dpf Mtm1KO and WT mice  either treated with PBS or valproic acid VPA starting at 21 days.", null, "pubmed:35844027", null, "Mtm1 KO  DMSO treatment  zebrafish  rep2", "GSM6434011", null, "source name:posterior half of larvae|tissue:posterior half of larvae|genotype:Mtm1 KO|treatment:DMSO treatment", "Mtm1 KO  DMSO treatment  zebrafish  rep2", "Sequencing reads were aligned to the mouseGRCm38 /zebrafish genomeGRCz9 using STAR. Read quality was assessed with FastQC  and adaptors were trimmed from reads using Cutadapt. STAR gene level counts ReadsPerGene.out.tab files were used for differential expression with DESeq2 package Assembly: Zebrafish: GRCz9 / Mus musculus: GRCm38 Supplementary files format and content: tab delimited text files include the raw count values for each Sample. Rows = genes; Columns = samples.", "posterior half of larvae", null, "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer\u2019s protocol Zebrafish: RNA libraries were generated using the QuantSeq 3\u2019 mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "tissue:posterior half of larvae|genotype:Mtm1 KO|treatment:DMSO treatment", "GSM6434011", "GSM6434011: Mtm1 KO  DMSO treatment  zebrafish  rep2; Danio rerio; RNA Seq", "GSM6434011 r1", "GSM6434011", "1", "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer's protocol Zebrafish: RNA libraries were generated using the QuantSeq three prime mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP390172", null, null, "WL1502_KY23_168_33_R1.fastq.gz", "fastq", 956592516.0, 14067537.0, "GSM6434011 r1", "0:68 1:0", "A:313998032;C:166431578;G:204849712;T:271283994;N:29200", 68, 0, null, null, 313998032, 166431578, 204849712, 271283994, 29200, "SRX16888177", "SRS14475661", "SRA1470408", "Hospital for Sick Children", "Hospital for Sick Children", 1, 0.76427, null, 0.08867, null, 0.8216, null, 0.47678, null, 68, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "lexogen", "bulk", "bulk", "bulk", null, "Canada", "2022-08-05", "Larval", "Larval", "Trunk", "Surface Structure"], [70894, "SRR20869076", "SRX16888176", "SRS14475660", "SRP390172", "PRJNA866536", "X linked myotubular myopathy is associated with epigenetic alterations and is ameliorated by HDAC inhibition", "GSE210642", "Other", "X linked myotubular myopathy XLMTM is a fatal neuromuscular disorder caused by loss of function mutations in MTM1 . At present  there are no directed therapies for XLMTM  and incomplete understanding of disease pathomechanisms. To address these knowledge gaps  we performed a drug screen in mtm1 mutant zebrafish andidentified four positive hits  including valproic acid  which functions as a potent suppressor of the mtm1 zebrafish phenotype via HDAC inhibition. We translated these findings to a mouse XLMTM model  and showed that valproic acid ameliorates the murine phenotype. Overall design: Zebrafish: At 1 dpf  embryos from single pair in crossings of mtm1+/zf711 adults were divided equally into three chemical treatment groups: DMSO  sodium valproate VPA  or trichostatin A. For tissue collection  the posterior section of larvae and fin fold tissues was dissected and snap frozen on dry ice at 4 dpf. A total of n=6 10 larvae per pool per condition with 5 biological replicates were used for RNA extraction.  Mice: Bulk RNA sequencing was performed on RNA extracts from tibialis anterior muscle from 35 dpf Mtm1KO and WT mice  either treated with PBS or valproic acid VPA starting at 21 days.", null, "pubmed:35844027", null, "Mtm1 KO  DMSO treatment  zebrafish  rep1", "GSM6434010", null, "source name:posterior half of larvae|tissue:posterior half of larvae|genotype:Mtm1 KO|treatment:DMSO treatment", "Mtm1 KO  DMSO treatment  zebrafish  rep1", "Sequencing reads were aligned to the mouseGRCm38 /zebrafish genomeGRCz9 using STAR. Read quality was assessed with FastQC  and adaptors were trimmed from reads using Cutadapt. STAR gene level counts ReadsPerGene.out.tab files were used for differential expression with DESeq2 package Assembly: Zebrafish: GRCz9 / Mus musculus: GRCm38 Supplementary files format and content: tab delimited text files include the raw count values for each Sample. Rows = genes; Columns = samples.", "posterior half of larvae", null, "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer\u2019s protocol Zebrafish: RNA libraries were generated using the QuantSeq 3\u2019 mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "tissue:posterior half of larvae|genotype:Mtm1 KO|treatment:DMSO treatment", "GSM6434010", "GSM6434010: Mtm1 KO  DMSO treatment  zebrafish  rep1; Danio rerio; RNA Seq", "GSM6434010 r1", "GSM6434010", "1", "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer's protocol Zebrafish: RNA libraries were generated using the QuantSeq three prime mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP390172", null, null, "WL1500_KY23_168_31_R1.fastq.gz", "fastq", 830931984.0, 12219588.0, "GSM6434010 r1", "0:68 1:0", "A:284740908;C:147201926;G:181724951;T:217238742;N:25457", 68, 0, null, null, 284740908, 147201926, 181724951, 217238742, 25457, "SRX16888176", "SRS14475660", "SRA1470408", "Hospital for Sick Children", "Hospital for Sick Children", 1, 0.76332, null, 0.10117, null, 0.82069, null, 0.54485, null, 68, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "lexogen", "bulk", "bulk", "bulk", null, "Canada", "2022-08-05", "Larval", "Larval", "Trunk", "Surface Structure"], [70895, "SRR20869077", "SRX16888175", "SRS14475659", "SRP390172", "PRJNA866536", "X linked myotubular myopathy is associated with epigenetic alterations and is ameliorated by HDAC inhibition", "GSE210642", "Other", "X linked myotubular myopathy XLMTM is a fatal neuromuscular disorder caused by loss of function mutations in MTM1 . At present  there are no directed therapies for XLMTM  and incomplete understanding of disease pathomechanisms. To address these knowledge gaps  we performed a drug screen in mtm1 mutant zebrafish andidentified four positive hits  including valproic acid  which functions as a potent suppressor of the mtm1 zebrafish phenotype via HDAC inhibition. We translated these findings to a mouse XLMTM model  and showed that valproic acid ameliorates the murine phenotype. Overall design: Zebrafish: At 1 dpf  embryos from single pair in crossings of mtm1+/zf711 adults were divided equally into three chemical treatment groups: DMSO  sodium valproate VPA  or trichostatin A. For tissue collection  the posterior section of larvae and fin fold tissues was dissected and snap frozen on dry ice at 4 dpf. A total of n=6 10 larvae per pool per condition with 5 biological replicates were used for RNA extraction.  Mice: Bulk RNA sequencing was performed on RNA extracts from tibialis anterior muscle from 35 dpf Mtm1KO and WT mice  either treated with PBS or valproic acid VPA starting at 21 days.", null, "pubmed:35844027", null, "HET  DMSO treatment  zebrafish  rep5", "GSM6434009", null, "source name:posterior half of larvae|tissue:posterior half of larvae|genotype:HET|treatment:DMSO treatment", "HET  DMSO treatment  zebrafish  rep5", "Sequencing reads were aligned to the mouseGRCm38 /zebrafish genomeGRCz9 using STAR. Read quality was assessed with FastQC  and adaptors were trimmed from reads using Cutadapt. STAR gene level counts ReadsPerGene.out.tab files were used for differential expression with DESeq2 package Assembly: Zebrafish: GRCz9 / Mus musculus: GRCm38 Supplementary files format and content: tab delimited text files include the raw count values for each Sample. Rows = genes; Columns = samples.", "posterior half of larvae", null, "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer\u2019s protocol Zebrafish: RNA libraries were generated using the QuantSeq 3\u2019 mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "tissue:posterior half of larvae|genotype:HET|treatment:DMSO treatment", "GSM6434009", "GSM6434009: HET  DMSO treatment  zebrafish  rep5; Danio rerio; RNA Seq", "GSM6434009 r1", "GSM6434009", "1", "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer's protocol Zebrafish: RNA libraries were generated using the QuantSeq three prime mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP390172", null, null, "WL1499_KY23_168_30_R1.fastq.gz", "fastq", 879671936.0, 12936352.0, "GSM6434009 r1", "0:68 1:0", "A:287361625;C:160168036;G:201822099;T:230293138;N:27038", 68, 0, null, null, 287361625, 160168036, 201822099, 230293138, 27038, "SRX16888175", "SRS14475659", "SRA1470408", "Hospital for Sick Children", "Hospital for Sick Children", 1, 0.79783, null, 0.11832, null, 0.81858, null, 0.53184, null, 68, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "lexogen", "bulk", "bulk", "bulk", null, "Canada", "2022-08-05", "Larval", "Larval", "Trunk", "Surface Structure"], [70896, "SRR20869078", "SRX16888174", "SRS14475658", "SRP390172", "PRJNA866536", "X linked myotubular myopathy is associated with epigenetic alterations and is ameliorated by HDAC inhibition", "GSE210642", "Other", "X linked myotubular myopathy XLMTM is a fatal neuromuscular disorder caused by loss of function mutations in MTM1 . At present  there are no directed therapies for XLMTM  and incomplete understanding of disease pathomechanisms. To address these knowledge gaps  we performed a drug screen in mtm1 mutant zebrafish andidentified four positive hits  including valproic acid  which functions as a potent suppressor of the mtm1 zebrafish phenotype via HDAC inhibition. We translated these findings to a mouse XLMTM model  and showed that valproic acid ameliorates the murine phenotype. Overall design: Zebrafish: At 1 dpf  embryos from single pair in crossings of mtm1+/zf711 adults were divided equally into three chemical treatment groups: DMSO  sodium valproate VPA  or trichostatin A. For tissue collection  the posterior section of larvae and fin fold tissues was dissected and snap frozen on dry ice at 4 dpf. A total of n=6 10 larvae per pool per condition with 5 biological replicates were used for RNA extraction.  Mice: Bulk RNA sequencing was performed on RNA extracts from tibialis anterior muscle from 35 dpf Mtm1KO and WT mice  either treated with PBS or valproic acid VPA starting at 21 days.", null, "pubmed:35844027", null, "HET  DMSO treatment  zebrafish  rep4", "GSM6434008", null, "source name:posterior half of larvae|tissue:posterior half of larvae|genotype:HET|treatment:DMSO treatment", "HET  DMSO treatment  zebrafish  rep4", "Sequencing reads were aligned to the mouseGRCm38 /zebrafish genomeGRCz9 using STAR. Read quality was assessed with FastQC  and adaptors were trimmed from reads using Cutadapt. STAR gene level counts ReadsPerGene.out.tab files were used for differential expression with DESeq2 package Assembly: Zebrafish: GRCz9 / Mus musculus: GRCm38 Supplementary files format and content: tab delimited text files include the raw count values for each Sample. Rows = genes; Columns = samples.", "posterior half of larvae", null, "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer\u2019s protocol Zebrafish: RNA libraries were generated using the QuantSeq 3\u2019 mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "tissue:posterior half of larvae|genotype:HET|treatment:DMSO treatment", "GSM6434008", "GSM6434008: HET  DMSO treatment  zebrafish  rep4; Danio rerio; RNA Seq", "GSM6434008 r1", "GSM6434008", "1", "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer's protocol Zebrafish: RNA libraries were generated using the QuantSeq three prime mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP390172", null, null, "WL1498_KY23_168_29_R1.fastq.gz", "fastq", 914400828.0, 13447071.0, "GSM6434008 r1", "0:68 1:0", "A:294008016;C:166492811;G:196902092;T:256969737;N:28172", 68, 0, null, null, 294008016, 166492811, 196902092, 256969737, 28172, "SRX16888174", "SRS14475658", "SRA1470408", "Hospital for Sick Children", "Hospital for Sick Children", 1, 0.80378, null, 0.09051, null, 0.81913, null, 0.53428, null, 68, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "lexogen", "bulk", "bulk", "bulk", null, "Canada", "2022-08-05", "Larval", "Larval", "Trunk", "Surface Structure"], [70897, "SRR20869079", "SRX16888173", "SRS14475657", "SRP390172", "PRJNA866536", "X linked myotubular myopathy is associated with epigenetic alterations and is ameliorated by HDAC inhibition", "GSE210642", "Other", "X linked myotubular myopathy XLMTM is a fatal neuromuscular disorder caused by loss of function mutations in MTM1 . At present  there are no directed therapies for XLMTM  and incomplete understanding of disease pathomechanisms. To address these knowledge gaps  we performed a drug screen in mtm1 mutant zebrafish andidentified four positive hits  including valproic acid  which functions as a potent suppressor of the mtm1 zebrafish phenotype via HDAC inhibition. We translated these findings to a mouse XLMTM model  and showed that valproic acid ameliorates the murine phenotype. Overall design: Zebrafish: At 1 dpf  embryos from single pair in crossings of mtm1+/zf711 adults were divided equally into three chemical treatment groups: DMSO  sodium valproate VPA  or trichostatin A. For tissue collection  the posterior section of larvae and fin fold tissues was dissected and snap frozen on dry ice at 4 dpf. A total of n=6 10 larvae per pool per condition with 5 biological replicates were used for RNA extraction.  Mice: Bulk RNA sequencing was performed on RNA extracts from tibialis anterior muscle from 35 dpf Mtm1KO and WT mice  either treated with PBS or valproic acid VPA starting at 21 days.", null, "pubmed:35844027", null, "HET  DMSO treatment  zebrafish  rep3", "GSM6434007", null, "source name:posterior half of larvae|tissue:posterior half of larvae|genotype:HET|treatment:DMSO treatment", "HET  DMSO treatment  zebrafish  rep3", "Sequencing reads were aligned to the mouseGRCm38 /zebrafish genomeGRCz9 using STAR. Read quality was assessed with FastQC  and adaptors were trimmed from reads using Cutadapt. STAR gene level counts ReadsPerGene.out.tab files were used for differential expression with DESeq2 package Assembly: Zebrafish: GRCz9 / Mus musculus: GRCm38 Supplementary files format and content: tab delimited text files include the raw count values for each Sample. Rows = genes; Columns = samples.", "posterior half of larvae", null, "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer\u2019s protocol Zebrafish: RNA libraries were generated using the QuantSeq 3\u2019 mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "tissue:posterior half of larvae|genotype:HET|treatment:DMSO treatment", "GSM6434007", "GSM6434007: HET  DMSO treatment  zebrafish  rep3; Danio rerio; RNA Seq", "GSM6434007 r1", "GSM6434007", "1", "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer's protocol Zebrafish: RNA libraries were generated using the QuantSeq three prime mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP390172", null, null, "WL1497_KY23_168_28_R1.fastq.gz", "fastq", 840953484.0, 12366963.0, "GSM6434007 r1", "0:68 1:0", "A:273539801;C:150455845;G:187644527;T:229287609;N:25702", 68, 0, null, null, 273539801, 150455845, 187644527, 229287609, 25702, "SRX16888173", "SRS14475657", "SRA1470408", "Hospital for Sick Children", "Hospital for Sick Children", 1, 0.8074, null, 0.10306, null, 0.816, null, 0.55004, null, 68, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "lexogen", "bulk", "bulk", "bulk", null, "Canada", "2022-08-05", "Larval", "Larval", "Trunk", "Surface Structure"], [70898, "SRR20869080", "SRX16888172", "SRS14475656", "SRP390172", "PRJNA866536", "X linked myotubular myopathy is associated with epigenetic alterations and is ameliorated by HDAC inhibition", "GSE210642", "Other", "X linked myotubular myopathy XLMTM is a fatal neuromuscular disorder caused by loss of function mutations in MTM1 . At present  there are no directed therapies for XLMTM  and incomplete understanding of disease pathomechanisms. To address these knowledge gaps  we performed a drug screen in mtm1 mutant zebrafish andidentified four positive hits  including valproic acid  which functions as a potent suppressor of the mtm1 zebrafish phenotype via HDAC inhibition. We translated these findings to a mouse XLMTM model  and showed that valproic acid ameliorates the murine phenotype. Overall design: Zebrafish: At 1 dpf  embryos from single pair in crossings of mtm1+/zf711 adults were divided equally into three chemical treatment groups: DMSO  sodium valproate VPA  or trichostatin A. For tissue collection  the posterior section of larvae and fin fold tissues was dissected and snap frozen on dry ice at 4 dpf. A total of n=6 10 larvae per pool per condition with 5 biological replicates were used for RNA extraction.  Mice: Bulk RNA sequencing was performed on RNA extracts from tibialis anterior muscle from 35 dpf Mtm1KO and WT mice  either treated with PBS or valproic acid VPA starting at 21 days.", null, "pubmed:35844027", null, "HET  DMSO treatment  zebrafish  rep2", "GSM6434006", null, "source name:posterior half of larvae|tissue:posterior half of larvae|genotype:HET|treatment:DMSO treatment", "HET  DMSO treatment  zebrafish  rep2", "Sequencing reads were aligned to the mouseGRCm38 /zebrafish genomeGRCz9 using STAR. Read quality was assessed with FastQC  and adaptors were trimmed from reads using Cutadapt. STAR gene level counts ReadsPerGene.out.tab files were used for differential expression with DESeq2 package Assembly: Zebrafish: GRCz9 / Mus musculus: GRCm38 Supplementary files format and content: tab delimited text files include the raw count values for each Sample. Rows = genes; Columns = samples.", "posterior half of larvae", null, "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer\u2019s protocol Zebrafish: RNA libraries were generated using the QuantSeq 3\u2019 mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "tissue:posterior half of larvae|genotype:HET|treatment:DMSO treatment", "GSM6434006", "GSM6434006: HET  DMSO treatment  zebrafish  rep2; Danio rerio; RNA Seq", "GSM6434006 r1", "GSM6434006", "1", "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer's protocol Zebrafish: RNA libraries were generated using the QuantSeq three prime mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP390172", null, null, "WL1496_KY23_168_27_R1.fastq.gz", "fastq", 866563304.0, 12743578.0, "GSM6434006 r1", "0:68 1:0", "A:281372378;C:156074885;G:192852640;T:236236763;N:26638", 68, 0, null, null, 281372378, 156074885, 192852640, 236236763, 26638, "SRX16888172", "SRS14475656", "SRA1470408", "Hospital for Sick Children", "Hospital for Sick Children", 1, 0.78328, null, 0.10093, null, 0.82483, null, 0.50637, null, 68, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "lexogen", "bulk", "bulk", "bulk", null, "Canada", "2022-08-05", "Larval", "Larval", "Trunk", "Surface Structure"], [70899, "SRR20869081", "SRX16888171", "SRS14475655", "SRP390172", "PRJNA866536", "X linked myotubular myopathy is associated with epigenetic alterations and is ameliorated by HDAC inhibition", "GSE210642", "Other", "X linked myotubular myopathy XLMTM is a fatal neuromuscular disorder caused by loss of function mutations in MTM1 . At present  there are no directed therapies for XLMTM  and incomplete understanding of disease pathomechanisms. To address these knowledge gaps  we performed a drug screen in mtm1 mutant zebrafish andidentified four positive hits  including valproic acid  which functions as a potent suppressor of the mtm1 zebrafish phenotype via HDAC inhibition. We translated these findings to a mouse XLMTM model  and showed that valproic acid ameliorates the murine phenotype. Overall design: Zebrafish: At 1 dpf  embryos from single pair in crossings of mtm1+/zf711 adults were divided equally into three chemical treatment groups: DMSO  sodium valproate VPA  or trichostatin A. For tissue collection  the posterior section of larvae and fin fold tissues was dissected and snap frozen on dry ice at 4 dpf. A total of n=6 10 larvae per pool per condition with 5 biological replicates were used for RNA extraction.  Mice: Bulk RNA sequencing was performed on RNA extracts from tibialis anterior muscle from 35 dpf Mtm1KO and WT mice  either treated with PBS or valproic acid VPA starting at 21 days.", null, "pubmed:35844027", null, "HET  DMSO treatment  zebrafish  rep1", "GSM6434005", null, "source name:posterior half of larvae|tissue:posterior half of larvae|genotype:HET|treatment:DMSO treatment", "HET  DMSO treatment  zebrafish  rep1", "Sequencing reads were aligned to the mouseGRCm38 /zebrafish genomeGRCz9 using STAR. Read quality was assessed with FastQC  and adaptors were trimmed from reads using Cutadapt. STAR gene level counts ReadsPerGene.out.tab files were used for differential expression with DESeq2 package Assembly: Zebrafish: GRCz9 / Mus musculus: GRCm38 Supplementary files format and content: tab delimited text files include the raw count values for each Sample. Rows = genes; Columns = samples.", "posterior half of larvae", null, "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer\u2019s protocol Zebrafish: RNA libraries were generated using the QuantSeq 3\u2019 mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "tissue:posterior half of larvae|genotype:HET|treatment:DMSO treatment", "GSM6434005", "GSM6434005: HET  DMSO treatment  zebrafish  rep1; Danio rerio; RNA Seq", "GSM6434005 r1", "GSM6434005", "1", "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer's protocol Zebrafish: RNA libraries were generated using the QuantSeq three prime mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP390172", null, null, "WL1495_KY23_168_26_R1.fastq.gz", "fastq", 843354632.0, 12402274.0, "GSM6434005 r1", "0:68 1:0", "A:272671962;C:152135239;G:192414605;T:226107225;N:25601", 68, 0, null, null, 272671962, 152135239, 192414605, 226107225, 25601, "SRX16888171", "SRS14475655", "SRA1470408", "Hospital for Sick Children", "Hospital for Sick Children", 1, 0.80999, null, 0.10836, null, 0.82087, null, 0.54692, null, 68, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "lexogen", "bulk", "bulk", "bulk", null, "Canada", "2022-08-05", "Larval", "Larval", "Trunk", "Surface Structure"], [70900, "SRR20869082", "SRX16888170", "SRS14475654", "SRP390172", "PRJNA866536", "X linked myotubular myopathy is associated with epigenetic alterations and is ameliorated by HDAC inhibition", "GSE210642", "Other", "X linked myotubular myopathy XLMTM is a fatal neuromuscular disorder caused by loss of function mutations in MTM1 . At present  there are no directed therapies for XLMTM  and incomplete understanding of disease pathomechanisms. To address these knowledge gaps  we performed a drug screen in mtm1 mutant zebrafish andidentified four positive hits  including valproic acid  which functions as a potent suppressor of the mtm1 zebrafish phenotype via HDAC inhibition. We translated these findings to a mouse XLMTM model  and showed that valproic acid ameliorates the murine phenotype. Overall design: Zebrafish: At 1 dpf  embryos from single pair in crossings of mtm1+/zf711 adults were divided equally into three chemical treatment groups: DMSO  sodium valproate VPA  or trichostatin A. For tissue collection  the posterior section of larvae and fin fold tissues was dissected and snap frozen on dry ice at 4 dpf. A total of n=6 10 larvae per pool per condition with 5 biological replicates were used for RNA extraction.  Mice: Bulk RNA sequencing was performed on RNA extracts from tibialis anterior muscle from 35 dpf Mtm1KO and WT mice  either treated with PBS or valproic acid VPA starting at 21 days.", null, "pubmed:35844027", null, "Mtm1 KO  VPA treatment  zebrafish  rep5", "GSM6434004", null, "source name:posterior half of larvae|tissue:posterior half of larvae|genotype:Mtm1 KO|treatment:VPA treatment", "Mtm1 KO  VPA treatment  zebrafish  rep5", "Sequencing reads were aligned to the mouseGRCm38 /zebrafish genomeGRCz9 using STAR. Read quality was assessed with FastQC  and adaptors were trimmed from reads using Cutadapt. STAR gene level counts ReadsPerGene.out.tab files were used for differential expression with DESeq2 package Assembly: Zebrafish: GRCz9 / Mus musculus: GRCm38 Supplementary files format and content: tab delimited text files include the raw count values for each Sample. Rows = genes; Columns = samples.", "posterior half of larvae", null, "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer\u2019s protocol Zebrafish: RNA libraries were generated using the QuantSeq 3\u2019 mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "tissue:posterior half of larvae|genotype:Mtm1 KO|treatment:VPA treatment", "GSM6434004", "GSM6434004: Mtm1 KO  VPA treatment  zebrafish  rep5; Danio rerio; RNA Seq", "GSM6434004 r1", "GSM6434004", "1", "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer's protocol Zebrafish: RNA libraries were generated using the QuantSeq three prime mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP390172", null, null, "WL1494_KY23_168_25_R1.fastq.gz", "fastq", 927311512.0, 13636934.0, "GSM6434004 r1", "0:68 1:0", "A:291725435;C:166577119;G:206636287;T:262343860;N:28811", 68, 0, null, null, 291725435, 166577119, 206636287, 262343860, 28811, "SRX16888170", "SRS14475654", "SRA1470408", "Hospital for Sick Children", "Hospital for Sick Children", 1, 0.82957, null, 0.07535, null, 0.80943, null, 0.52892, null, 68, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "lexogen", "bulk", "bulk", "bulk", null, "Canada", "2022-08-05", "Larval", "Larval", "Trunk", "Surface Structure"], [70901, "SRR20869083", "SRX16888169", "SRS14475653", "SRP390172", "PRJNA866536", "X linked myotubular myopathy is associated with epigenetic alterations and is ameliorated by HDAC inhibition", "GSE210642", "Other", "X linked myotubular myopathy XLMTM is a fatal neuromuscular disorder caused by loss of function mutations in MTM1 . At present  there are no directed therapies for XLMTM  and incomplete understanding of disease pathomechanisms. To address these knowledge gaps  we performed a drug screen in mtm1 mutant zebrafish andidentified four positive hits  including valproic acid  which functions as a potent suppressor of the mtm1 zebrafish phenotype via HDAC inhibition. We translated these findings to a mouse XLMTM model  and showed that valproic acid ameliorates the murine phenotype. Overall design: Zebrafish: At 1 dpf  embryos from single pair in crossings of mtm1+/zf711 adults were divided equally into three chemical treatment groups: DMSO  sodium valproate VPA  or trichostatin A. For tissue collection  the posterior section of larvae and fin fold tissues was dissected and snap frozen on dry ice at 4 dpf. A total of n=6 10 larvae per pool per condition with 5 biological replicates were used for RNA extraction.  Mice: Bulk RNA sequencing was performed on RNA extracts from tibialis anterior muscle from 35 dpf Mtm1KO and WT mice  either treated with PBS or valproic acid VPA starting at 21 days.", null, "pubmed:35844027", null, "Mtm1 KO  VPA treatment  zebrafish  rep4", "GSM6434003", null, "source name:posterior half of larvae|tissue:posterior half of larvae|genotype:Mtm1 KO|treatment:VPA treatment", "Mtm1 KO  VPA treatment  zebrafish  rep4", "Sequencing reads were aligned to the mouseGRCm38 /zebrafish genomeGRCz9 using STAR. Read quality was assessed with FastQC  and adaptors were trimmed from reads using Cutadapt. STAR gene level counts ReadsPerGene.out.tab files were used for differential expression with DESeq2 package Assembly: Zebrafish: GRCz9 / Mus musculus: GRCm38 Supplementary files format and content: tab delimited text files include the raw count values for each Sample. Rows = genes; Columns = samples.", "posterior half of larvae", null, "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer\u2019s protocol Zebrafish: RNA libraries were generated using the QuantSeq 3\u2019 mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "tissue:posterior half of larvae|genotype:Mtm1 KO|treatment:VPA treatment", "GSM6434003", "GSM6434003: Mtm1 KO  VPA treatment  zebrafish  rep4; Danio rerio; RNA Seq", "GSM6434003 r1", "GSM6434003", "1", "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer's protocol Zebrafish: RNA libraries were generated using the QuantSeq three prime mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP390172", null, null, "WL1493_KY23_168_24_R1.fastq.gz", "fastq", 911599840.0, 13405880.0, "GSM6434003 r1", "0:68 1:0", "A:287750544;C:163096141;G:204309196;T:256416158;N:27801", 68, 0, null, null, 287750544, 163096141, 204309196, 256416158, 27801, "SRX16888169", "SRS14475653", "SRA1470408", "Hospital for Sick Children", "Hospital for Sick Children", 1, 0.83046, null, 0.10327, null, 0.81109, null, 0.53449, null, 68, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "lexogen", "bulk", "bulk", "bulk", null, "Canada", "2022-08-05", "Larval", "Larval", "Trunk", "Surface Structure"], [70902, "SRR20869084", "SRX16888168", "SRS14475652", "SRP390172", "PRJNA866536", "X linked myotubular myopathy is associated with epigenetic alterations and is ameliorated by HDAC inhibition", "GSE210642", "Other", "X linked myotubular myopathy XLMTM is a fatal neuromuscular disorder caused by loss of function mutations in MTM1 . At present  there are no directed therapies for XLMTM  and incomplete understanding of disease pathomechanisms. To address these knowledge gaps  we performed a drug screen in mtm1 mutant zebrafish andidentified four positive hits  including valproic acid  which functions as a potent suppressor of the mtm1 zebrafish phenotype via HDAC inhibition. We translated these findings to a mouse XLMTM model  and showed that valproic acid ameliorates the murine phenotype. Overall design: Zebrafish: At 1 dpf  embryos from single pair in crossings of mtm1+/zf711 adults were divided equally into three chemical treatment groups: DMSO  sodium valproate VPA  or trichostatin A. For tissue collection  the posterior section of larvae and fin fold tissues was dissected and snap frozen on dry ice at 4 dpf. A total of n=6 10 larvae per pool per condition with 5 biological replicates were used for RNA extraction.  Mice: Bulk RNA sequencing was performed on RNA extracts from tibialis anterior muscle from 35 dpf Mtm1KO and WT mice  either treated with PBS or valproic acid VPA starting at 21 days.", null, "pubmed:35844027", null, "Mtm1 KO  VPA treatment  zebrafish  rep3", "GSM6434002", null, "source name:posterior half of larvae|tissue:posterior half of larvae|genotype:Mtm1 KO|treatment:VPA treatment", "Mtm1 KO  VPA treatment  zebrafish  rep3", "Sequencing reads were aligned to the mouseGRCm38 /zebrafish genomeGRCz9 using STAR. Read quality was assessed with FastQC  and adaptors were trimmed from reads using Cutadapt. STAR gene level counts ReadsPerGene.out.tab files were used for differential expression with DESeq2 package Assembly: Zebrafish: GRCz9 / Mus musculus: GRCm38 Supplementary files format and content: tab delimited text files include the raw count values for each Sample. Rows = genes; Columns = samples.", "posterior half of larvae", null, "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer\u2019s protocol Zebrafish: RNA libraries were generated using the QuantSeq 3\u2019 mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "tissue:posterior half of larvae|genotype:Mtm1 KO|treatment:VPA treatment", "GSM6434002", "GSM6434002: Mtm1 KO  VPA treatment  zebrafish  rep3; Danio rerio; RNA Seq", "GSM6434002 r1", "GSM6434002", "1", "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer's protocol Zebrafish: RNA libraries were generated using the QuantSeq three prime mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP390172", null, null, "WL1492_KY23_168_23_R1.fastq.gz", "fastq", 929837440.0, 13674080.0, "GSM6434002 r1", "0:68 1:0", "A:303836655;C:166378150;G:210423283;T:249170835;N:28517", 68, 0, null, null, 303836655, 166378150, 210423283, 249170835, 28517, "SRX16888168", "SRS14475652", "SRA1470408", "Hospital for Sick Children", "Hospital for Sick Children", 1, 0.80469, null, 0.11617, null, 0.81371, null, 0.5335, null, 68, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "lexogen", "bulk", "bulk", "bulk", null, "Canada", "2022-08-05", "Larval", "Larval", "Trunk", "Surface Structure"], [70903, "SRR20869085", "SRX16888167", "SRS14475651", "SRP390172", "PRJNA866536", "X linked myotubular myopathy is associated with epigenetic alterations and is ameliorated by HDAC inhibition", "GSE210642", "Other", "X linked myotubular myopathy XLMTM is a fatal neuromuscular disorder caused by loss of function mutations in MTM1 . At present  there are no directed therapies for XLMTM  and incomplete understanding of disease pathomechanisms. To address these knowledge gaps  we performed a drug screen in mtm1 mutant zebrafish andidentified four positive hits  including valproic acid  which functions as a potent suppressor of the mtm1 zebrafish phenotype via HDAC inhibition. We translated these findings to a mouse XLMTM model  and showed that valproic acid ameliorates the murine phenotype. Overall design: Zebrafish: At 1 dpf  embryos from single pair in crossings of mtm1+/zf711 adults were divided equally into three chemical treatment groups: DMSO  sodium valproate VPA  or trichostatin A. For tissue collection  the posterior section of larvae and fin fold tissues was dissected and snap frozen on dry ice at 4 dpf. A total of n=6 10 larvae per pool per condition with 5 biological replicates were used for RNA extraction.  Mice: Bulk RNA sequencing was performed on RNA extracts from tibialis anterior muscle from 35 dpf Mtm1KO and WT mice  either treated with PBS or valproic acid VPA starting at 21 days.", null, "pubmed:35844027", null, "Mtm1 KO  VPA treatment  zebrafish  rep2", "GSM6434001", null, "source name:posterior half of larvae|tissue:posterior half of larvae|genotype:Mtm1 KO|treatment:VPA treatment", "Mtm1 KO  VPA treatment  zebrafish  rep2", "Sequencing reads were aligned to the mouseGRCm38 /zebrafish genomeGRCz9 using STAR. Read quality was assessed with FastQC  and adaptors were trimmed from reads using Cutadapt. STAR gene level counts ReadsPerGene.out.tab files were used for differential expression with DESeq2 package Assembly: Zebrafish: GRCz9 / Mus musculus: GRCm38 Supplementary files format and content: tab delimited text files include the raw count values for each Sample. Rows = genes; Columns = samples.", "posterior half of larvae", null, "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer\u2019s protocol Zebrafish: RNA libraries were generated using the QuantSeq 3\u2019 mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "tissue:posterior half of larvae|genotype:Mtm1 KO|treatment:VPA treatment", "GSM6434001", "GSM6434001: Mtm1 KO  VPA treatment  zebrafish  rep2; Danio rerio; RNA Seq", "GSM6434001 r1", "GSM6434001", "1", "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer's protocol Zebrafish: RNA libraries were generated using the QuantSeq three prime mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP390172", null, null, "WL1491_KY23_168_22_R1.fastq.gz", "fastq", 856283132.0, 12592399.0, "GSM6434001 r1", "0:68 1:0", "A:298516548;C:149218718;G:188328193;T:220193538;N:26135", 68, 0, null, null, 298516548, 149218718, 188328193, 220193538, 26135, "SRX16888167", "SRS14475651", "SRA1470408", "Hospital for Sick Children", "Hospital for Sick Children", 1, 0.74816, null, 0.1133, null, 0.82012, null, 0.54102, null, 68, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "lexogen", "bulk", "bulk", "bulk", null, "Canada", "2022-08-05", "Larval", "Larval", "Trunk", "Surface Structure"], [70904, "SRR20869086", "SRX16888166", "SRS14475650", "SRP390172", "PRJNA866536", "X linked myotubular myopathy is associated with epigenetic alterations and is ameliorated by HDAC inhibition", "GSE210642", "Other", "X linked myotubular myopathy XLMTM is a fatal neuromuscular disorder caused by loss of function mutations in MTM1 . At present  there are no directed therapies for XLMTM  and incomplete understanding of disease pathomechanisms. To address these knowledge gaps  we performed a drug screen in mtm1 mutant zebrafish andidentified four positive hits  including valproic acid  which functions as a potent suppressor of the mtm1 zebrafish phenotype via HDAC inhibition. We translated these findings to a mouse XLMTM model  and showed that valproic acid ameliorates the murine phenotype. Overall design: Zebrafish: At 1 dpf  embryos from single pair in crossings of mtm1+/zf711 adults were divided equally into three chemical treatment groups: DMSO  sodium valproate VPA  or trichostatin A. For tissue collection  the posterior section of larvae and fin fold tissues was dissected and snap frozen on dry ice at 4 dpf. A total of n=6 10 larvae per pool per condition with 5 biological replicates were used for RNA extraction.  Mice: Bulk RNA sequencing was performed on RNA extracts from tibialis anterior muscle from 35 dpf Mtm1KO and WT mice  either treated with PBS or valproic acid VPA starting at 21 days.", null, "pubmed:35844027", null, "Mtm1 KO  VPA treatment  zebrafish  rep1", "GSM6434000", null, "source name:posterior half of larvae|tissue:posterior half of larvae|genotype:Mtm1 KO|treatment:VPA treatment", "Mtm1 KO  VPA treatment  zebrafish  rep1", "Sequencing reads were aligned to the mouseGRCm38 /zebrafish genomeGRCz9 using STAR. Read quality was assessed with FastQC  and adaptors were trimmed from reads using Cutadapt. STAR gene level counts ReadsPerGene.out.tab files were used for differential expression with DESeq2 package Assembly: Zebrafish: GRCz9 / Mus musculus: GRCm38 Supplementary files format and content: tab delimited text files include the raw count values for each Sample. Rows = genes; Columns = samples.", "posterior half of larvae", null, "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer\u2019s protocol Zebrafish: RNA libraries were generated using the QuantSeq 3\u2019 mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "tissue:posterior half of larvae|genotype:Mtm1 KO|treatment:VPA treatment", "GSM6434000", "GSM6434000: Mtm1 KO  VPA treatment  zebrafish  rep1; Danio rerio; RNA Seq", "GSM6434000 r1", "GSM6434000", "1", "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer's protocol Zebrafish: RNA libraries were generated using the QuantSeq three prime mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP390172", null, null, "WL1490_KY23_168_21_R1.fastq.gz", "fastq", 840998840.0, 12367630.0, "GSM6434000 r1", "0:68 1:0", "A:269574792;C:155617312;G:189177931;T:226602805;N:26000", 68, 0, null, null, 269574792, 155617312, 189177931, 226602805, 26000, "SRX16888166", "SRS14475650", "SRA1470408", "Hospital for Sick Children", "Hospital for Sick Children", 1, 0.82682, null, 0.11442, null, 0.81428, null, 0.56002, null, 68, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "lexogen", "bulk", "bulk", "bulk", null, "Canada", "2022-08-05", "Larval", "Larval", "Trunk", "Surface Structure"], [70905, "SRR20869087", "SRX16888165", "SRS14475649", "SRP390172", "PRJNA866536", "X linked myotubular myopathy is associated with epigenetic alterations and is ameliorated by HDAC inhibition", "GSE210642", "Other", "X linked myotubular myopathy XLMTM is a fatal neuromuscular disorder caused by loss of function mutations in MTM1 . At present  there are no directed therapies for XLMTM  and incomplete understanding of disease pathomechanisms. To address these knowledge gaps  we performed a drug screen in mtm1 mutant zebrafish andidentified four positive hits  including valproic acid  which functions as a potent suppressor of the mtm1 zebrafish phenotype via HDAC inhibition. We translated these findings to a mouse XLMTM model  and showed that valproic acid ameliorates the murine phenotype. Overall design: Zebrafish: At 1 dpf  embryos from single pair in crossings of mtm1+/zf711 adults were divided equally into three chemical treatment groups: DMSO  sodium valproate VPA  or trichostatin A. For tissue collection  the posterior section of larvae and fin fold tissues was dissected and snap frozen on dry ice at 4 dpf. A total of n=6 10 larvae per pool per condition with 5 biological replicates were used for RNA extraction.  Mice: Bulk RNA sequencing was performed on RNA extracts from tibialis anterior muscle from 35 dpf Mtm1KO and WT mice  either treated with PBS or valproic acid VPA starting at 21 days.", null, "pubmed:35844027", null, "HET  VPA treatment  zebrafish  rep5", "GSM6433999", null, "source name:posterior half of larvae|tissue:posterior half of larvae|genotype:HET|treatment:VPA treatment", "HET  VPA treatment  zebrafish  rep5", "Sequencing reads were aligned to the mouseGRCm38 /zebrafish genomeGRCz9 using STAR. Read quality was assessed with FastQC  and adaptors were trimmed from reads using Cutadapt. STAR gene level counts ReadsPerGene.out.tab files were used for differential expression with DESeq2 package Assembly: Zebrafish: GRCz9 / Mus musculus: GRCm38 Supplementary files format and content: tab delimited text files include the raw count values for each Sample. Rows = genes; Columns = samples.", "posterior half of larvae", null, "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer\u2019s protocol Zebrafish: RNA libraries were generated using the QuantSeq 3\u2019 mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "tissue:posterior half of larvae|genotype:HET|treatment:VPA treatment", "GSM6433999", "GSM6433999: HET  VPA treatment  zebrafish  rep5; Danio rerio; RNA Seq", "GSM6433999 r1", "GSM6433999", "1", "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer's protocol Zebrafish: RNA libraries were generated using the QuantSeq three prime mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP390172", null, null, "WL1489_KY23_168_20_R1.fastq.gz", "fastq", 901828240.0, 13262180.0, "GSM6433999 r1", "0:68 1:0", "A:291763235;C:163163197;G:196793555;T:250080362;N:27891", 68, 0, null, null, 291763235, 163163197, 196793555, 250080362, 27891, "SRX16888165", "SRS14475649", "SRA1470408", "Hospital for Sick Children", "Hospital for Sick Children", 1, 0.81103, null, 0.09106, null, 0.81397, null, 0.55141, null, 68, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "lexogen", "bulk", "bulk", "bulk", null, "Canada", "2022-08-05", "Larval", "Larval", "Trunk", "Surface Structure"], [70906, "SRR20869088", "SRX16888164", "SRS14475648", "SRP390172", "PRJNA866536", "X linked myotubular myopathy is associated with epigenetic alterations and is ameliorated by HDAC inhibition", "GSE210642", "Other", "X linked myotubular myopathy XLMTM is a fatal neuromuscular disorder caused by loss of function mutations in MTM1 . At present  there are no directed therapies for XLMTM  and incomplete understanding of disease pathomechanisms. To address these knowledge gaps  we performed a drug screen in mtm1 mutant zebrafish andidentified four positive hits  including valproic acid  which functions as a potent suppressor of the mtm1 zebrafish phenotype via HDAC inhibition. We translated these findings to a mouse XLMTM model  and showed that valproic acid ameliorates the murine phenotype. Overall design: Zebrafish: At 1 dpf  embryos from single pair in crossings of mtm1+/zf711 adults were divided equally into three chemical treatment groups: DMSO  sodium valproate VPA  or trichostatin A. For tissue collection  the posterior section of larvae and fin fold tissues was dissected and snap frozen on dry ice at 4 dpf. A total of n=6 10 larvae per pool per condition with 5 biological replicates were used for RNA extraction.  Mice: Bulk RNA sequencing was performed on RNA extracts from tibialis anterior muscle from 35 dpf Mtm1KO and WT mice  either treated with PBS or valproic acid VPA starting at 21 days.", null, "pubmed:35844027", null, "HET  VPA treatment  zebrafish  rep4", "GSM6433998", null, "source name:posterior half of larvae|tissue:posterior half of larvae|genotype:HET|treatment:VPA treatment", "HET  VPA treatment  zebrafish  rep4", "Sequencing reads were aligned to the mouseGRCm38 /zebrafish genomeGRCz9 using STAR. Read quality was assessed with FastQC  and adaptors were trimmed from reads using Cutadapt. STAR gene level counts ReadsPerGene.out.tab files were used for differential expression with DESeq2 package Assembly: Zebrafish: GRCz9 / Mus musculus: GRCm38 Supplementary files format and content: tab delimited text files include the raw count values for each Sample. Rows = genes; Columns = samples.", "posterior half of larvae", null, "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer\u2019s protocol Zebrafish: RNA libraries were generated using the QuantSeq 3\u2019 mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "tissue:posterior half of larvae|genotype:HET|treatment:VPA treatment", "GSM6433998", "GSM6433998: HET  VPA treatment  zebrafish  rep4; Danio rerio; RNA Seq", "GSM6433998 r1", "GSM6433998", "1", "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer's protocol Zebrafish: RNA libraries were generated using the QuantSeq three prime mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP390172", null, null, "WL1488_KY23_168_19_R1.fastq.gz", "fastq", 1002197600.0, 14738200.0, "GSM6433998 r1", "0:68 1:0", "A:322076969;C:182902068;G:222775191;T:274412708;N:30664", 68, 0, null, null, 322076969, 182902068, 222775191, 274412708, 30664, "SRX16888164", "SRS14475648", "SRA1470408", "Hospital for Sick Children", "Hospital for Sick Children", 1, 0.8214, null, 0.09555, null, 0.81708, null, 0.5555, null, 68, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "lexogen", "bulk", "bulk", "bulk", null, "Canada", "2022-08-05", "Larval", "Larval", "Trunk", "Surface Structure"], [70907, "SRR20869089", "SRX16888163", "SRS14475647", "SRP390172", "PRJNA866536", "X linked myotubular myopathy is associated with epigenetic alterations and is ameliorated by HDAC inhibition", "GSE210642", "Other", "X linked myotubular myopathy XLMTM is a fatal neuromuscular disorder caused by loss of function mutations in MTM1 . At present  there are no directed therapies for XLMTM  and incomplete understanding of disease pathomechanisms. To address these knowledge gaps  we performed a drug screen in mtm1 mutant zebrafish andidentified four positive hits  including valproic acid  which functions as a potent suppressor of the mtm1 zebrafish phenotype via HDAC inhibition. We translated these findings to a mouse XLMTM model  and showed that valproic acid ameliorates the murine phenotype. Overall design: Zebrafish: At 1 dpf  embryos from single pair in crossings of mtm1+/zf711 adults were divided equally into three chemical treatment groups: DMSO  sodium valproate VPA  or trichostatin A. For tissue collection  the posterior section of larvae and fin fold tissues was dissected and snap frozen on dry ice at 4 dpf. A total of n=6 10 larvae per pool per condition with 5 biological replicates were used for RNA extraction.  Mice: Bulk RNA sequencing was performed on RNA extracts from tibialis anterior muscle from 35 dpf Mtm1KO and WT mice  either treated with PBS or valproic acid VPA starting at 21 days.", null, "pubmed:35844027", null, "HET  VPA treatment  zebrafish  rep3", "GSM6433997", null, "source name:posterior half of larvae|tissue:posterior half of larvae|genotype:HET|treatment:VPA treatment", "HET  VPA treatment  zebrafish  rep3", "Sequencing reads were aligned to the mouseGRCm38 /zebrafish genomeGRCz9 using STAR. Read quality was assessed with FastQC  and adaptors were trimmed from reads using Cutadapt. STAR gene level counts ReadsPerGene.out.tab files were used for differential expression with DESeq2 package Assembly: Zebrafish: GRCz9 / Mus musculus: GRCm38 Supplementary files format and content: tab delimited text files include the raw count values for each Sample. Rows = genes; Columns = samples.", "posterior half of larvae", null, "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer\u2019s protocol Zebrafish: RNA libraries were generated using the QuantSeq 3\u2019 mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "tissue:posterior half of larvae|genotype:HET|treatment:VPA treatment", "GSM6433997", "GSM6433997: HET  VPA treatment  zebrafish  rep3; Danio rerio; RNA Seq", "GSM6433997 r1", "GSM6433997", "1", "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer's protocol Zebrafish: RNA libraries were generated using the QuantSeq three prime mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP390172", null, null, "WL1487_KY23_168_18_R1.fastq.gz", "fastq", 913436452.0, 13432889.0, "GSM6433997 r1", "0:68 1:0", "A:298763838;C:164686057;G:208498185;T:241460289;N:28083", 68, 0, null, null, 298763838, 164686057, 208498185, 241460289, 28083, "SRX16888163", "SRS14475647", "SRA1470408", "Hospital for Sick Children", "Hospital for Sick Children", 1, 0.80018, null, 0.11373, null, 0.81438, null, 0.36042, null, 68, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "lexogen", "bulk", "bulk", "bulk", null, "Canada", "2022-08-05", "Larval", "Larval", "Trunk", "Surface Structure"], [70908, "SRR20869090", "SRX16888162", "SRS14475646", "SRP390172", "PRJNA866536", "X linked myotubular myopathy is associated with epigenetic alterations and is ameliorated by HDAC inhibition", "GSE210642", "Other", "X linked myotubular myopathy XLMTM is a fatal neuromuscular disorder caused by loss of function mutations in MTM1 . At present  there are no directed therapies for XLMTM  and incomplete understanding of disease pathomechanisms. To address these knowledge gaps  we performed a drug screen in mtm1 mutant zebrafish andidentified four positive hits  including valproic acid  which functions as a potent suppressor of the mtm1 zebrafish phenotype via HDAC inhibition. We translated these findings to a mouse XLMTM model  and showed that valproic acid ameliorates the murine phenotype. Overall design: Zebrafish: At 1 dpf  embryos from single pair in crossings of mtm1+/zf711 adults were divided equally into three chemical treatment groups: DMSO  sodium valproate VPA  or trichostatin A. For tissue collection  the posterior section of larvae and fin fold tissues was dissected and snap frozen on dry ice at 4 dpf. A total of n=6 10 larvae per pool per condition with 5 biological replicates were used for RNA extraction.  Mice: Bulk RNA sequencing was performed on RNA extracts from tibialis anterior muscle from 35 dpf Mtm1KO and WT mice  either treated with PBS or valproic acid VPA starting at 21 days.", null, "pubmed:35844027", null, "HET  VPA treatment  zebrafish  rep2", "GSM6433996", null, "source name:posterior half of larvae|tissue:posterior half of larvae|genotype:HET|treatment:VPA treatment", "HET  VPA treatment  zebrafish  rep2", "Sequencing reads were aligned to the mouseGRCm38 /zebrafish genomeGRCz9 using STAR. Read quality was assessed with FastQC  and adaptors were trimmed from reads using Cutadapt. STAR gene level counts ReadsPerGene.out.tab files were used for differential expression with DESeq2 package Assembly: Zebrafish: GRCz9 / Mus musculus: GRCm38 Supplementary files format and content: tab delimited text files include the raw count values for each Sample. Rows = genes; Columns = samples.", "posterior half of larvae", null, "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer\u2019s protocol Zebrafish: RNA libraries were generated using the QuantSeq 3\u2019 mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "tissue:posterior half of larvae|genotype:HET|treatment:VPA treatment", "GSM6433996", "GSM6433996: HET  VPA treatment  zebrafish  rep2; Danio rerio; RNA Seq", "GSM6433996 r1", "GSM6433996", "1", "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer's protocol Zebrafish: RNA libraries were generated using the QuantSeq three prime mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP390172", null, null, "WL1486_KY23_168_17_R1.fastq.gz", "fastq", 820142016.0, 12060912.0, "GSM6433996 r1", "0:68 1:0", "A:263283593;C:147216450;G:177773419;T:231843239;N:25315", 68, 0, null, null, 263283593, 147216450, 177773419, 231843239, 25315, "SRX16888162", "SRS14475646", "SRA1470408", "Hospital for Sick Children", "Hospital for Sick Children", 1, 0.81, null, 0.08525, null, 0.81335, null, 0.54085, null, 68, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "lexogen", "bulk", "bulk", "bulk", null, "Canada", "2022-08-05", "Larval", "Larval", "Trunk", "Surface Structure"], [70909, "SRR20869091", "SRX16888161", "SRS14475645", "SRP390172", "PRJNA866536", "X linked myotubular myopathy is associated with epigenetic alterations and is ameliorated by HDAC inhibition", "GSE210642", "Other", "X linked myotubular myopathy XLMTM is a fatal neuromuscular disorder caused by loss of function mutations in MTM1 . At present  there are no directed therapies for XLMTM  and incomplete understanding of disease pathomechanisms. To address these knowledge gaps  we performed a drug screen in mtm1 mutant zebrafish andidentified four positive hits  including valproic acid  which functions as a potent suppressor of the mtm1 zebrafish phenotype via HDAC inhibition. We translated these findings to a mouse XLMTM model  and showed that valproic acid ameliorates the murine phenotype. Overall design: Zebrafish: At 1 dpf  embryos from single pair in crossings of mtm1+/zf711 adults were divided equally into three chemical treatment groups: DMSO  sodium valproate VPA  or trichostatin A. For tissue collection  the posterior section of larvae and fin fold tissues was dissected and snap frozen on dry ice at 4 dpf. A total of n=6 10 larvae per pool per condition with 5 biological replicates were used for RNA extraction.  Mice: Bulk RNA sequencing was performed on RNA extracts from tibialis anterior muscle from 35 dpf Mtm1KO and WT mice  either treated with PBS or valproic acid VPA starting at 21 days.", null, "pubmed:35844027", null, "HET  VPA treatment  zebrafish  rep1", "GSM6433995", null, "source name:posterior half of larvae|tissue:posterior half of larvae|genotype:HET|treatment:VPA treatment", "HET  VPA treatment  zebrafish  rep1", "Sequencing reads were aligned to the mouseGRCm38 /zebrafish genomeGRCz9 using STAR. Read quality was assessed with FastQC  and adaptors were trimmed from reads using Cutadapt. STAR gene level counts ReadsPerGene.out.tab files were used for differential expression with DESeq2 package Assembly: Zebrafish: GRCz9 / Mus musculus: GRCm38 Supplementary files format and content: tab delimited text files include the raw count values for each Sample. Rows = genes; Columns = samples.", "posterior half of larvae", null, "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer\u2019s protocol Zebrafish: RNA libraries were generated using the QuantSeq 3\u2019 mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "tissue:posterior half of larvae|genotype:HET|treatment:VPA treatment", "GSM6433995", "GSM6433995: HET  VPA treatment  zebrafish  rep1; Danio rerio; RNA Seq", "GSM6433995 r1", "GSM6433995", "1", "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer's protocol Zebrafish: RNA libraries were generated using the QuantSeq three prime mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP390172", null, null, "WL1485_KY23_168_16_R1.fastq.gz", "fastq", 935648924.0, 13759543.0, "GSM6433995 r1", "0:68 1:0", "A:311986085;C:169749709;G:201471642;T:252412819;N:28669", 68, 0, null, null, 311986085, 169749709, 201471642, 252412819, 28669, "SRX16888161", "SRS14475645", "SRA1470408", "Hospital for Sick Children", "Hospital for Sick Children", 1, 0.71797, null, 0.09744, null, 0.81645, null, 0.56605, null, 68, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "lexogen", "bulk", "bulk", "bulk", null, "Canada", "2022-08-05", "Larval", "Larval", "Trunk", "Surface Structure"], [70910, "SRR20869092", "SRX16888160", "SRS14475644", "SRP390172", "PRJNA866536", "X linked myotubular myopathy is associated with epigenetic alterations and is ameliorated by HDAC inhibition", "GSE210642", "Other", "X linked myotubular myopathy XLMTM is a fatal neuromuscular disorder caused by loss of function mutations in MTM1 . At present  there are no directed therapies for XLMTM  and incomplete understanding of disease pathomechanisms. To address these knowledge gaps  we performed a drug screen in mtm1 mutant zebrafish andidentified four positive hits  including valproic acid  which functions as a potent suppressor of the mtm1 zebrafish phenotype via HDAC inhibition. We translated these findings to a mouse XLMTM model  and showed that valproic acid ameliorates the murine phenotype. Overall design: Zebrafish: At 1 dpf  embryos from single pair in crossings of mtm1+/zf711 adults were divided equally into three chemical treatment groups: DMSO  sodium valproate VPA  or trichostatin A. For tissue collection  the posterior section of larvae and fin fold tissues was dissected and snap frozen on dry ice at 4 dpf. A total of n=6 10 larvae per pool per condition with 5 biological replicates were used for RNA extraction.  Mice: Bulk RNA sequencing was performed on RNA extracts from tibialis anterior muscle from 35 dpf Mtm1KO and WT mice  either treated with PBS or valproic acid VPA starting at 21 days.", null, "pubmed:35844027", null, "Mtm1 KO  TSA treatment  zebrafish  rep5", "GSM6433994", null, "source name:posterior half of larvae|tissue:posterior half of larvae|genotype:Mtm1 KO|treatment:TSA treatment", "Mtm1 KO  TSA treatment  zebrafish  rep5", "Sequencing reads were aligned to the mouseGRCm38 /zebrafish genomeGRCz9 using STAR. Read quality was assessed with FastQC  and adaptors were trimmed from reads using Cutadapt. STAR gene level counts ReadsPerGene.out.tab files were used for differential expression with DESeq2 package Assembly: Zebrafish: GRCz9 / Mus musculus: GRCm38 Supplementary files format and content: tab delimited text files include the raw count values for each Sample. Rows = genes; Columns = samples.", "posterior half of larvae", null, "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer\u2019s protocol Zebrafish: RNA libraries were generated using the QuantSeq 3\u2019 mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "tissue:posterior half of larvae|genotype:Mtm1 KO|treatment:TSA treatment", "GSM6433994", "GSM6433994: Mtm1 KO  TSA treatment  zebrafish  rep5; Danio rerio; RNA Seq", "GSM6433994 r1", "GSM6433994", "1", "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer's protocol Zebrafish: RNA libraries were generated using the QuantSeq three prime mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP390172", null, null, "WL1484_KY23_168_15_R1.fastq.gz", "fastq", 867623492.0, 12759169.0, "GSM6433994 r1", "0:68 1:0", "A:289234513;C:155221667;G:194434609;T:228706315;N:26388", 68, 0, null, null, 289234513, 155221667, 194434609, 228706315, 26388, "SRX16888160", "SRS14475644", "SRA1470408", "Hospital for Sick Children", "Hospital for Sick Children", 1, 0.78415, null, 0.11088, null, 0.81355, null, 0.51504, null, 68, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "lexogen", "bulk", "bulk", "bulk", null, "Canada", "2022-08-05", "Larval", "Larval", "Trunk", "Surface Structure"], [70911, "SRR20869093", "SRX16888159", "SRS14475643", "SRP390172", "PRJNA866536", "X linked myotubular myopathy is associated with epigenetic alterations and is ameliorated by HDAC inhibition", "GSE210642", "Other", "X linked myotubular myopathy XLMTM is a fatal neuromuscular disorder caused by loss of function mutations in MTM1 . At present  there are no directed therapies for XLMTM  and incomplete understanding of disease pathomechanisms. To address these knowledge gaps  we performed a drug screen in mtm1 mutant zebrafish andidentified four positive hits  including valproic acid  which functions as a potent suppressor of the mtm1 zebrafish phenotype via HDAC inhibition. We translated these findings to a mouse XLMTM model  and showed that valproic acid ameliorates the murine phenotype. Overall design: Zebrafish: At 1 dpf  embryos from single pair in crossings of mtm1+/zf711 adults were divided equally into three chemical treatment groups: DMSO  sodium valproate VPA  or trichostatin A. For tissue collection  the posterior section of larvae and fin fold tissues was dissected and snap frozen on dry ice at 4 dpf. A total of n=6 10 larvae per pool per condition with 5 biological replicates were used for RNA extraction.  Mice: Bulk RNA sequencing was performed on RNA extracts from tibialis anterior muscle from 35 dpf Mtm1KO and WT mice  either treated with PBS or valproic acid VPA starting at 21 days.", null, "pubmed:35844027", null, "Mtm1 KO  TSA treatment  zebrafish  rep4", "GSM6433993", null, "source name:posterior half of larvae|tissue:posterior half of larvae|genotype:Mtm1 KO|treatment:TSA treatment", "Mtm1 KO  TSA treatment  zebrafish  rep4", "Sequencing reads were aligned to the mouseGRCm38 /zebrafish genomeGRCz9 using STAR. Read quality was assessed with FastQC  and adaptors were trimmed from reads using Cutadapt. STAR gene level counts ReadsPerGene.out.tab files were used for differential expression with DESeq2 package Assembly: Zebrafish: GRCz9 / Mus musculus: GRCm38 Supplementary files format and content: tab delimited text files include the raw count values for each Sample. Rows = genes; Columns = samples.", "posterior half of larvae", null, "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer\u2019s protocol Zebrafish: RNA libraries were generated using the QuantSeq 3\u2019 mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "tissue:posterior half of larvae|genotype:Mtm1 KO|treatment:TSA treatment", "GSM6433993", "GSM6433993: Mtm1 KO  TSA treatment  zebrafish  rep4; Danio rerio; RNA Seq", "GSM6433993 r1", "GSM6433993", "1", "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer's protocol Zebrafish: RNA libraries were generated using the QuantSeq three prime mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP390172", null, null, "WL1483_KY23_168_14_R1.fastq.gz", "fastq", 866595060.0, 12744045.0, "GSM6433993 r1", "0:68 1:0", "A:307372835;C:152869818;G:183626188;T:222699713;N:26506", 68, 0, null, null, 307372835, 152869818, 183626188, 222699713, 26506, "SRX16888159", "SRS14475643", "SRA1470408", "Hospital for Sick Children", "Hospital for Sick Children", 1, 0.71566, null, 0.11015, null, 0.82917, null, 0.50431, null, 68, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "lexogen", "bulk", "bulk", "bulk", null, "Canada", "2022-08-05", "Larval", "Larval", "Trunk", "Surface Structure"], [70912, "SRR20869094", "SRX16888158", "SRS14475642", "SRP390172", "PRJNA866536", "X linked myotubular myopathy is associated with epigenetic alterations and is ameliorated by HDAC inhibition", "GSE210642", "Other", "X linked myotubular myopathy XLMTM is a fatal neuromuscular disorder caused by loss of function mutations in MTM1 . At present  there are no directed therapies for XLMTM  and incomplete understanding of disease pathomechanisms. To address these knowledge gaps  we performed a drug screen in mtm1 mutant zebrafish andidentified four positive hits  including valproic acid  which functions as a potent suppressor of the mtm1 zebrafish phenotype via HDAC inhibition. We translated these findings to a mouse XLMTM model  and showed that valproic acid ameliorates the murine phenotype. Overall design: Zebrafish: At 1 dpf  embryos from single pair in crossings of mtm1+/zf711 adults were divided equally into three chemical treatment groups: DMSO  sodium valproate VPA  or trichostatin A. For tissue collection  the posterior section of larvae and fin fold tissues was dissected and snap frozen on dry ice at 4 dpf. A total of n=6 10 larvae per pool per condition with 5 biological replicates were used for RNA extraction.  Mice: Bulk RNA sequencing was performed on RNA extracts from tibialis anterior muscle from 35 dpf Mtm1KO and WT mice  either treated with PBS or valproic acid VPA starting at 21 days.", null, "pubmed:35844027", null, "Mtm1 KO  TSA treatment  zebrafish  rep3", "GSM6433992", null, "source name:posterior half of larvae|tissue:posterior half of larvae|genotype:Mtm1 KO|treatment:TSA treatment", "Mtm1 KO  TSA treatment  zebrafish  rep3", "Sequencing reads were aligned to the mouseGRCm38 /zebrafish genomeGRCz9 using STAR. Read quality was assessed with FastQC  and adaptors were trimmed from reads using Cutadapt. STAR gene level counts ReadsPerGene.out.tab files were used for differential expression with DESeq2 package Assembly: Zebrafish: GRCz9 / Mus musculus: GRCm38 Supplementary files format and content: tab delimited text files include the raw count values for each Sample. Rows = genes; Columns = samples.", "posterior half of larvae", null, "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer\u2019s protocol Zebrafish: RNA libraries were generated using the QuantSeq 3\u2019 mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "tissue:posterior half of larvae|genotype:Mtm1 KO|treatment:TSA treatment", "GSM6433992", "GSM6433992: Mtm1 KO  TSA treatment  zebrafish  rep3; Danio rerio; RNA Seq", "GSM6433992 r1", "GSM6433992", "1", "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer's protocol Zebrafish: RNA libraries were generated using the QuantSeq three prime mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP390172", null, null, "WL1482_KY23_168_13_R1.fastq.gz", "fastq", 908450692.0, 13359569.0, "GSM6433992 r1", "0:68 1:0", "A:294288974;C:166101496;G:195409922;T:252622316;N:27984", 68, 0, null, null, 294288974, 166101496, 195409922, 252622316, 27984, "SRX16888158", "SRS14475642", "SRA1470408", "Hospital for Sick Children", "Hospital for Sick Children", 1, 0.80995, null, 0.0914, null, 0.81389, null, 0.54466, null, 68, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "lexogen", "bulk", "bulk", "bulk", null, "Canada", "2022-08-05", "Larval", "Larval", "Trunk", "Surface Structure"], [70913, "SRR20869095", "SRX16888157", "SRS14475641", "SRP390172", "PRJNA866536", "X linked myotubular myopathy is associated with epigenetic alterations and is ameliorated by HDAC inhibition", "GSE210642", "Other", "X linked myotubular myopathy XLMTM is a fatal neuromuscular disorder caused by loss of function mutations in MTM1 . At present  there are no directed therapies for XLMTM  and incomplete understanding of disease pathomechanisms. To address these knowledge gaps  we performed a drug screen in mtm1 mutant zebrafish andidentified four positive hits  including valproic acid  which functions as a potent suppressor of the mtm1 zebrafish phenotype via HDAC inhibition. We translated these findings to a mouse XLMTM model  and showed that valproic acid ameliorates the murine phenotype. Overall design: Zebrafish: At 1 dpf  embryos from single pair in crossings of mtm1+/zf711 adults were divided equally into three chemical treatment groups: DMSO  sodium valproate VPA  or trichostatin A. For tissue collection  the posterior section of larvae and fin fold tissues was dissected and snap frozen on dry ice at 4 dpf. A total of n=6 10 larvae per pool per condition with 5 biological replicates were used for RNA extraction.  Mice: Bulk RNA sequencing was performed on RNA extracts from tibialis anterior muscle from 35 dpf Mtm1KO and WT mice  either treated with PBS or valproic acid VPA starting at 21 days.", null, "pubmed:35844027", null, "Mtm1 KO  TSA treatment  zebrafish  rep2", "GSM6433991", null, "source name:posterior half of larvae|tissue:posterior half of larvae|genotype:Mtm1 KO|treatment:TSA treatment", "Mtm1 KO  TSA treatment  zebrafish  rep2", "Sequencing reads were aligned to the mouseGRCm38 /zebrafish genomeGRCz9 using STAR. Read quality was assessed with FastQC  and adaptors were trimmed from reads using Cutadapt. STAR gene level counts ReadsPerGene.out.tab files were used for differential expression with DESeq2 package Assembly: Zebrafish: GRCz9 / Mus musculus: GRCm38 Supplementary files format and content: tab delimited text files include the raw count values for each Sample. Rows = genes; Columns = samples.", "posterior half of larvae", null, "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer\u2019s protocol Zebrafish: RNA libraries were generated using the QuantSeq 3\u2019 mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "tissue:posterior half of larvae|genotype:Mtm1 KO|treatment:TSA treatment", "GSM6433991", "GSM6433991: Mtm1 KO  TSA treatment  zebrafish  rep2; Danio rerio; RNA Seq", "GSM6433991 r1", "GSM6433991", "1", "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer's protocol Zebrafish: RNA libraries were generated using the QuantSeq three prime mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP390172", null, null, "WL1481_KY23_168_12_R1.fastq.gz", "fastq", 880023496.0, 12941522.0, "GSM6433991 r1", "0:68 1:0", "A:287151954;C:160498388;G:192579956;T:239765774;N:27424", 68, 0, null, null, 287151954, 160498388, 192579956, 239765774, 27424, "SRX16888157", "SRS14475641", "SRA1470408", "Hospital for Sick Children", "Hospital for Sick Children", 1, 0.8031, null, 0.09849, null, 0.81501, null, 0.55513, null, 68, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "lexogen", "bulk", "bulk", "bulk", null, "Canada", "2022-08-05", "Larval", "Larval", "Trunk", "Surface Structure"], [70914, "SRR20869096", "SRX16888156", "SRS14475640", "SRP390172", "PRJNA866536", "X linked myotubular myopathy is associated with epigenetic alterations and is ameliorated by HDAC inhibition", "GSE210642", "Other", "X linked myotubular myopathy XLMTM is a fatal neuromuscular disorder caused by loss of function mutations in MTM1 . At present  there are no directed therapies for XLMTM  and incomplete understanding of disease pathomechanisms. To address these knowledge gaps  we performed a drug screen in mtm1 mutant zebrafish andidentified four positive hits  including valproic acid  which functions as a potent suppressor of the mtm1 zebrafish phenotype via HDAC inhibition. We translated these findings to a mouse XLMTM model  and showed that valproic acid ameliorates the murine phenotype. Overall design: Zebrafish: At 1 dpf  embryos from single pair in crossings of mtm1+/zf711 adults were divided equally into three chemical treatment groups: DMSO  sodium valproate VPA  or trichostatin A. For tissue collection  the posterior section of larvae and fin fold tissues was dissected and snap frozen on dry ice at 4 dpf. A total of n=6 10 larvae per pool per condition with 5 biological replicates were used for RNA extraction.  Mice: Bulk RNA sequencing was performed on RNA extracts from tibialis anterior muscle from 35 dpf Mtm1KO and WT mice  either treated with PBS or valproic acid VPA starting at 21 days.", null, "pubmed:35844027", null, "Mtm1 KO  TSA treatment  zebrafish  rep1", "GSM6433990", null, "source name:posterior half of larvae|tissue:posterior half of larvae|genotype:Mtm1 KO|treatment:TSA treatment", "Mtm1 KO  TSA treatment  zebrafish  rep1", "Sequencing reads were aligned to the mouseGRCm38 /zebrafish genomeGRCz9 using STAR. Read quality was assessed with FastQC  and adaptors were trimmed from reads using Cutadapt. STAR gene level counts ReadsPerGene.out.tab files were used for differential expression with DESeq2 package Assembly: Zebrafish: GRCz9 / Mus musculus: GRCm38 Supplementary files format and content: tab delimited text files include the raw count values for each Sample. Rows = genes; Columns = samples.", "posterior half of larvae", null, "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer\u2019s protocol Zebrafish: RNA libraries were generated using the QuantSeq 3\u2019 mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "tissue:posterior half of larvae|genotype:Mtm1 KO|treatment:TSA treatment", "GSM6433990", "GSM6433990: Mtm1 KO  TSA treatment  zebrafish  rep1; Danio rerio; RNA Seq", "GSM6433990 r1", "GSM6433990", "1", "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer's protocol Zebrafish: RNA libraries were generated using the QuantSeq three prime mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP390172", null, null, "WL1480_KY23_168_11_R1.fastq.gz", "fastq", 1003182444.0, 14752683.0, "GSM6433990 r1", "0:68 1:0", "A:328950780;C:180702054;G:217909263;T:275589304;N:31043", 68, 0, null, null, 328950780, 180702054, 217909263, 275589304, 31043, "SRX16888156", "SRS14475640", "SRA1470408", "Hospital for Sick Children", "Hospital for Sick Children", 1, 0.80451, null, 0.09789, null, 0.81533, null, 0.55074, null, 68, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "lexogen", "bulk", "bulk", "bulk", null, "Canada", "2022-08-05", "Larval", "Larval", "Trunk", "Surface Structure"], [70915, "SRR20869097", "SRX16888155", "SRS14475639", "SRP390172", "PRJNA866536", "X linked myotubular myopathy is associated with epigenetic alterations and is ameliorated by HDAC inhibition", "GSE210642", "Other", "X linked myotubular myopathy XLMTM is a fatal neuromuscular disorder caused by loss of function mutations in MTM1 . At present  there are no directed therapies for XLMTM  and incomplete understanding of disease pathomechanisms. To address these knowledge gaps  we performed a drug screen in mtm1 mutant zebrafish andidentified four positive hits  including valproic acid  which functions as a potent suppressor of the mtm1 zebrafish phenotype via HDAC inhibition. We translated these findings to a mouse XLMTM model  and showed that valproic acid ameliorates the murine phenotype. Overall design: Zebrafish: At 1 dpf  embryos from single pair in crossings of mtm1+/zf711 adults were divided equally into three chemical treatment groups: DMSO  sodium valproate VPA  or trichostatin A. For tissue collection  the posterior section of larvae and fin fold tissues was dissected and snap frozen on dry ice at 4 dpf. A total of n=6 10 larvae per pool per condition with 5 biological replicates were used for RNA extraction.  Mice: Bulk RNA sequencing was performed on RNA extracts from tibialis anterior muscle from 35 dpf Mtm1KO and WT mice  either treated with PBS or valproic acid VPA starting at 21 days.", null, "pubmed:35844027", null, "HET  TSA treatment  zebrafish  rep4", "GSM6433989", null, "source name:posterior half of larvae|tissue:posterior half of larvae|genotype:HET|treatment:TSA treatment", "HET  TSA treatment  zebrafish  rep4", "Sequencing reads were aligned to the mouseGRCm38 /zebrafish genomeGRCz9 using STAR. Read quality was assessed with FastQC  and adaptors were trimmed from reads using Cutadapt. STAR gene level counts ReadsPerGene.out.tab files were used for differential expression with DESeq2 package Assembly: Zebrafish: GRCz9 / Mus musculus: GRCm38 Supplementary files format and content: tab delimited text files include the raw count values for each Sample. Rows = genes; Columns = samples.", "posterior half of larvae", null, "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer\u2019s protocol Zebrafish: RNA libraries were generated using the QuantSeq 3\u2019 mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "tissue:posterior half of larvae|genotype:HET|treatment:TSA treatment", "GSM6433989", "GSM6433989: HET  TSA treatment  zebrafish  rep4; Danio rerio; RNA Seq", "GSM6433989 r1", "GSM6433989", "1", "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer's protocol Zebrafish: RNA libraries were generated using the QuantSeq three prime mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP390172", null, null, "WL1479_KY23_168_10_R1.fastq.gz", "fastq", 895564760.0, 13170070.0, "GSM6433989 r1", "0:68 1:0", "A:300989941;C:166218035;G:200751247;T:227578514;N:27023", 68, 0, null, null, 300989941, 166218035, 200751247, 227578514, 27023, "SRX16888155", "SRS14475639", "SRA1470408", "Hospital for Sick Children", "Hospital for Sick Children", 1, 0.65575, null, 0.09506, null, 0.83224, null, 0.52894, null, 68, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "lexogen", "bulk", "bulk", "bulk", null, "Canada", "2022-08-05", "Larval", "Larval", "Trunk", "Surface Structure"], [70916, "SRR20869098", "SRX16888154", "SRS14475638", "SRP390172", "PRJNA866536", "X linked myotubular myopathy is associated with epigenetic alterations and is ameliorated by HDAC inhibition", "GSE210642", "Other", "X linked myotubular myopathy XLMTM is a fatal neuromuscular disorder caused by loss of function mutations in MTM1 . At present  there are no directed therapies for XLMTM  and incomplete understanding of disease pathomechanisms. To address these knowledge gaps  we performed a drug screen in mtm1 mutant zebrafish andidentified four positive hits  including valproic acid  which functions as a potent suppressor of the mtm1 zebrafish phenotype via HDAC inhibition. We translated these findings to a mouse XLMTM model  and showed that valproic acid ameliorates the murine phenotype. Overall design: Zebrafish: At 1 dpf  embryos from single pair in crossings of mtm1+/zf711 adults were divided equally into three chemical treatment groups: DMSO  sodium valproate VPA  or trichostatin A. For tissue collection  the posterior section of larvae and fin fold tissues was dissected and snap frozen on dry ice at 4 dpf. A total of n=6 10 larvae per pool per condition with 5 biological replicates were used for RNA extraction.  Mice: Bulk RNA sequencing was performed on RNA extracts from tibialis anterior muscle from 35 dpf Mtm1KO and WT mice  either treated with PBS or valproic acid VPA starting at 21 days.", null, "pubmed:35844027", null, "HET  TSA treatment  zebrafish  rep3", "GSM6433988", null, "source name:posterior half of larvae|tissue:posterior half of larvae|genotype:HET|treatment:TSA treatment", "HET  TSA treatment  zebrafish  rep3", "Sequencing reads were aligned to the mouseGRCm38 /zebrafish genomeGRCz9 using STAR. Read quality was assessed with FastQC  and adaptors were trimmed from reads using Cutadapt. STAR gene level counts ReadsPerGene.out.tab files were used for differential expression with DESeq2 package Assembly: Zebrafish: GRCz9 / Mus musculus: GRCm38 Supplementary files format and content: tab delimited text files include the raw count values for each Sample. Rows = genes; Columns = samples.", "posterior half of larvae", null, "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer\u2019s protocol Zebrafish: RNA libraries were generated using the QuantSeq 3\u2019 mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "tissue:posterior half of larvae|genotype:HET|treatment:TSA treatment", "GSM6433988", "GSM6433988: HET  TSA treatment  zebrafish  rep3; Danio rerio; RNA Seq", "GSM6433988 r1", "GSM6433988", "1", "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer's protocol Zebrafish: RNA libraries were generated using the QuantSeq three prime mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP390172", null, null, "WL1477_KY23_168_8_R1.fastq.gz", "fastq", 1021524628.0, 15022421.0, "GSM6433988 r1", "0:68 1:0", "A:386300445;C:167964779;G:205371083;T:261856684;N:31637", 68, 0, null, null, 386300445, 167964779, 205371083, 261856684, 31637, "SRX16888154", "SRS14475638", "SRA1470408", "Hospital for Sick Children", "Hospital for Sick Children", 1, 0.73302, null, 0.10328, null, 0.81466, null, 0.55873, null, 68, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "lexogen", "bulk", "bulk", "bulk", null, "Canada", "2022-08-05", "Larval", "Larval", "Trunk", "Surface Structure"], [70917, "SRR20869099", "SRX16888153", "SRS14475637", "SRP390172", "PRJNA866536", "X linked myotubular myopathy is associated with epigenetic alterations and is ameliorated by HDAC inhibition", "GSE210642", "Other", "X linked myotubular myopathy XLMTM is a fatal neuromuscular disorder caused by loss of function mutations in MTM1 . At present  there are no directed therapies for XLMTM  and incomplete understanding of disease pathomechanisms. To address these knowledge gaps  we performed a drug screen in mtm1 mutant zebrafish andidentified four positive hits  including valproic acid  which functions as a potent suppressor of the mtm1 zebrafish phenotype via HDAC inhibition. We translated these findings to a mouse XLMTM model  and showed that valproic acid ameliorates the murine phenotype. Overall design: Zebrafish: At 1 dpf  embryos from single pair in crossings of mtm1+/zf711 adults were divided equally into three chemical treatment groups: DMSO  sodium valproate VPA  or trichostatin A. For tissue collection  the posterior section of larvae and fin fold tissues was dissected and snap frozen on dry ice at 4 dpf. A total of n=6 10 larvae per pool per condition with 5 biological replicates were used for RNA extraction.  Mice: Bulk RNA sequencing was performed on RNA extracts from tibialis anterior muscle from 35 dpf Mtm1KO and WT mice  either treated with PBS or valproic acid VPA starting at 21 days.", null, "pubmed:35844027", null, "HET  TSA treatment  zebrafish  rep2", "GSM6433987", null, "source name:posterior half of larvae|tissue:posterior half of larvae|genotype:HET|treatment:TSA treatment", "HET  TSA treatment  zebrafish  rep2", "Sequencing reads were aligned to the mouseGRCm38 /zebrafish genomeGRCz9 using STAR. Read quality was assessed with FastQC  and adaptors were trimmed from reads using Cutadapt. STAR gene level counts ReadsPerGene.out.tab files were used for differential expression with DESeq2 package Assembly: Zebrafish: GRCz9 / Mus musculus: GRCm38 Supplementary files format and content: tab delimited text files include the raw count values for each Sample. Rows = genes; Columns = samples.", "posterior half of larvae", null, "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer\u2019s protocol Zebrafish: RNA libraries were generated using the QuantSeq 3\u2019 mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "tissue:posterior half of larvae|genotype:HET|treatment:TSA treatment", "GSM6433987", "GSM6433987: HET  TSA treatment  zebrafish  rep2; Danio rerio; RNA Seq", "GSM6433987 r1", "GSM6433987", "1", "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer's protocol Zebrafish: RNA libraries were generated using the QuantSeq three prime mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP390172", null, null, "WL1476_KY23_168_7_R1.fastq.gz", "fastq", 951668296.0, 13995122.0, "GSM6433987 r1", "0:68 1:0", "A:339449944;C:164483500;G:198328177;T:249377598;N:29077", 68, 0, null, null, 339449944, 164483500, 198328177, 249377598, 29077, "SRX16888153", "SRS14475637", "SRA1470408", "Hospital for Sick Children", "Hospital for Sick Children", 1, 0.73604, null, 0.0885, null, 0.82187, null, 0.54577, null, 68, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "lexogen", "bulk", "bulk", "bulk", null, "Canada", "2022-08-05", "Larval", "Larval", "Trunk", "Surface Structure"], [70918, "SRR20869100", "SRX16888152", "SRS14475636", "SRP390172", "PRJNA866536", "X linked myotubular myopathy is associated with epigenetic alterations and is ameliorated by HDAC inhibition", "GSE210642", "Other", "X linked myotubular myopathy XLMTM is a fatal neuromuscular disorder caused by loss of function mutations in MTM1 . At present  there are no directed therapies for XLMTM  and incomplete understanding of disease pathomechanisms. To address these knowledge gaps  we performed a drug screen in mtm1 mutant zebrafish andidentified four positive hits  including valproic acid  which functions as a potent suppressor of the mtm1 zebrafish phenotype via HDAC inhibition. We translated these findings to a mouse XLMTM model  and showed that valproic acid ameliorates the murine phenotype. Overall design: Zebrafish: At 1 dpf  embryos from single pair in crossings of mtm1+/zf711 adults were divided equally into three chemical treatment groups: DMSO  sodium valproate VPA  or trichostatin A. For tissue collection  the posterior section of larvae and fin fold tissues was dissected and snap frozen on dry ice at 4 dpf. A total of n=6 10 larvae per pool per condition with 5 biological replicates were used for RNA extraction.  Mice: Bulk RNA sequencing was performed on RNA extracts from tibialis anterior muscle from 35 dpf Mtm1KO and WT mice  either treated with PBS or valproic acid VPA starting at 21 days.", null, "pubmed:35844027", null, "HET  TSA treatment  zebrafish  rep1", "GSM6433986", null, "source name:posterior half of larvae|tissue:posterior half of larvae|genotype:HET|treatment:TSA treatment", "HET  TSA treatment  zebrafish  rep1", "Sequencing reads were aligned to the mouseGRCm38 /zebrafish genomeGRCz9 using STAR. Read quality was assessed with FastQC  and adaptors were trimmed from reads using Cutadapt. STAR gene level counts ReadsPerGene.out.tab files were used for differential expression with DESeq2 package Assembly: Zebrafish: GRCz9 / Mus musculus: GRCm38 Supplementary files format and content: tab delimited text files include the raw count values for each Sample. Rows = genes; Columns = samples.", "posterior half of larvae", null, "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer\u2019s protocol Zebrafish: RNA libraries were generated using the QuantSeq 3\u2019 mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "tissue:posterior half of larvae|genotype:HET|treatment:TSA treatment", "GSM6433986", "GSM6433986: HET  TSA treatment  zebrafish  rep1; Danio rerio; RNA Seq", "GSM6433986 r1", "GSM6433986", "1", "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer's protocol Zebrafish: RNA libraries were generated using the QuantSeq three prime mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP390172", null, null, "WL1475_KY23_168_6_R1.fastq.gz", "fastq", 882802180.0, 12982385.0, "GSM6433986 r1", "0:68 1:0", "A:303896452;C:155568953;G:193507200;T:229802351;N:27224", 68, 0, null, null, 303896452, 155568953, 193507200, 229802351, 27224, "SRX16888152", "SRS14475636", "SRA1470408", "Hospital for Sick Children", "Hospital for Sick Children", 1, 0.7587, null, 0.1005, null, 0.82071, null, 0.54149, null, 68, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "lexogen", "bulk", "bulk", "bulk", null, "Canada", "2022-08-05", "Larval", "Larval", "Trunk", "Surface Structure"], [70919, "SRR20869101", "SRX16888151", "SRS14475635", "SRP390172", "PRJNA866536", "X linked myotubular myopathy is associated with epigenetic alterations and is ameliorated by HDAC inhibition", "GSE210642", "Other", "X linked myotubular myopathy XLMTM is a fatal neuromuscular disorder caused by loss of function mutations in MTM1 . At present  there are no directed therapies for XLMTM  and incomplete understanding of disease pathomechanisms. To address these knowledge gaps  we performed a drug screen in mtm1 mutant zebrafish andidentified four positive hits  including valproic acid  which functions as a potent suppressor of the mtm1 zebrafish phenotype via HDAC inhibition. We translated these findings to a mouse XLMTM model  and showed that valproic acid ameliorates the murine phenotype. Overall design: Zebrafish: At 1 dpf  embryos from single pair in crossings of mtm1+/zf711 adults were divided equally into three chemical treatment groups: DMSO  sodium valproate VPA  or trichostatin A. For tissue collection  the posterior section of larvae and fin fold tissues was dissected and snap frozen on dry ice at 4 dpf. A total of n=6 10 larvae per pool per condition with 5 biological replicates were used for RNA extraction.  Mice: Bulk RNA sequencing was performed on RNA extracts from tibialis anterior muscle from 35 dpf Mtm1KO and WT mice  either treated with PBS or valproic acid VPA starting at 21 days.", null, "pubmed:35844027", null, "WT  DMSO treatment  zebrafish  rep5", "GSM6433985", null, "source name:posterior half of larvae|tissue:posterior half of larvae|genotype:WT|treatment:DMSO treatment", "WT  DMSO treatment  zebrafish  rep5", "Sequencing reads were aligned to the mouseGRCm38 /zebrafish genomeGRCz9 using STAR. Read quality was assessed with FastQC  and adaptors were trimmed from reads using Cutadapt. STAR gene level counts ReadsPerGene.out.tab files were used for differential expression with DESeq2 package Assembly: Zebrafish: GRCz9 / Mus musculus: GRCm38 Supplementary files format and content: tab delimited text files include the raw count values for each Sample. Rows = genes; Columns = samples.", "posterior half of larvae", null, "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer\u2019s protocol Zebrafish: RNA libraries were generated using the QuantSeq 3\u2019 mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "tissue:posterior half of larvae|genotype:WT|treatment:DMSO treatment", "GSM6433985", "GSM6433985: WT  DMSO treatment  zebrafish  rep5; Danio rerio; RNA Seq", "GSM6433985 r1", "GSM6433985", "1", "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer's protocol Zebrafish: RNA libraries were generated using the QuantSeq three prime mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP390172", null, null, "WL1474_KY23_168_5_R1.fastq.gz", "fastq", 912959636.0, 13425877.0, "GSM6433985 r1", "0:68 1:0", "A:308365583;C:164030703;G:197218474;T:243316551;N:28325", 68, 0, null, null, 308365583, 164030703, 197218474, 243316551, 28325, "SRX16888151", "SRS14475635", "SRA1470408", "Hospital for Sick Children", "Hospital for Sick Children", 1, 0.7904, null, 0.09253, null, 0.81886, null, 0.57028, null, 68, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "lexogen", "bulk", "bulk", "bulk", null, "Canada", "2022-08-05", "Larval", "Larval", "Trunk", "Surface Structure"], [70920, "SRR20869102", "SRX16888150", "SRS14475634", "SRP390172", "PRJNA866536", "X linked myotubular myopathy is associated with epigenetic alterations and is ameliorated by HDAC inhibition", "GSE210642", "Other", "X linked myotubular myopathy XLMTM is a fatal neuromuscular disorder caused by loss of function mutations in MTM1 . At present  there are no directed therapies for XLMTM  and incomplete understanding of disease pathomechanisms. To address these knowledge gaps  we performed a drug screen in mtm1 mutant zebrafish andidentified four positive hits  including valproic acid  which functions as a potent suppressor of the mtm1 zebrafish phenotype via HDAC inhibition. We translated these findings to a mouse XLMTM model  and showed that valproic acid ameliorates the murine phenotype. Overall design: Zebrafish: At 1 dpf  embryos from single pair in crossings of mtm1+/zf711 adults were divided equally into three chemical treatment groups: DMSO  sodium valproate VPA  or trichostatin A. For tissue collection  the posterior section of larvae and fin fold tissues was dissected and snap frozen on dry ice at 4 dpf. A total of n=6 10 larvae per pool per condition with 5 biological replicates were used for RNA extraction.  Mice: Bulk RNA sequencing was performed on RNA extracts from tibialis anterior muscle from 35 dpf Mtm1KO and WT mice  either treated with PBS or valproic acid VPA starting at 21 days.", null, "pubmed:35844027", null, "WT  DMSO treatment  zebrafish  rep4", "GSM6433984", null, "source name:posterior half of larvae|tissue:posterior half of larvae|genotype:WT|treatment:DMSO treatment", "WT  DMSO treatment  zebrafish  rep4", "Sequencing reads were aligned to the mouseGRCm38 /zebrafish genomeGRCz9 using STAR. Read quality was assessed with FastQC  and adaptors were trimmed from reads using Cutadapt. STAR gene level counts ReadsPerGene.out.tab files were used for differential expression with DESeq2 package Assembly: Zebrafish: GRCz9 / Mus musculus: GRCm38 Supplementary files format and content: tab delimited text files include the raw count values for each Sample. Rows = genes; Columns = samples.", "posterior half of larvae", null, "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer\u2019s protocol Zebrafish: RNA libraries were generated using the QuantSeq 3\u2019 mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "tissue:posterior half of larvae|genotype:WT|treatment:DMSO treatment", "GSM6433984", "GSM6433984: WT  DMSO treatment  zebrafish  rep4; Danio rerio; RNA Seq", "GSM6433984 r1", "GSM6433984", "1", "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer's protocol Zebrafish: RNA libraries were generated using the QuantSeq three prime mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP390172", null, null, "WL1473_KY23_168_4_R1.fastq.gz", "fastq", 886745704.0, 13040378.0, "GSM6433984 r1", "0:68 1:0", "A:304159499;C:157062642;G:192987191;T:232509378;N:26994", 68, 0, null, null, 304159499, 157062642, 192987191, 232509378, 26994, "SRX16888150", "SRS14475634", "SRA1470408", "Hospital for Sick Children", "Hospital for Sick Children", 1, 0.77072, null, 0.08161, null, 0.82294, null, 0.56065, null, 68, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "lexogen", "bulk", "bulk", "bulk", null, "Canada", "2022-08-05", "Larval", "Larval", "Trunk", "Surface Structure"], [70921, "SRR20869103", "SRX16888149", "SRS14475633", "SRP390172", "PRJNA866536", "X linked myotubular myopathy is associated with epigenetic alterations and is ameliorated by HDAC inhibition", "GSE210642", "Other", "X linked myotubular myopathy XLMTM is a fatal neuromuscular disorder caused by loss of function mutations in MTM1 . At present  there are no directed therapies for XLMTM  and incomplete understanding of disease pathomechanisms. To address these knowledge gaps  we performed a drug screen in mtm1 mutant zebrafish andidentified four positive hits  including valproic acid  which functions as a potent suppressor of the mtm1 zebrafish phenotype via HDAC inhibition. We translated these findings to a mouse XLMTM model  and showed that valproic acid ameliorates the murine phenotype. Overall design: Zebrafish: At 1 dpf  embryos from single pair in crossings of mtm1+/zf711 adults were divided equally into three chemical treatment groups: DMSO  sodium valproate VPA  or trichostatin A. For tissue collection  the posterior section of larvae and fin fold tissues was dissected and snap frozen on dry ice at 4 dpf. A total of n=6 10 larvae per pool per condition with 5 biological replicates were used for RNA extraction.  Mice: Bulk RNA sequencing was performed on RNA extracts from tibialis anterior muscle from 35 dpf Mtm1KO and WT mice  either treated with PBS or valproic acid VPA starting at 21 days.", null, "pubmed:35844027", null, "WT  DMSO treatment  zebrafish  rep3", "GSM6433983", null, "source name:posterior half of larvae|tissue:posterior half of larvae|genotype:WT|treatment:DMSO treatment", "WT  DMSO treatment  zebrafish  rep3", "Sequencing reads were aligned to the mouseGRCm38 /zebrafish genomeGRCz9 using STAR. Read quality was assessed with FastQC  and adaptors were trimmed from reads using Cutadapt. STAR gene level counts ReadsPerGene.out.tab files were used for differential expression with DESeq2 package Assembly: Zebrafish: GRCz9 / Mus musculus: GRCm38 Supplementary files format and content: tab delimited text files include the raw count values for each Sample. Rows = genes; Columns = samples.", "posterior half of larvae", null, "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer\u2019s protocol Zebrafish: RNA libraries were generated using the QuantSeq 3\u2019 mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "tissue:posterior half of larvae|genotype:WT|treatment:DMSO treatment", "GSM6433983", "GSM6433983: WT  DMSO treatment  zebrafish  rep3; Danio rerio; RNA Seq", "GSM6433983 r1", "GSM6433983", "1", "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer's protocol Zebrafish: RNA libraries were generated using the QuantSeq three prime mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP390172", null, null, "WL1472_KY23_168_3_R1.fastq.gz", "fastq", 852365924.0, 12534793.0, "GSM6433983 r1", "0:68 1:0", "A:288118744;C:154342074;G:181602972;T:228275755;N:26379", 68, 0, null, null, 288118744, 154342074, 181602972, 228275755, 26379, "SRX16888149", "SRS14475633", "SRA1470408", "Hospital for Sick Children", "Hospital for Sick Children", 1, 0.78952, null, 0.07137, null, 0.81941, null, 0.55642, null, 68, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "lexogen", "bulk", "bulk", "bulk", null, "Canada", "2022-08-05", "Larval", "Larval", "Trunk", "Surface Structure"], [70922, "SRR20869104", "SRX16888148", "SRS14475632", "SRP390172", "PRJNA866536", "X linked myotubular myopathy is associated with epigenetic alterations and is ameliorated by HDAC inhibition", "GSE210642", "Other", "X linked myotubular myopathy XLMTM is a fatal neuromuscular disorder caused by loss of function mutations in MTM1 . At present  there are no directed therapies for XLMTM  and incomplete understanding of disease pathomechanisms. To address these knowledge gaps  we performed a drug screen in mtm1 mutant zebrafish andidentified four positive hits  including valproic acid  which functions as a potent suppressor of the mtm1 zebrafish phenotype via HDAC inhibition. We translated these findings to a mouse XLMTM model  and showed that valproic acid ameliorates the murine phenotype. Overall design: Zebrafish: At 1 dpf  embryos from single pair in crossings of mtm1+/zf711 adults were divided equally into three chemical treatment groups: DMSO  sodium valproate VPA  or trichostatin A. For tissue collection  the posterior section of larvae and fin fold tissues was dissected and snap frozen on dry ice at 4 dpf. A total of n=6 10 larvae per pool per condition with 5 biological replicates were used for RNA extraction.  Mice: Bulk RNA sequencing was performed on RNA extracts from tibialis anterior muscle from 35 dpf Mtm1KO and WT mice  either treated with PBS or valproic acid VPA starting at 21 days.", null, "pubmed:35844027", null, "WT  DMSO treatment  zebrafish  rep2", "GSM6433982", null, "source name:posterior half of larvae|tissue:posterior half of larvae|genotype:WT|treatment:DMSO treatment", "WT  DMSO treatment  zebrafish  rep2", "Sequencing reads were aligned to the mouseGRCm38 /zebrafish genomeGRCz9 using STAR. Read quality was assessed with FastQC  and adaptors were trimmed from reads using Cutadapt. STAR gene level counts ReadsPerGene.out.tab files were used for differential expression with DESeq2 package Assembly: Zebrafish: GRCz9 / Mus musculus: GRCm38 Supplementary files format and content: tab delimited text files include the raw count values for each Sample. Rows = genes; Columns = samples.", "posterior half of larvae", null, "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer\u2019s protocol Zebrafish: RNA libraries were generated using the QuantSeq 3\u2019 mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "tissue:posterior half of larvae|genotype:WT|treatment:DMSO treatment", "GSM6433982", "GSM6433982: WT  DMSO treatment  zebrafish  rep2; Danio rerio; RNA Seq", "GSM6433982 r1", "GSM6433982", "1", "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer's protocol Zebrafish: RNA libraries were generated using the QuantSeq three prime mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP390172", null, null, "WL1471_KY23_168_2_R1.fastq.gz", "fastq", 915622584.0, 13465038.0, "GSM6433982 r1", "0:68 1:0", "A:314839314;C:161960932;G:199970507;T:238823895;N:27936", 68, 0, null, null, 314839314, 161960932, 199970507, 238823895, 27936, "SRX16888148", "SRS14475632", "SRA1470408", "Hospital for Sick Children", "Hospital for Sick Children", 1, 0.76878, null, 0.08743, null, 0.82304, null, 0.57384, null, 68, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "lexogen", "bulk", "bulk", "bulk", null, "Canada", "2022-08-05", "Larval", "Larval", "Trunk", "Surface Structure"], [70923, "SRR20869105", "SRX16888147", "SRS14475631", "SRP390172", "PRJNA866536", "X linked myotubular myopathy is associated with epigenetic alterations and is ameliorated by HDAC inhibition", "GSE210642", "Other", "X linked myotubular myopathy XLMTM is a fatal neuromuscular disorder caused by loss of function mutations in MTM1 . At present  there are no directed therapies for XLMTM  and incomplete understanding of disease pathomechanisms. To address these knowledge gaps  we performed a drug screen in mtm1 mutant zebrafish andidentified four positive hits  including valproic acid  which functions as a potent suppressor of the mtm1 zebrafish phenotype via HDAC inhibition. We translated these findings to a mouse XLMTM model  and showed that valproic acid ameliorates the murine phenotype. Overall design: Zebrafish: At 1 dpf  embryos from single pair in crossings of mtm1+/zf711 adults were divided equally into three chemical treatment groups: DMSO  sodium valproate VPA  or trichostatin A. For tissue collection  the posterior section of larvae and fin fold tissues was dissected and snap frozen on dry ice at 4 dpf. A total of n=6 10 larvae per pool per condition with 5 biological replicates were used for RNA extraction.  Mice: Bulk RNA sequencing was performed on RNA extracts from tibialis anterior muscle from 35 dpf Mtm1KO and WT mice  either treated with PBS or valproic acid VPA starting at 21 days.", null, "pubmed:35844027", null, "WT  DMSO treatment  zebrafish  rep1", "GSM6433981", null, "source name:posterior half of larvae|tissue:posterior half of larvae|genotype:WT|treatment:DMSO treatment", "WT  DMSO treatment  zebrafish  rep1", "Sequencing reads were aligned to the mouseGRCm38 /zebrafish genomeGRCz9 using STAR. Read quality was assessed with FastQC  and adaptors were trimmed from reads using Cutadapt. STAR gene level counts ReadsPerGene.out.tab files were used for differential expression with DESeq2 package Assembly: Zebrafish: GRCz9 / Mus musculus: GRCm38 Supplementary files format and content: tab delimited text files include the raw count values for each Sample. Rows = genes; Columns = samples.", "posterior half of larvae", null, "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer\u2019s protocol Zebrafish: RNA libraries were generated using the QuantSeq 3\u2019 mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "tissue:posterior half of larvae|genotype:WT|treatment:DMSO treatment", "GSM6433981", "GSM6433981: WT  DMSO treatment  zebrafish  rep1; Danio rerio; RNA Seq", "GSM6433981 r1", "GSM6433981", "1", "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer's protocol Zebrafish: RNA libraries were generated using the QuantSeq three prime mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP390172", null, null, "WL1470_KY23_168_1_R1.fastq.gz", "fastq", 997885244.0, 14674783.0, "GSM6433981 r1", "0:68 1:0", "A:351989460;C:174189591;G:216129629;T:255546296;N:30268", 68, 0, null, null, 351989460, 174189591, 216129629, 255546296, 30268, "SRX16888147", "SRS14475631", "SRA1470408", "Hospital for Sick Children", "Hospital for Sick Children", 1, 0.7455, null, 0.08488, null, 0.82611, null, 0.57074, null, 68, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "lexogen", "bulk", "bulk", "bulk", null, "Canada", "2022-08-05", "Larval", "Larval", "Trunk", "Surface Structure"]], "truncated": false, "filtered_table_rows_count": 40, "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", 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[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], 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